Query 020247
Match_columns 329
No_of_seqs 119 out of 197
Neff 5.1
Searched_HMMs 46136
Date Fri Mar 29 08:12:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020247.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020247hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3471 RNA polymerase II tran 100.0 2E-111 4E-116 822.4 22.8 307 16-329 147-463 (465)
2 TIGR00625 tfb2 Transcription f 100.0 3E-109 7E-114 824.1 30.7 306 17-329 134-448 (448)
3 COG5144 TFB2 RNA polymerase II 100.0 1.4E-98 3E-103 715.3 17.6 305 17-328 135-445 (447)
4 PF03849 Tfb2: Transcription f 100.0 2.3E-78 5E-83 594.0 20.5 222 17-243 132-366 (366)
5 PF13625 Helicase_C_3: Helicas 99.7 4.7E-16 1E-20 132.0 12.2 118 176-301 2-121 (129)
6 TIGR00603 rad25 DNA repair hel 97.4 0.0016 3.4E-08 70.4 12.2 106 173-293 22-132 (732)
7 PF08671 SinI: Anti-repressor 92.5 0.12 2.7E-06 34.1 2.5 22 219-240 8-29 (30)
8 PRK06015 keto-hydroxyglutarate 84.2 7.2 0.00016 36.2 9.0 126 172-326 27-164 (201)
9 PRK05718 keto-hydroxyglutarate 80.3 20 0.00043 33.4 10.3 162 124-326 1-175 (212)
10 PF01081 Aldolase: KDPG and KH 79.5 3.2 7E-05 38.3 4.8 126 172-326 31-168 (196)
11 TIGR01615 A_thal_3542 uncharac 76.9 1.3 2.7E-05 38.8 1.2 65 172-254 47-112 (131)
12 TIGR01182 eda Entner-Doudoroff 75.8 24 0.00052 32.8 9.5 125 173-326 32-168 (204)
13 PRK07114 keto-hydroxyglutarate 75.2 34 0.00075 32.2 10.4 156 130-326 7-180 (222)
14 KOG1123 RNA polymerase II tran 72.9 6.9 0.00015 41.6 5.6 89 172-272 81-169 (776)
15 PF08356 EF_assoc_2: EF hand a 63.3 10 0.00022 31.0 3.7 43 45-89 10-57 (89)
16 PRK14529 adenylate kinase; Pro 62.9 51 0.0011 30.9 8.8 80 204-298 23-103 (223)
17 PF14947 HTH_45: Winged helix- 62.3 3.6 7.9E-05 31.9 0.9 31 45-75 37-67 (77)
18 PF00406 ADK: Adenylate kinase 57.3 18 0.0004 30.5 4.5 81 204-298 19-100 (151)
19 PRK06552 keto-hydroxyglutarate 56.2 1.1E+02 0.0023 28.5 9.7 154 131-326 6-175 (213)
20 COG1420 HrcA Transcriptional r 54.4 9.9 0.00021 38.1 2.7 62 82-159 12-73 (346)
21 COG3432 Predicted transcriptio 50.1 11 0.00025 31.1 1.9 33 42-74 46-82 (95)
22 PRK09333 30S ribosomal protein 50.0 12 0.00027 33.4 2.3 35 41-75 95-129 (150)
23 PF10711 DUF2513: Hypothetical 49.1 13 0.00029 30.4 2.2 42 48-89 41-92 (102)
24 PF01978 TrmB: Sugar-specific 48.9 15 0.00032 27.3 2.3 32 124-156 34-66 (68)
25 TIGR03853 matur_matur probable 48.8 25 0.00053 28.2 3.5 27 215-241 18-58 (77)
26 PF06969 HemN_C: HemN C-termin 48.1 10 0.00022 27.9 1.3 27 45-71 39-65 (66)
27 COG1313 PflX Uncharacterized F 48.0 23 0.00051 35.2 4.0 52 230-299 273-329 (335)
28 COG2238 RPS19A Ribosomal prote 48.0 13 0.00028 33.0 2.0 35 40-74 94-128 (147)
29 PF02244 Propep_M14: Carboxype 47.3 77 0.0017 23.7 6.1 46 282-327 6-55 (74)
30 PF03428 RP-C: Replication pro 46.2 83 0.0018 28.7 7.0 73 80-152 23-113 (177)
31 PF09639 YjcQ: YjcQ protein; 43.8 13 0.00027 29.8 1.3 31 46-76 29-69 (88)
32 COG1412 Uncharacterized protei 41.9 66 0.0014 28.3 5.5 18 172-189 9-26 (136)
33 PF04720 DUF506: Protein of un 41.8 12 0.00025 35.4 0.9 66 171-254 135-201 (218)
34 PRK13824 replication initiatio 40.3 1E+02 0.0022 31.6 7.4 68 81-151 36-124 (404)
35 PRK11183 D-lactate dehydrogena 40.1 1.2E+02 0.0025 32.7 7.9 80 184-265 272-363 (564)
36 PF10678 DUF2492: Protein of u 39.5 42 0.00091 26.9 3.6 26 215-240 20-59 (78)
37 smart00195 DSPc Dual specifici 39.2 69 0.0015 26.4 5.1 51 208-265 80-137 (138)
38 TIGR02425 decarb_PcaC 4-carbox 37.1 41 0.00088 28.7 3.4 25 217-241 76-100 (123)
39 PF03444 HrcA_DNA-bdg: Winged 36.7 36 0.00078 27.3 2.8 35 125-160 37-71 (78)
40 TIGR02010 IscR iron-sulfur clu 35.9 37 0.0008 28.8 3.0 53 103-156 10-69 (135)
41 PF01726 LexA_DNA_bind: LexA D 34.3 49 0.0011 25.1 3.1 57 75-147 4-62 (65)
42 PRK03911 heat-inducible transc 33.2 28 0.0006 33.8 1.9 47 111-159 24-70 (260)
43 PTZ00095 40S ribosomal protein 33.0 30 0.00064 31.6 2.0 36 39-74 117-154 (169)
44 KOG4175 Tryptophan synthase al 32.8 1.8E+02 0.0039 27.8 7.1 77 218-301 67-151 (268)
45 PF09713 A_thal_3526: Plant pr 30.8 73 0.0016 23.8 3.4 24 218-241 3-26 (54)
46 TIGR03147 cyt_nit_nrfF cytochr 30.3 95 0.0021 27.0 4.6 39 217-255 63-101 (126)
47 PF03918 CcmH: Cytochrome C bi 30.2 48 0.001 29.3 2.8 31 217-247 63-93 (148)
48 PF14338 Mrr_N: Mrr N-terminal 30.0 43 0.00092 26.6 2.3 31 47-77 60-91 (92)
49 PF09330 Lact-deh-memb: D-lact 29.9 2E+02 0.0043 28.5 7.1 119 185-326 3-133 (291)
50 PF09821 AAA_assoc_C: C-termin 29.8 45 0.00097 28.4 2.5 36 46-81 16-51 (120)
51 COG0563 Adk Adenylate kinase a 29.7 33 0.00071 30.8 1.7 79 205-298 24-104 (178)
52 PF13833 EF-hand_8: EF-hand do 29.6 63 0.0014 22.4 2.9 21 213-233 3-27 (54)
53 PF01316 Arg_repressor: Argini 28.4 70 0.0015 24.9 3.1 29 124-152 34-62 (70)
54 PF04023 FeoA: FeoA domain; I 28.4 18 0.00039 27.1 -0.2 35 109-143 2-36 (74)
55 cd00115 LMWPc Substituted upda 28.3 35 0.00075 28.8 1.6 67 4-70 6-73 (141)
56 PRK10144 formate-dependent nit 28.1 1.1E+02 0.0024 26.6 4.6 39 217-255 63-101 (126)
57 PF12637 TSCPD: TSCPD domain; 28.0 1E+02 0.0022 25.0 4.2 54 194-263 37-90 (95)
58 PF00782 DSPc: Dual specificit 26.7 1.3E+02 0.0027 24.5 4.7 44 215-265 84-132 (133)
59 PLN02459 probable adenylate ki 26.6 1.3E+02 0.0027 29.2 5.2 69 204-284 52-120 (261)
60 PF00085 Thioredoxin: Thioredo 26.5 1.4E+02 0.003 22.5 4.6 37 184-220 22-60 (103)
61 PF01216 Calsequestrin: Calseq 25.4 1.7E+02 0.0036 30.0 5.9 135 178-326 163-322 (383)
62 PF08784 RPA_C: Replication pr 25.0 95 0.0021 24.9 3.5 53 75-144 45-98 (102)
63 COG3355 Predicted transcriptio 24.9 61 0.0013 28.2 2.4 21 126-146 57-77 (126)
64 PLN02674 adenylate kinase 24.9 3.4E+02 0.0074 25.8 7.8 81 204-298 54-135 (244)
65 smart00529 HTH_DTXR Helix-turn 24.8 3.2E+02 0.0069 21.0 6.5 62 45-111 17-80 (96)
66 PF05184 SapB_1: Saposin-like 24.4 74 0.0016 20.8 2.3 21 219-239 13-33 (39)
67 COG1497 Predicted transcriptio 24.3 24 0.00053 34.0 -0.1 39 41-80 40-79 (260)
68 PRK13808 adenylate kinase; Pro 23.5 2.2E+02 0.0047 28.5 6.4 78 204-296 23-102 (333)
69 PRK14526 adenylate kinase; Pro 22.9 1.6E+02 0.0034 27.1 5.0 74 206-293 25-99 (211)
70 PRK10857 DNA-binding transcrip 22.3 85 0.0019 28.0 3.0 53 103-156 10-69 (164)
71 PF02082 Rrf2: Transcriptional 21.8 91 0.002 24.1 2.7 25 128-152 42-66 (83)
72 PRK11235 bifunctional antitoxi 21.1 2.5E+02 0.0054 22.5 5.1 45 93-137 20-64 (80)
73 PF01090 Ribosomal_S19e: Ribos 21.1 21 0.00045 31.6 -1.2 34 41-74 94-128 (139)
74 TIGR00738 rrf2_super rrf2 fami 20.6 1E+02 0.0023 25.4 3.0 29 127-156 41-69 (132)
75 PRK11014 transcriptional repre 20.5 1.1E+02 0.0023 26.1 3.2 50 103-152 10-66 (141)
76 PRK00279 adk adenylate kinase; 20.1 6.3E+02 0.014 22.6 9.9 101 204-323 23-124 (215)
No 1
>KOG3471 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB2 [Transcription; Replication, recombination and repair]
Probab=100.00 E-value=1.9e-111 Score=822.37 Aligned_cols=307 Identities=36% Similarity=0.661 Sum_probs=292.6
Q ss_pred cccCccceecceeccCCCCCCCCCCCCCcHHHHHHHHhCCCccCCCCCCccchhchhhhccChhhHHHHHHHHHHHHHHH
Q 020247 16 QGFQPWRTLRPMPLDNGSSTQAERPTNFSSSMMKVFQRGLLSRRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQE 95 (329)
Q Consensus 16 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~v~~lL~~~gL~~~~~~~~~IT~~GfqFLL~d~~~Q~W~lll~yl~~~e~ 95 (329)
-+.+|||||+||||+++.+ ..+|+++.++|+++|||+.+...+.||++||||||+|+++|+|+++++||++.+.
T Consensus 147 ya~~rwe~ILh~mvgt~~a------~~~se~v~~ll~~a~lm~~~~~~~~IT~~GFQFLL~~~~aQlW~~~LqyLk~~~~ 220 (465)
T KOG3471|consen 147 YASERWECILHFMVGTPEA------KAVSEGVLNLLKHAGLMSRDENQIEITNAGFQFLLLDINAQLWTLVLQYLKLFES 220 (465)
T ss_pred HHHHHHHHHHHHHhCCccc------cccChhHHHHHHhcCccCCCCCCceEeecchhhhhcCcHHHHHHHHHHHHHHHHh
Confidence 3689999999999955533 7899999999999999998888999999999999999999999999999999999
Q ss_pred cCCChHHHHHHHHHhcccccCccccCCCCCHHHHHHHHHHhhcCceeeecCCCccccccchhhhhcccccCC--------
Q 020247 96 RGINQADLISFLLELSFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTD-------- 167 (329)
Q Consensus 96 ~g~~~~e~L~fLf~Ls~~~~G~~Y~~~~lt~~q~~~L~~L~d~GLVy~~~~~~~~fy~pT~La~~L~~~~~~-------- 167 (329)
+|+|++|+|+|||+||++++|++|+++++|++|+.||+||+|+|||||+|.+..+|| ||+||++++++-.+
T Consensus 221 ~~~dlvevL~~LfqL~~~~~G~~Ysvd~~~~~~~~~lq~Lre~GlvfQrk~k~~rfy-ptrla~~~ss~~~~~~~~~~~~ 299 (465)
T KOG3471|consen 221 SGMDLVEVLEFLFQLSALALGRAYSVDALTETQRILLQHLRELGLVFQRKIKILRFY-PTRLAIGLSSDQLGAASLVHQN 299 (465)
T ss_pred cCCCHHHHHHHHHHHHHHHhcccceeehhhHHHHHHHHHHHHhhHHHHhhhhhheec-chhhhhccchhhhhhhhhhhcc
Confidence 999999999999999999999999999999999999999999999999999999999 99999999875431
Q ss_pred ccccccceEEEeeceeEEeecCChhHHHHHHHhhhhhhccCceEEEEeCHHHHHHHHHcCCCHHHHHHHHHhcCCccccc
Q 020247 168 SSARKEGFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVAD 247 (329)
Q Consensus 168 ~~~~~~g~IIVETNFrvYAYT~S~lqiaiL~lF~el~~r~PNlvvg~iTReSV~~Al~~GITA~QII~fL~~hAHp~m~~ 247 (329)
..+++.|||||||||||||||+||||+|+|+||||+.|||||||||+|||||||+|+++||||+|||+||++||||||+.
T Consensus 300 ~~edd~G~iIVETN~riYAYT~S~lQiAvi~LF~~l~~rf~nlvvG~iTreSVr~Al~~GITa~QII~fLet~ahpqm~~ 379 (465)
T KOG3471|consen 300 RNEDDVGFIIVETNYRIYAYTNSPLQIAVIALFTELTYRFPNLVVGVITRESVRRALDNGITAEQIIHFLETHAHPQMRM 379 (465)
T ss_pred cccccCceEEEEeccEEEEecCCHHHHHHHHHHHHHHhhccccceeeeeHHHHHHHHhcCCcHHHHHHHHHhccCchhhh
Confidence 12355699999999999999999999999999999999999999999999999999999999999999999999999988
Q ss_pred cC--CCCChhHHHHHHHHHHhcCceeeeceeeecCCCCHHHHHHHHHHHHHcCeEeeecCCCceEEEeccccHHHHHHHh
Q 020247 248 RM--PSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEAACDYARDQSGLLWEDPKKMRLVVKAEIHMHMREFLR 325 (329)
Q Consensus 248 ~~--~~iP~tV~dQI~lWe~Er~Rl~~~~g~Ly~~f~s~~~fe~v~~yA~~~g~llw~~~~kr~~~V~~~~h~~vr~f~k 325 (329)
.. |++||||+|||||||.||||+.++||+||++|.|..||+.+++||+++|+|+|+|+.||+|||+.+||++||+|||
T Consensus 380 ~~~~~~LPpTv~dQIrLWElernR~~~~~g~LYs~Fls~~df~~l~eya~~~~vLvw~d~~kr~~vV~~~Ghs~Vk~f~K 459 (465)
T KOG3471|consen 380 LSPVPCLPPTVVDQIRLWELERNRLRMTEGYLYSDFLSLSDFQLLLEYAREIGVLVWSDSDKRMFVVTKEGHSLVKRFWK 459 (465)
T ss_pred cCCCCCCCchHHhHHHHHHHhhcceecccchhHHhhhhhhhHHHHHHHHHHcCeEEEecCcceEEEEecCccHHHHHHHH
Confidence 76 9999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hccC
Q 020247 326 GQNK 329 (329)
Q Consensus 326 ~~~~ 329 (329)
+++|
T Consensus 460 r~~k 463 (465)
T KOG3471|consen 460 RKSK 463 (465)
T ss_pred Hhhc
Confidence 9764
No 2
>TIGR00625 tfb2 Transcription factor tfb2. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=100.00 E-value=3.2e-109 Score=824.10 Aligned_cols=306 Identities=35% Similarity=0.663 Sum_probs=289.5
Q ss_pred ccCccceecceeccCCCCCCCCCCCCCcHHHHHHHHhCCCccCC--CCCCccchhchhhhccChhhHHHHHHHHHHHHHH
Q 020247 17 GFQPWRTLRPMPLDNGSSTQAERPTNFSSSMMKVFQRGLLSRRD--KEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQ 94 (329)
Q Consensus 17 ~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~v~~lL~~~gL~~~~--~~~~~IT~~GfqFLL~d~~~Q~W~lll~yl~~~e 94 (329)
+.++||||+||||++++. ..||++|+++|+++|||+.+ ++.+.||++||||||+|+++|+|+||++||+++|
T Consensus 134 A~~~WE~IL~fmVgs~~~------~~~s~~v~~lL~~~~Lm~~~~~~~~~~IT~~GFqFLLqd~n~QvW~lll~YL~~~e 207 (448)
T TIGR00625 134 AEERWETILHFMVGTPSA------KVPSEDVLQLLKQAGLMKSTEPGEPPCITSAGFQFLLQDINAQLWTLLLQYLKTAE 207 (448)
T ss_pred HHHHHHHHHHHHcCCCCc------CCCchHHHHHHHhCCCCcccCCCCCccCchhhHHHHcCChhHHHHHHHHHHHHHHH
Confidence 568999999999944322 56899999999999999873 3358999999999999999999999999999999
Q ss_pred HcCCChHHHHHHHHHhcccccCccccCCCCCHHHHHHHHHHhhcCceeeecCCCccccccchhhhhcccccCC----cc-
Q 020247 95 ERGINQADLISFLLELSFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTD----SS- 169 (329)
Q Consensus 95 ~~g~~~~e~L~fLf~Ls~~~~G~~Y~~~~lt~~q~~~L~~L~d~GLVy~~~~~~~~fy~pT~La~~L~~~~~~----~~- 169 (329)
++|+|.+|+|+|||+||++++|++|++++||++|++||+||+|+||||++++++++|| |||||++|+++.++ ++
T Consensus 208 ~~g~d~vevLsFLf~Ls~l~lG~~Y~~~~Lt~tq~~~L~dL~dlGLVy~~~~~~~~fY-PTrLAt~Lts~~~~l~~~~~~ 286 (448)
T TIGR00625 208 SRGMDLVEVLHFLFMLGFLTLGKAYSVDGLSDTQLIMLQDLREYGLVFQRKRKSRRFY-PTRLAINLTSDTKTVSGAGGT 286 (448)
T ss_pred hcCCCHHHHHHHHHHHhccccCCccCCCCCCHHHHHHHHHHHHcCeEEEecCCCCccc-chHHHHHHhcCcccccccccc
Confidence 9999999999999999999999999999999999999999999999999999999999 99999999876542 11
Q ss_pred -ccccceEEEeeceeEEeecCChhHHHHHHHhhhhhhccCceEEEEeCHHHHHHHHHcCCCHHHHHHHHHhcCCcccc-c
Q 020247 170 -ARKEGFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVA-D 247 (329)
Q Consensus 170 -~~~~g~IIVETNFrvYAYT~S~lqiaiL~lF~el~~r~PNlvvg~iTReSV~~Al~~GITA~QII~fL~~hAHp~m~-~ 247 (329)
..++|||||||||||||||+||||++||++||++.||||||+||+|||+||++|+++||||||||+||++||||+|+ +
T Consensus 287 ~~~~~g~iivEtNfrvYaYt~s~l~~~il~lF~~~~~r~pnlvvg~iTr~Sv~~A~~~GITa~qIi~fl~~~ahp~~~~~ 366 (448)
T TIGR00625 287 VDDDLGFIIVETNYRLYAYTESPLQIALIALFSELLARFPNMVVGQITRESIRRALANGITAQQIIHYLRTHAHPQMRKE 366 (448)
T ss_pred ccCCCceEEEEecceEEEecCCHHHHHHHHHHHHHHhcCCceEEEEecHHHHHHHHHcCCCHHHHHHHHHhcCChhhhcc
Confidence 25679999999999999999999999999999999999999999999999999999999999999999999999998 4
Q ss_pred cCCCCChhHHHHHHHHHHhcCceeeeceeeecCCCCHHHHHHHHHHHHHcCeEeeecCCCceEEEeccccHHHHHHHhhc
Q 020247 248 RMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEAACDYARDQSGLLWEDPKKMRLVVKAEIHMHMREFLRGQ 327 (329)
Q Consensus 248 ~~~~iP~tV~dQI~lWe~Er~Rl~~~~g~Ly~~f~s~~~fe~v~~yA~~~g~llw~~~~kr~~~V~~~~h~~vr~f~k~~ 327 (329)
+.|+|||||+|||||||.||||+++++|+||++|.|++||+++++||+++|+|+|+|+.||+|||+.+||++||+|||++
T Consensus 367 ~~~~lP~tv~dQi~lWe~e~~R~~~~~~~l~~~f~s~~~y~~~~~ya~~~~~l~w~~~~kr~~~V~~~gh~~v~~f~k~~ 446 (448)
T TIGR00625 367 QTPVLPPTIVDQIRLWELERDRLRFTEGVLYNDFLTQVDFELLLAYARELGVLVWENSAKRLFFITPAGHSDVKRFWKRQ 446 (448)
T ss_pred CCCCCChHHHHHHHHHHHHhcceEeecceeeeecCCHHHHHHHHHHHHHcCEEEEecCCceEEEEeccchHHHHHHHHhh
Confidence 78999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cC
Q 020247 328 NK 329 (329)
Q Consensus 328 ~~ 329 (329)
|+
T Consensus 447 ~~ 448 (448)
T TIGR00625 447 KH 448 (448)
T ss_pred cC
Confidence 86
No 3
>COG5144 TFB2 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB2 [Transcription / DNA replication, recombination, and repair]
Probab=100.00 E-value=1.4e-98 Score=715.27 Aligned_cols=305 Identities=32% Similarity=0.574 Sum_probs=291.2
Q ss_pred ccCccceecceeccCCCCCCCCCCCCCcHHHHHHHHhCCCccCCCCCCccchhchhhhccChhhHHHHHHHHHHHHHHHc
Q 020247 17 GFQPWRTLRPMPLDNGSSTQAERPTNFSSSMMKVFQRGLLSRRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQER 96 (329)
Q Consensus 17 ~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~v~~lL~~~gL~~~~~~~~~IT~~GfqFLL~d~~~Q~W~lll~yl~~~e~~ 96 (329)
+-++|||++|+|| |++.+ .-|++.|+++|+++|||..+...++||++|||||||+.|+|+|++++.||++.|..
T Consensus 135 s~~kwEtILhfmV--gtpea----kip~egVl~lLk~ggLm~~~~ne~kITn~GFqFLLq~in~QlWtLlL~yLK~~e~s 208 (447)
T COG5144 135 SSRKWETILHFMV--GTPEA----KIPAEGVLELLKFGGLMGRDRNEFKITNRGFQFLLQTINEQLWTLLLLYLKYFEGS 208 (447)
T ss_pred hhhhHHHHHHHHh--CCccc----cCcchhHHHHHHhcccccCCcccceeehhHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence 4578999999999 66544 77999999999999999988889999999999999999999999999999999999
Q ss_pred CCChHHHHHHHHHhcccccCccccCCCCCHHHHHHHHHHhhcCceeeecCCCccccccchhhhhcccccC----C--ccc
Q 020247 97 GINQADLISFLLELSFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLT----D--SSA 170 (329)
Q Consensus 97 g~~~~e~L~fLf~Ls~~~~G~~Y~~~~lt~~q~~~L~~L~d~GLVy~~~~~~~~fy~pT~La~~L~~~~~----~--~~~ 170 (329)
-||++++|+|||+||.+++|++|+++.||++|+-+|+|+|++|||++++-.+++|| ||+||+.++++-- . ...
T Consensus 209 ~md~v~VLhflFmLgal~vG~aY~id~lsdtqqiml~D~R~yglv~q~~i~~~~fY-pt~LA~glt~d~~~~~s~qnr~e 287 (447)
T COG5144 209 VMDEVAVLHFLFMLGALAVGTAYKIDALSDTQQIMLMDRRLYGLVEQLGILRKIFY-PTGLAIGLTFDQLFEASEQNRRE 287 (447)
T ss_pred cccHHHHHHHHHHhcchhhcceeeecccchHHHHHHHHHHHhhHHHHhccchhhcc-ccccchhhhhHHHHHhhhhcccc
Confidence 99999999999999999999999999999999999999999999999998889999 9999999876422 1 233
Q ss_pred cccceEEEeeceeEEeecCChhHHHHHHHhhhhhhccCceEEEEeCHHHHHHHHHcCCCHHHHHHHHHhcCCccccccCC
Q 020247 171 RKEGFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRMP 250 (329)
Q Consensus 171 ~~~g~IIVETNFrvYAYT~S~lqiaiL~lF~el~~r~PNlvvg~iTReSV~~Al~~GITA~QII~fL~~hAHp~m~~~~~ 250 (329)
++.|||||||||||||||+||+|+|+++|||++.+||||||+|+|||||||+|+.+||||+|||.||++||||+|+++.|
T Consensus 288 dd~gfiIVETN~kiYaYtnSplqiavi~LF~nl~arf~Nlv~GiITreSirrAl~nGIta~QII~yLethahpqmr~~l~ 367 (447)
T COG5144 288 DDKGFIIVETNNKIYAYTNSPLQIAVIHLFCNLTARFPNLVKGIITRESIRRALDNGITAKQIIHYLETHAHPQMRKKLE 367 (447)
T ss_pred ccCceEEEEecceEEEecCChHHHHHHHHhhhhhcccchhhhhhccHHHHHHHHhcCccHHHHHHHHHhccChhhhhcCC
Confidence 66799999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCChhHHHHHHHHHHhcCceeeeceeeecCCCCHHHHHHHHHHHHHcCeEeeecCCCceEEEeccccHHHHHHHhhcc
Q 020247 251 SVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEAACDYARDQSGLLWEDPKKMRLVVKAEIHMHMREFLRGQN 328 (329)
Q Consensus 251 ~iP~tV~dQI~lWe~Er~Rl~~~~g~Ly~~f~s~~~fe~v~~yA~~~g~llw~~~~kr~~~V~~~~h~~vr~f~k~~~ 328 (329)
.+||||+|||++||.|+||+...||+||+||.+..+|+.+.+||++.|+|+|++..||+|||+.+||..|++|.|++-
T Consensus 368 llPPtivdQI~lWele~nRi~~~pG~LysdFlt~s~y~~~~eya~~~gvLvw~d~~Krmffi~~eG~s~v~~f~Kr~l 445 (447)
T COG5144 368 LLPPTIVDQIVLWELERNRIFMVPGYLYSDFLTLSDYQKVLEYAIRGGVLVWSDVDKRMFFIKLEGHSLVKEFVKRIL 445 (447)
T ss_pred CCChhhhhheeeeeeccCcEEeecchHHhhhhchhhHHHHHHHHHhcCeEEeecccceEEEEEccCcHHHHHHHHHHh
Confidence 999999999999999999999999999999999999999999999999999999999999999999999999999964
No 4
>PF03849 Tfb2: Transcription factor Tfb2; InterPro: IPR004598 Members of this family are part of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. The core-TFIIH basal transcription factor complex has six subunits, this is the p52 subunit.; GO: 0006281 DNA repair, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=100.00 E-value=2.3e-78 Score=593.97 Aligned_cols=222 Identities=44% Similarity=0.770 Sum_probs=207.8
Q ss_pred ccCccceecceeccCCCCCCCCCCCCCcHHHHHHHHhCCCccC--CCCCCccchhchhhhccChhhHHHHHHHHHHHHHH
Q 020247 17 GFQPWRTLRPMPLDNGSSTQAERPTNFSSSMMKVFQRGLLSRR--DKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQ 94 (329)
Q Consensus 17 ~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~v~~lL~~~gL~~~--~~~~~~IT~~GfqFLL~d~~~Q~W~lll~yl~~~e 94 (329)
+.++||||+||||++++... ..||++|+++|+++|||+. ++++..||++||||||+|+++|+|+||++||+++|
T Consensus 132 A~~rWE~IL~~mVgs~~~~~----~~~s~~v~~lL~~sgLm~~~~~~~~~~IT~~GFqFLL~d~~~QlW~lll~yL~~~e 207 (366)
T PF03849_consen 132 ARERWESILHYMVGSSSSSN----SSPSQDVKQLLKRSGLMKRSESGGSLKITSKGFQFLLQDTNAQLWTLLLQYLKMAE 207 (366)
T ss_pred HHHHHHHHHHHHhcCccccc----CCCCHHHHHHHHHcCCCcCcCCCCCCcEehhheeeecCChHHHHHHHHHHHHHHHH
Confidence 67899999999995444322 2299999999999999998 55689999999999999999999999999999999
Q ss_pred HcCCChHHHHHHHHHhcccccCccccCCCCCHHHHHHHHHHhhcCceeeecCCCccccccchhhhhcccccCC-------
Q 020247 95 ERGINQADLISFLLELSFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTD------- 167 (329)
Q Consensus 95 ~~g~~~~e~L~fLf~Ls~~~~G~~Y~~~~lt~~q~~~L~~L~d~GLVy~~~~~~~~fy~pT~La~~L~~~~~~------- 167 (329)
++|++.+|+|+|||+||++++|++|++++||++|++||+||+|+||||++++++++|| |||||++|+++.+.
T Consensus 208 ~~~~~~~~~l~flf~L~~~~~g~~Y~~~~ls~~q~~~L~~l~~~GLvy~~~~~~~~fy-pT~La~~l~~~~~~~~~~~~~ 286 (366)
T PF03849_consen 208 ARGMDLVEVLSFLFQLSFLELGKAYSTEGLSETQKNMLQDLRELGLVYQRKRKSRRFY-PTRLATNLTSGSSALRSASSA 286 (366)
T ss_pred hcCCCHHHHHHHHHHhcccccCCcCcCCCCCHHHHHHHHHHHHCCeEEEecCCCCeEe-chHHHHHHhcCCCcccccccc
Confidence 9999999999999999999999999999999999999999999999999999999999 99999999887652
Q ss_pred ----ccccccceEEEeeceeEEeecCChhHHHHHHHhhhhhhccCceEEEEeCHHHHHHHHHcCCCHHHHHHHHHhcCCc
Q 020247 168 ----SSARKEGFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHP 243 (329)
Q Consensus 168 ----~~~~~~g~IIVETNFrvYAYT~S~lqiaiL~lF~el~~r~PNlvvg~iTReSV~~Al~~GITA~QII~fL~~hAHp 243 (329)
....++|||||||||||||||+||||||||++||++.|||||||||+||||||++|+++||||||||+||++||||
T Consensus 287 ~~~~~~~~~~g~iivETNfrvYAYT~s~l~iaiL~lF~~~~~r~pnlvvg~iTr~Sv~~A~~~GIta~qIi~fL~~~aHp 366 (366)
T PF03849_consen 287 LDSSSSSNKEGFIIVETNFRVYAYTNSPLQIAILSLFCELKYRFPNLVVGQITRESVRRALKNGITADQIISFLRSHAHP 366 (366)
T ss_pred cccccccccCceEEEEecceEEEecCCHHHHHHHHHHHHHHhcCCCeEEEEEcHHHHHHHHHcCCCHHHHHHHHHhcCCC
Confidence 1346789999999999999999999999999999999999999999999999999999999999999999999999
No 5
>PF13625 Helicase_C_3: Helicase conserved C-terminal domain
Probab=99.68 E-value=4.7e-16 Score=132.01 Aligned_cols=118 Identities=23% Similarity=0.361 Sum_probs=105.3
Q ss_pred EEEeeceeEEeecCCh--hHHHHHHHhhhhhhccCceEEEEeCHHHHHHHHHcCCCHHHHHHHHHhcCCccccccCCCCC
Q 020247 176 IVVETNFRMYAYSTSK--LHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRMPSVP 253 (329)
Q Consensus 176 IIVETNFrvYAYT~S~--lqiaiL~lF~el~~r~PNlvvg~iTReSV~~Al~~GITA~QII~fL~~hAHp~m~~~~~~iP 253 (329)
+||++||.|.+++.+| -..+.|..|+++ .+..+|.+++||+.|+.+|++.|+|+++|++||+.|+.. .||
T Consensus 2 liVqpd~~I~v~~~~~~~~~~~~L~~fae~-~s~~~~~~yrlT~~Sl~~A~~~G~~~e~i~~~L~~~S~~-------~lP 73 (129)
T PF13625_consen 2 LIVQPDFEILVEPGHPSPADAWFLARFAEL-KSPDTMHVYRLTPASLWRAASAGLTAEEIIEFLERYSKN-------PLP 73 (129)
T ss_pred EEECCCCEEEEeCCCCCHHHHHHHHHHhcc-cccCceEEEEECHHHHHHHHHcCCCHHHHHHHHHHHcCC-------CCC
Confidence 7999999999977766 344999999999 567999999999999999999999999999999999954 699
Q ss_pred hhHHHHHHHHHHhcCceeeeceeeecCCCCHHHHHHHHHHHHHcCeEe
Q 020247 254 ENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEAACDYARDQSGLL 301 (329)
Q Consensus 254 ~tV~dQI~lWe~Er~Rl~~~~g~Ly~~f~s~~~fe~v~~yA~~~g~ll 301 (329)
++|..+|+-|+...+|+++.++..|-.+.+.+..+.+.+..+-.++.+
T Consensus 74 ~~v~~~i~~w~~~~g~v~l~~~~~~l~~~d~~~l~~l~~~~~~~~~~~ 121 (129)
T PF13625_consen 74 QNVEQSIEDWARRYGRVRLYKGAYLLECDDPELLDELLADPELAKLIL 121 (129)
T ss_pred HHHHHHHHHHHHhcCCEEEecCeEEEEECCHHHHHHHHhChhhhhhhc
Confidence 999999999999999999999676669999999999988877665443
No 6
>TIGR00603 rad25 DNA repair helicase rad25. All proteins in this family for which functions are known are DNA-DNA helicases used for the initiation of nucleotide excision repair and transacription as part of the TFIIH complex.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.39 E-value=0.0016 Score=70.36 Aligned_cols=106 Identities=24% Similarity=0.380 Sum_probs=84.3
Q ss_pred cceEEEeeceeEEeecCChhH--H-HHHHHhhhhhhccCceEEEEeCHHHHHHHHHcCCCHHHHHHHHHhcCCccccccC
Q 020247 173 EGFIVVETNFRMYAYSTSKLH--C-EILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRM 249 (329)
Q Consensus 173 ~g~IIVETNFrvYAYT~S~lq--i-aiL~lF~el~~r~PNlvvg~iTReSV~~Al~~GITA~QII~fL~~hAHp~m~~~~ 249 (329)
+|.|++|| .||+- . .-|..|+|+.+|--+|..++||-=|+-.|...|+++++||++|..++-.
T Consensus 22 d~~i~lE~--------~~p~~~~a~~fl~~~aEp~~rp~~iHeY~lT~~sl~~A~s~g~~~~~ii~~L~~~sk~------ 87 (732)
T TIGR00603 22 DGHIFLES--------FSPLYKQAQDFLVAIAEPVCRPEHIHEYKLTAYSLYAAVSVGLETEDIIEVLGRLSKT------ 87 (732)
T ss_pred CCeEEEEe--------CCccHHHHHHHHHHhcccccChhheEEEeccHHHHHHHHHcCCCHHHHHHHHHHHhCC------
Confidence 45666666 34443 3 7899999999999999999999999999999999999999999999844
Q ss_pred CCCChhHHHHHHHHHHhcCceeee--ceeeecCCCCHHHHHHHHHH
Q 020247 250 PSVPENVCDQIRLWESDLNRVEMT--PAHYYDEFPSRDVFEAACDY 293 (329)
Q Consensus 250 ~~iP~tV~dQI~lWe~Er~Rl~~~--~g~Ly~~f~s~~~fe~v~~y 293 (329)
.||++|.+.|+.+-.-.+++++. +.--|-+-.+.+..+.+.+.
T Consensus 88 -~~p~~i~~~i~~~~~~ygk~klv~~~~~~~~es~~~~~l~~l~~~ 132 (732)
T TIGR00603 88 -PIPKGIIEFIRLCTQSYGKVKLVLKHNRYFVESPHPEVLQRLLKD 132 (732)
T ss_pred -CCCHHHHHHHHHHHHhcCcEEEEEcCCceEEecCCHHHHHHHHhc
Confidence 79999999999999999999883 22113244555555555543
No 7
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=92.48 E-value=0.12 Score=34.08 Aligned_cols=22 Identities=36% Similarity=0.525 Sum_probs=17.7
Q ss_pred HHHHHHHcCCCHHHHHHHHHhc
Q 020247 219 SLYNAFENGITAEQIISFLQQN 240 (329)
Q Consensus 219 SV~~Al~~GITA~QII~fL~~h 240 (329)
=|++|...|||.+||-+||+.+
T Consensus 8 Li~eA~~~Gls~eeir~FL~~~ 29 (30)
T PF08671_consen 8 LIKEAKESGLSKEEIREFLEFN 29 (30)
T ss_dssp HHHHHHHTT--HHHHHHHHHHH
T ss_pred HHHHHHHcCCCHHHHHHHHHhC
Confidence 3789999999999999999864
No 8
>PRK06015 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional
Probab=84.22 E-value=7.2 Score=36.16 Aligned_cols=126 Identities=16% Similarity=0.242 Sum_probs=87.5
Q ss_pred ccceEEEeeceeEEeecCChhHHHHHHHhhhhhhccCceEEE---EeCHHHHHHHHHcCC-------CHHHHHHHHHhcC
Q 020247 172 KEGFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVG---AITKESLYNAFENGI-------TAEQIISFLQQNA 241 (329)
Q Consensus 172 ~~g~IIVETNFrvYAYT~S~lqiaiL~lF~el~~r~PNlvvg---~iTReSV~~Al~~GI-------TA~QII~fL~~hA 241 (329)
+.|.=++|-.|+ +|--. ..+.++..++|++.|| ++|.|.+++|.+.|- .-+.++++-+.+-
T Consensus 27 ~gGi~~iEit~~------tp~a~---~~I~~l~~~~~~~~vGAGTVl~~e~a~~ai~aGA~FivSP~~~~~vi~~a~~~~ 97 (201)
T PRK06015 27 AGGLPAIEITLR------TPAAL---DAIRAVAAEVEEAIVGAGTILNAKQFEDAAKAGSRFIVSPGTTQELLAAANDSD 97 (201)
T ss_pred HCCCCEEEEeCC------CccHH---HHHHHHHHHCCCCEEeeEeCcCHHHHHHHHHcCCCEEECCCCCHHHHHHHHHcC
Confidence 346667777765 44333 3344566678999999 899999999999995 4678888888776
Q ss_pred CccccccCCCCCh--hHHHHHHHHHHhcCceeeeceeeecCCCCHHHHHHHHHHHHHcCeEeeecCCCceEEEeccccHH
Q 020247 242 HPRVADRMPSVPE--NVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEAACDYARDQSGLLWEDPKKMRLVVKAEIHMH 319 (329)
Q Consensus 242 Hp~m~~~~~~iP~--tV~dQI~lWe~Er~Rl~~~~g~Ly~~f~s~~~fe~v~~yA~~~g~llw~~~~kr~~~V~~~~h~~ 319 (329)
.| .+|= |..+=..-|+.=-+-+|+.|+-.+- . .+|.+.+...+ +.-++|-+.-=.-++
T Consensus 98 i~-------~iPG~~TptEi~~A~~~Ga~~vK~FPa~~~G---G-------~~yikal~~pl---p~~~l~ptGGV~~~n 157 (201)
T PRK06015 98 VP-------LLPGAATPSEVMALREEGYTVLKFFPAEQAG---G-------AAFLKALSSPL---AGTFFCPTGGISLKN 157 (201)
T ss_pred CC-------EeCCCCCHHHHHHHHHCCCCEEEECCchhhC---C-------HHHHHHHHhhC---CCCcEEecCCCCHHH
Confidence 66 7775 7788888999999999998864441 0 34556655444 344444433333478
Q ss_pred HHHHHhh
Q 020247 320 MREFLRG 326 (329)
Q Consensus 320 vr~f~k~ 326 (329)
+.+|++.
T Consensus 158 ~~~~l~a 164 (201)
T PRK06015 158 ARDYLSL 164 (201)
T ss_pred HHHHHhC
Confidence 8888874
No 9
>PRK05718 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional
Probab=80.25 E-value=20 Score=33.40 Aligned_cols=162 Identities=18% Similarity=0.229 Sum_probs=103.6
Q ss_pred CCHHHHHHHHHHhhcCceeeecCC-CccccccchhhhhcccccCCccccccceEEEeeceeEEeecCChhHHHHHHHhhh
Q 020247 124 LSEIQKSMIKDFADLGLVKLQQGR-KENWFIPTKLATNLSMSLTDSSARKEGFIVVETNFRMYAYSTSKLHCEILRLFSK 202 (329)
Q Consensus 124 lt~~q~~~L~~L~d~GLVy~~~~~-~~~fy~pT~La~~L~~~~~~~~~~~~g~IIVETNFrvYAYT~S~lqiaiL~lF~e 202 (329)
+++++..+++.|.+.|+|-.-+.. ..... +++-.+ .+.|.=++|--++ +|-- +..+.+
T Consensus 1 ~~~~~~~~~~~l~~~~~iaV~r~~~~~~a~---~i~~al---------~~~Gi~~iEitl~------~~~~---~~~I~~ 59 (212)
T PRK05718 1 MKNWKTSIEEILRAGPVVPVIVINKLEDAV---PLAKAL---------VAGGLPVLEVTLR------TPAA---LEAIRL 59 (212)
T ss_pred CchhHHHHHHHHHHCCEEEEEEcCCHHHHH---HHHHHH---------HHcCCCEEEEecC------CccH---HHHHHH
Confidence 367888899999999999665432 11111 111111 2335556776643 4433 344455
Q ss_pred hhhccCceEEE---EeCHHHHHHHHHcCC-------CHHHHHHHHHhcCCccccccCCCCCh--hHHHHHHHHHHhcCce
Q 020247 203 VEYQLPNLIVG---AITKESLYNAFENGI-------TAEQIISFLQQNAHPRVADRMPSVPE--NVCDQIRLWESDLNRV 270 (329)
Q Consensus 203 l~~r~PNlvvg---~iTReSV~~Al~~GI-------TA~QII~fL~~hAHp~m~~~~~~iP~--tV~dQI~lWe~Er~Rl 270 (329)
+..+||++.|| ++|.+.++.|++.|- ..+.+|++-..+-.| .+|- |..+=...|+.--+-+
T Consensus 60 l~~~~p~~~IGAGTVl~~~~a~~a~~aGA~FivsP~~~~~vi~~a~~~~i~-------~iPG~~TptEi~~a~~~Ga~~v 132 (212)
T PRK05718 60 IAKEVPEALIGAGTVLNPEQLAQAIEAGAQFIVSPGLTPPLLKAAQEGPIP-------LIPGVSTPSELMLGMELGLRTF 132 (212)
T ss_pred HHHHCCCCEEEEeeccCHHHHHHHHHcCCCEEECCCCCHHHHHHHHHcCCC-------EeCCCCCHHHHHHHHHCCCCEE
Confidence 55679999999 899999999999984 456899988876555 7775 4466445888888888
Q ss_pred eeeceeeecCCCCHHHHHHHHHHHHHcCeEeeecCCCceEEEeccccHHHHHHHhh
Q 020247 271 EMTPAHYYDEFPSRDVFEAACDYARDQSGLLWEDPKKMRLVVKAEIHMHMREFLRG 326 (329)
Q Consensus 271 ~~~~g~Ly~~f~s~~~fe~v~~yA~~~g~llw~~~~kr~~~V~~~~h~~vr~f~k~ 326 (329)
++.|+-.+- =.+|-+.+...+ +.-+.+.+.-=.-+++++|++.
T Consensus 133 KlFPa~~~g----------g~~~lk~l~~p~---p~~~~~ptGGV~~~ni~~~l~a 175 (212)
T PRK05718 133 KFFPAEASG----------GVKMLKALAGPF---PDVRFCPTGGISPANYRDYLAL 175 (212)
T ss_pred EEccchhcc----------CHHHHHHHhccC---CCCeEEEeCCCCHHHHHHHHhC
Confidence 886533220 145666655444 4455555444445889999874
No 10
>PF01081 Aldolase: KDPG and KHG aldolase; InterPro: IPR000887 4-Hydroxy-2-oxoglutarate aldolase (4.1.3.16 from EC) (KHG-aldolase) catalyzes the interconversion of 4-hydroxy-2-oxoglutarate into pyruvate and glyoxylate. Phospho-2-dehydro-3-deoxygluconate aldolase (4.1.2.14 from EC) (KDPG-aldolase) catalyzes the interconversion of 6-phospho-2-dehydro-3-deoxy-D-gluconate into pyruvate and glyceraldehyde 3-phosphate. These two enzymes are structurally and functionally related []. They are both homotrimeric proteins of approximately 220 amino-acid residues. They are class I aldolases whose catalytic mechanism involves the formation of a Schiff-base intermediate between the substrate and the epsilon-amino group of a lysine residue. In both enzymes, an arginine is required for catalytic activity.; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 3VCR_A 1FQ0_A 1EUN_A 1EUA_B 1FWR_A 2C0A_B 1WBH_A 1WAU_A 2YW3_B 2YW4_A ....
Probab=79.50 E-value=3.2 Score=38.28 Aligned_cols=126 Identities=19% Similarity=0.333 Sum_probs=81.1
Q ss_pred ccceEEEeeceeEEeecCChhHHHHHHHhhhhhhccCceEEE---EeCHHHHHHHHHcCC-------CHHHHHHHHHhcC
Q 020247 172 KEGFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVG---AITKESLYNAFENGI-------TAEQIISFLQQNA 241 (329)
Q Consensus 172 ~~g~IIVETNFrvYAYT~S~lqiaiL~lF~el~~r~PNlvvg---~iTReSV~~Al~~GI-------TA~QII~fL~~hA 241 (329)
+.|.=++|--|| +|--.. ...++..++|+|.|| ++|.|.+++|.+.|- .-++++++-+.|-
T Consensus 31 ~gGi~~iEiT~~------t~~a~~---~I~~l~~~~p~~~vGAGTV~~~e~a~~a~~aGA~FivSP~~~~~v~~~~~~~~ 101 (196)
T PF01081_consen 31 EGGIRAIEITLR------TPNALE---AIEALRKEFPDLLVGAGTVLTAEQAEAAIAAGAQFIVSPGFDPEVIEYAREYG 101 (196)
T ss_dssp HTT--EEEEETT------STTHHH---HHHHHHHHHTTSEEEEES--SHHHHHHHHHHT-SEEEESS--HHHHHHHHHHT
T ss_pred HCCCCEEEEecC------CccHHH---HHHHHHHHCCCCeeEEEeccCHHHHHHHHHcCCCEEECCCCCHHHHHHHHHcC
Confidence 346667887776 333223 334455678999999 899999999999994 4678999998887
Q ss_pred CccccccCCCCC--hhHHHHHHHHHHhcCceeeeceeeecCCCCHHHHHHHHHHHHHcCeEeeecCCCceEEEeccccHH
Q 020247 242 HPRVADRMPSVP--ENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEAACDYARDQSGLLWEDPKKMRLVVKAEIHMH 319 (329)
Q Consensus 242 Hp~m~~~~~~iP--~tV~dQI~lWe~Er~Rl~~~~g~Ly~~f~s~~~fe~v~~yA~~~g~llw~~~~kr~~~V~~~~h~~ 319 (329)
.| .+| -|..+=...|+.-.+-+|+.|+-.+- =.+|.+++...+ +.-+.+.+.-=.-++
T Consensus 102 i~-------~iPG~~TptEi~~A~~~G~~~vK~FPA~~~G----------G~~~ik~l~~p~---p~~~~~ptGGV~~~N 161 (196)
T PF01081_consen 102 IP-------YIPGVMTPTEIMQALEAGADIVKLFPAGALG----------GPSYIKALRGPF---PDLPFMPTGGVNPDN 161 (196)
T ss_dssp SE-------EEEEESSHHHHHHHHHTT-SEEEETTTTTTT----------HHHHHHHHHTTT---TT-EEEEBSS--TTT
T ss_pred Cc-------ccCCcCCHHHHHHHHHCCCCEEEEecchhcC----------cHHHHHHHhccC---CCCeEEEcCCCCHHH
Confidence 77 777 37777788899999999999976651 134556644332 333444433334567
Q ss_pred HHHHHhh
Q 020247 320 MREFLRG 326 (329)
Q Consensus 320 vr~f~k~ 326 (329)
+++|++.
T Consensus 162 ~~~~l~a 168 (196)
T PF01081_consen 162 LAEYLKA 168 (196)
T ss_dssp HHHHHTS
T ss_pred HHHHHhC
Confidence 9999875
No 11
>TIGR01615 A_thal_3542 uncharacterized plant-specific domain TIGR01615. of a number of uncharacterized plant proteins. The domain is strongly conserved (greater than 30 % sequence identity between most pairs of members) but flanked by highly divergent regions including stretches of low-complexity sequence.
Probab=76.88 E-value=1.3 Score=38.76 Aligned_cols=65 Identities=17% Similarity=0.383 Sum_probs=50.5
Q ss_pred ccceEEEeeceeEEeecCChhHHH-HHHHhhhhhhccCceEEEEeCHHHHHHHHHcCCCHHHHHHHHHhcCCccccccCC
Q 020247 172 KEGFIVVETNFRMYAYSTSKLHCE-ILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRMP 250 (329)
Q Consensus 172 ~~g~IIVETNFrvYAYT~S~lqia-iL~lF~el~~r~PNlvvg~iTReSV~~Al~~GITA~QII~fL~~hAHp~m~~~~~ 250 (329)
....+|||.||| +.+.|| ==.-+.++...+|.+.||...| -.||++.+-..|--.|+++.-
T Consensus 47 ~~~R~iVd~dFr------~~FeiARpt~~Y~~ll~~LP~vFVG~~~r------------L~~iV~~mc~Aak~Slk~~gm 108 (131)
T TIGR01615 47 QEMRVIIDLDFR------SEFEIARPTEEYKRLLESLPEVFVGTTER------------LRQLVRLMCDAAKKSLKKKGM 108 (131)
T ss_pred CcceEEEeccch------hhceecCCCHHHHHHHHhCCcceECCHHH------------HHHHHHHHHHHHHHHHHHcCC
Confidence 445799999998 666652 2234667777899999996655 368999999999999999887
Q ss_pred CCCh
Q 020247 251 SVPE 254 (329)
Q Consensus 251 ~iP~ 254 (329)
-+||
T Consensus 109 hlPP 112 (131)
T TIGR01615 109 PLPP 112 (131)
T ss_pred CCCC
Confidence 8888
No 12
>TIGR01182 eda Entner-Doudoroff aldolase. 2-deydro-3-deoxyphosphogluconate aldolase (EC 4.1.2.14) is an enzyme of the Entner-Doudoroff pathway. This aldolase has another function, 4-hydroxy-2-oxoglutarate aldolase (EC 4.1.3.16) shown experimentally in Escherichia coli and Pseudomonas putida
Probab=75.80 E-value=24 Score=32.76 Aligned_cols=125 Identities=16% Similarity=0.318 Sum_probs=85.2
Q ss_pred cceEEEeeceeEEeecCChhHHHHHHHhhhhhhccCceEEE---EeCHHHHHHHHHcCC-------CHHHHHHHHHhcCC
Q 020247 173 EGFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVG---AITKESLYNAFENGI-------TAEQIISFLQQNAH 242 (329)
Q Consensus 173 ~g~IIVETNFrvYAYT~S~lqiaiL~lF~el~~r~PNlvvg---~iTReSV~~Al~~GI-------TA~QII~fL~~hAH 242 (329)
.|.=++|--|+ +|--...+ .++..++|++.|| ++|.|.+++|.+.|- .-..++.+.+.+--
T Consensus 32 ~Gi~~iEit~~------t~~a~~~i---~~l~~~~~~~~vGAGTVl~~~~a~~a~~aGA~FivsP~~~~~v~~~~~~~~i 102 (204)
T TIGR01182 32 GGLRVLEVTLR------TPVALDAI---RLLRKEVPDALIGAGTVLNPEQLRQAVDAGAQFIVSPGLTPELAKHAQDHGI 102 (204)
T ss_pred cCCCEEEEeCC------CccHHHHH---HHHHHHCCCCEEEEEeCCCHHHHHHHHHcCCCEEECCCCCHHHHHHHHHcCC
Confidence 35556666663 45444443 4445578999999 899999999999994 34677777776544
Q ss_pred ccccccCCCCCh--hHHHHHHHHHHhcCceeeeceeeecCCCCHHHHHHHHHHHHHcCeEeeecCCCceEEEeccccHHH
Q 020247 243 PRVADRMPSVPE--NVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEAACDYARDQSGLLWEDPKKMRLVVKAEIHMHM 320 (329)
Q Consensus 243 p~m~~~~~~iP~--tV~dQI~lWe~Er~Rl~~~~g~Ly~~f~s~~~fe~v~~yA~~~g~llw~~~~kr~~~V~~~~h~~v 320 (329)
|.+|= |-.+=..-|+.--+-+|+.|+-.+-. .+|-+.+...+ +.-+.+.+.-=.-+++
T Consensus 103 -------~~iPG~~TptEi~~A~~~Ga~~vKlFPA~~~GG----------~~yikal~~pl---p~i~~~ptGGV~~~N~ 162 (204)
T TIGR01182 103 -------PIIPGVATPSEIMLALELGITALKLFPAEVSGG----------VKMLKALAGPF---PQVRFCPTGGINLANV 162 (204)
T ss_pred -------cEECCCCCHHHHHHHHHCCCCEEEECCchhcCC----------HHHHHHHhccC---CCCcEEecCCCCHHHH
Confidence 46774 77788889999999999988655410 35667766554 4455554433344889
Q ss_pred HHHHhh
Q 020247 321 REFLRG 326 (329)
Q Consensus 321 r~f~k~ 326 (329)
.+|++.
T Consensus 163 ~~~l~a 168 (204)
T TIGR01182 163 RDYLAA 168 (204)
T ss_pred HHHHhC
Confidence 999874
No 13
>PRK07114 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional
Probab=75.18 E-value=34 Score=32.15 Aligned_cols=156 Identities=15% Similarity=0.194 Sum_probs=100.5
Q ss_pred HHHHHHhhcCceeeecCC-CccccccchhhhhcccccCCccccccceEEEeeceeEEeecCChhHHHHHHHhh-hhhhcc
Q 020247 130 SMIKDFADLGLVKLQQGR-KENWFIPTKLATNLSMSLTDSSARKEGFIVVETNFRMYAYSTSKLHCEILRLFS-KVEYQL 207 (329)
Q Consensus 130 ~~L~~L~d~GLVy~~~~~-~~~fy~pT~La~~L~~~~~~~~~~~~g~IIVETNFrvYAYT~S~lqiaiL~lF~-el~~r~ 207 (329)
.+++.|.+.|+|-.-... ...-. +++-.| .+.|.=++|-=|| +|--...+.... +...++
T Consensus 7 ~~~~~l~~~~vi~Vvr~~~~~~a~---~~~~al---------~~gGi~~iEiT~~------tp~a~~~i~~l~~~~~~~~ 68 (222)
T PRK07114 7 AVLTAMKATGMVPVFYHADVEVAK---KVIKAC---------YDGGARVFEFTNR------GDFAHEVFAELVKYAAKEL 68 (222)
T ss_pred HHHHHHHhCCEEEEEEcCCHHHHH---HHHHHH---------HHCCCCEEEEeCC------CCcHHHHHHHHHHHHHhhC
Confidence 467888888888664432 11111 111111 2345556776664 444443443332 444579
Q ss_pred CceEEE---EeCHHHHHHHHHcCC-------CHHHHHHHHHhcCCccccccCCCCCh--hHHHHHHHHHHhcCceeeece
Q 020247 208 PNLIVG---AITKESLYNAFENGI-------TAEQIISFLQQNAHPRVADRMPSVPE--NVCDQIRLWESDLNRVEMTPA 275 (329)
Q Consensus 208 PNlvvg---~iTReSV~~Al~~GI-------TA~QII~fL~~hAHp~m~~~~~~iP~--tV~dQI~lWe~Er~Rl~~~~g 275 (329)
|++.|| ++|.|.++.|.+.|- .-..++++.+.+-.| .+|= |..+=..-|+.=.+-+|+.|+
T Consensus 69 p~~~vGaGTVl~~e~a~~a~~aGA~FiVsP~~~~~v~~~~~~~~i~-------~iPG~~TpsEi~~A~~~Ga~~vKlFPA 141 (222)
T PRK07114 69 PGMILGVGSIVDAATAALYIQLGANFIVTPLFNPDIAKVCNRRKVP-------YSPGCGSLSEIGYAEELGCEIVKLFPG 141 (222)
T ss_pred CCeEEeeEeCcCHHHHHHHHHcCCCEEECCCCCHHHHHHHHHcCCC-------EeCCCCCHHHHHHHHHCCCCEEEECcc
Confidence 999999 899999999999995 457888888887766 7775 777888899999999999986
Q ss_pred eeecCCCCHHHHHHHHHHHHHcCeEeeecCCCceEEEecccc----HHHHHHHhh
Q 020247 276 HYYDEFPSRDVFEAACDYARDQSGLLWEDPKKMRLVVKAEIH----MHMREFLRG 326 (329)
Q Consensus 276 ~Ly~~f~s~~~fe~v~~yA~~~g~llw~~~~kr~~~V~~~~h----~~vr~f~k~ 326 (329)
-.+ . .+|-+.+...+ +.-+ |+...|- +++.+|++.
T Consensus 142 ~~~----------G-~~~ikal~~p~---p~i~--~~ptGGV~~~~~n~~~yl~a 180 (222)
T PRK07114 142 SVY----------G-PGFVKAIKGPM---PWTK--IMPTGGVEPTEENLKKWFGA 180 (222)
T ss_pred ccc----------C-HHHHHHHhccC---CCCe--EEeCCCCCcchhcHHHHHhC
Confidence 543 1 45666655444 3333 3334443 588998873
No 14
>KOG1123 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, 3'-5' helicase subunit SSL2 [Transcription; Replication, recombination and repair]
Probab=72.95 E-value=6.9 Score=41.62 Aligned_cols=89 Identities=24% Similarity=0.359 Sum_probs=69.8
Q ss_pred ccceEEEeeceeEEeecCChhHHHHHHHhhhhhhccCceEEEEeCHHHHHHHHHcCCCHHHHHHHHHhcCCccccccCCC
Q 020247 172 KEGFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRMPS 251 (329)
Q Consensus 172 ~~g~IIVETNFrvYAYT~S~lqiaiL~lF~el~~r~PNlvvg~iTReSV~~Al~~GITA~QII~fL~~hAHp~m~~~~~~ 251 (329)
-+|.||+||==-+|-+- ...|--.+|..+|=-.+.=+.||-=|+-.|..-|.+-+.||++|..-+.. .
T Consensus 81 ~dG~IfLEsFsp~ykqA-----~DFLiaIaEPvcRP~~iHEy~lTaySLYAAVSVGL~T~dIie~L~rlSKt-------~ 148 (776)
T KOG1123|consen 81 PDGHIFLETFSPLYKQA-----QDFLIAIAEPVCRPEHIHEYKLTAYSLYAAVSVGLQTEDIIEVLDRLSKT-------P 148 (776)
T ss_pred CCCeEEeeecCHHHHhH-----hhhhhhhccccCChhhhhhhcchhhhhhhhhccccchHHHHHHHHHhccC-------C
Confidence 46889999742222211 14455567888888889999999999999999999999999999987644 7
Q ss_pred CChhHHHHHHHHHHhcCceee
Q 020247 252 VPENVCDQIRLWESDLNRVEM 272 (329)
Q Consensus 252 iP~tV~dQI~lWe~Er~Rl~~ 272 (329)
||+.|++=|++=-..-+.++.
T Consensus 149 lp~~ii~FI~~cT~sYGKVKL 169 (776)
T KOG1123|consen 149 LPESIIEFIRACTVSYGKVKL 169 (776)
T ss_pred CCHHHHHHHHHHhhccccEEE
Confidence 999999999988777666554
No 15
>PF08356 EF_assoc_2: EF hand associated; InterPro: IPR013567 This region predominantly appears near EF-hands (IPR002048 from INTERPRO) in GTP-binding proteins. It is found in all three eukaryotic kingdoms.
Probab=63.29 E-value=10 Score=30.97 Aligned_cols=43 Identities=21% Similarity=0.423 Sum_probs=30.1
Q ss_pred HHHHHHHHhCCCccCCCCCCccchhchhhh-----ccChhhHHHHHHHHH
Q 020247 45 SSMMKVFQRGLLSRRDKEAPRLTESGFQFL-----LMDTNAQLWYIVREY 89 (329)
Q Consensus 45 ~~v~~lL~~~gL~~~~~~~~~IT~~GfqFL-----L~d~~~Q~W~lll~y 89 (329)
.+|+++.+.. +..+...-.||.+||=|| -..+++-.|++|+.+
T Consensus 10 ~~ik~~v~~~--~~~gv~~~GiT~~GFl~L~~lfierGR~ETtW~vLR~F 57 (89)
T PF08356_consen 10 EDIKKVVREN--IPDGVNDNGITLDGFLFLNKLFIERGRHETTWTVLRKF 57 (89)
T ss_pred HHHHHHHHHH--CCCCcCCCccchhhHHHHHHHHHHhCcchHHHHHHHHc
Confidence 4455555554 322222346999999866 889999999999987
No 16
>PRK14529 adenylate kinase; Provisional
Probab=62.92 E-value=51 Score=30.87 Aligned_cols=80 Identities=16% Similarity=0.243 Sum_probs=57.2
Q ss_pred hhccCceEEEEeCHHHHHHHHHcCCCHHHHHHHHHhcCCccccccCCCCChhHHHHHHHHHHhcCceeeeceeeecCCCC
Q 020247 204 EYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPS 283 (329)
Q Consensus 204 ~~r~PNlvvg~iTReSV~~Al~~GITA~QII~fL~~hAHp~m~~~~~~iP~tV~dQI~lWe~Er~Rl~~~~g~Ly~~f~s 283 (329)
.+.++.+.+|.+.|+.+.. ..-.+++|=.|+.. ...+|..++-++-.+.....- ..|++++.|+-
T Consensus 23 ~~~~~~is~gdllr~~i~~---~t~lg~~i~~~i~~---------G~lvpdei~~~lv~~~l~~~~---~~g~iLDGfPR 87 (223)
T PRK14529 23 KYDLAHIESGAIFREHIGG---GTELGKKAKEYIDR---------GDLVPDDITIPMILETLKQDG---KNGWLLDGFPR 87 (223)
T ss_pred HHCCCCcccchhhhhhccC---CChHHHHHHHHHhc---------cCcchHHHHHHHHHHHHhccC---CCcEEEeCCCC
Confidence 4568999999999998753 22234566666654 348999999999888886653 78999999998
Q ss_pred H-HHHHHHHHHHHHcC
Q 020247 284 R-DVFEAACDYARDQS 298 (329)
Q Consensus 284 ~-~~fe~v~~yA~~~g 298 (329)
. +..+.+-+..++.|
T Consensus 88 t~~Qa~~l~~~l~~~~ 103 (223)
T PRK14529 88 NKVQAEKLWEALQKEG 103 (223)
T ss_pred CHHHHHHHHHHHHhcC
Confidence 5 45555555555555
No 17
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=62.33 E-value=3.6 Score=31.93 Aligned_cols=31 Identities=29% Similarity=0.379 Sum_probs=25.3
Q ss_pred HHHHHHHHhCCCccCCCCCCccchhchhhhc
Q 020247 45 SSMMKVFQRGLLSRRDKEAPRLTESGFQFLL 75 (329)
Q Consensus 45 ~~v~~lL~~~gL~~~~~~~~~IT~~GfqFLL 75 (329)
...++-|...||++.+++...||++|-+||-
T Consensus 37 ~~yL~~L~~~gLI~~~~~~Y~lTekG~~~l~ 67 (77)
T PF14947_consen 37 KKYLKELEEKGLIKKKDGKYRLTEKGKEFLE 67 (77)
T ss_dssp HHHHHHHHHTTSEEEETTEEEE-HHHHHHHH
T ss_pred HHHHHHHHHCcCeeCCCCEEEECccHHHHHH
Confidence 4457788999999887788999999999874
No 18
>PF00406 ADK: Adenylate kinase; InterPro: IPR000850 Adenylate kinases (ADK) are phosphotransferases that catalyse the reversible reaction AMP + MgATP = ADP + MgADP an essential reaction for many processes in living cells. Two ADK isozymes have been identified in mammalian cells. These specifically bind AMP and favour binding to ATP over other nucleotide triphosphates (AK1 is cytosolic and AK2 is located in the mitochondria). A third ADK has been identified in bovine heart and human cells [], this is a mitochondrial GTP:AMP phosphotransferase, also specific for the phosphorylation of AMP, but can only use GTP or ITP as a substrate []. ADK has also been identified in different bacterial species and in yeast []. Two further enzymes are known to be related to the ADK family, i.e. yeast uridine monophosphokinase and slime mold UMP-CMP kinase. Within the ADK family there are several conserved regions, including the ATP-binding domains. One of the most conserved areas includes an Arg residue, whose modification inactivates the enzyme, together with an Asp that resides in the catalytic cleft of the enzyme and participates in a salt bridge.; GO: 0005524 ATP binding, 0019205 nucleobase-containing compound kinase activity, 0006139 nucleobase-containing compound metabolic process; PDB: 1ZD8_A 3TLX_D 1TEV_A 1ZAK_B 3CM0_A 3ADK_A 1ZIP_A 1ZIO_A 1ZIN_A 3NDP_A ....
Probab=57.26 E-value=18 Score=30.54 Aligned_cols=81 Identities=19% Similarity=0.308 Sum_probs=51.8
Q ss_pred hhccCceEEEEeCHHHHHHHHHcCCCHHHHHHHHHhcCCccccccCCCCChhHHHHHHHHHHhcCceeeeceeeecCCCC
Q 020247 204 EYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPS 283 (329)
Q Consensus 204 ~~r~PNlvvg~iTReSV~~Al~~GITA~QII~fL~~hAHp~m~~~~~~iP~tV~dQI~lWe~Er~Rl~~~~g~Ly~~f~s 283 (329)
.+.++.+.+|.+=|+.+++ ..-.+++|-++|.+. ..||+.++-++-.++.+.. .-..|++.+.|+.
T Consensus 19 ~~~~~~is~~~llr~~~~~---~s~~g~~i~~~l~~g---------~~vp~~~v~~ll~~~l~~~--~~~~g~ildGfPr 84 (151)
T PF00406_consen 19 RYGLVHISVGDLLREEIKS---DSELGKQIQEYLDNG---------ELVPDELVIELLKERLEQP--PCNRGFILDGFPR 84 (151)
T ss_dssp HHTSEEEEHHHHHHHHHHT---TSHHHHHHHHHHHTT---------SS--HHHHHHHHHHHHHSG--GTTTEEEEESB-S
T ss_pred hcCcceechHHHHHHHHhh---hhHHHHHHHHHHHhh---------ccchHHHHHHHHHHHHhhh--cccceeeeeeccc
Confidence 3456666666555555532 222357888887754 3899999999998888876 6679999999998
Q ss_pred H-HHHHHHHHHHHHcC
Q 020247 284 R-DVFEAACDYARDQS 298 (329)
Q Consensus 284 ~-~~fe~v~~yA~~~g 298 (329)
. ++++...+.....+
T Consensus 85 t~~Qa~~l~~~~~~~~ 100 (151)
T PF00406_consen 85 TLEQAEALEEILEEEG 100 (151)
T ss_dssp SHHHHHHHHHHHHHTT
T ss_pred cHHHHHHHHHHHhhcc
Confidence 5 44555544333334
No 19
>PRK06552 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional
Probab=56.23 E-value=1.1e+02 Score=28.49 Aligned_cols=154 Identities=16% Similarity=0.292 Sum_probs=91.7
Q ss_pred HHHHHhhcCceeeecCC-CccccccchhhhhcccccCCccccccceEEEeeceeEEeecCChhHHHHHHHhhhhhhcc--
Q 020247 131 MIKDFADLGLVKLQQGR-KENWFIPTKLATNLSMSLTDSSARKEGFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQL-- 207 (329)
Q Consensus 131 ~L~~L~d~GLVy~~~~~-~~~fy~pT~La~~L~~~~~~~~~~~~g~IIVETNFrvYAYT~S~lqiaiL~lF~el~~r~-- 207 (329)
+++.|.+.+++-.-+.. ..... +++-.| .+.|.=++|-=|| +|--.. .+.++..++
T Consensus 6 ~~~~l~~~~vi~vir~~~~~~a~---~~~~al---------~~~Gi~~iEit~~------~~~a~~---~i~~l~~~~~~ 64 (213)
T PRK06552 6 ILTKLKANGVVAVVRGESKEEAL---KISLAV---------IKGGIKAIEVTYT------NPFASE---VIKELVELYKD 64 (213)
T ss_pred HHHHHHHCCEEEEEECCCHHHHH---HHHHHH---------HHCCCCEEEEECC------CccHHH---HHHHHHHHcCC
Confidence 67788888888665432 11111 111111 2346667776665 444333 344444456
Q ss_pred -CceEEE---EeCHHHHHHHHHcCC-------CHHHHHHHHHhcCCccccccCCCCCh--hHHHHHHHHHHhcCceeeec
Q 020247 208 -PNLIVG---AITKESLYNAFENGI-------TAEQIISFLQQNAHPRVADRMPSVPE--NVCDQIRLWESDLNRVEMTP 274 (329)
Q Consensus 208 -PNlvvg---~iTReSV~~Al~~GI-------TA~QII~fL~~hAHp~m~~~~~~iP~--tV~dQI~lWe~Er~Rl~~~~ 274 (329)
|++.|| ++|.+.+++|.+.|- .-+.++++-+.+-.| .+|= |..+=.+.|+.--+-+++.+
T Consensus 65 ~p~~~vGaGTV~~~~~~~~a~~aGA~FivsP~~~~~v~~~~~~~~i~-------~iPG~~T~~E~~~A~~~Gad~vklFP 137 (213)
T PRK06552 65 DPEVLIGAGTVLDAVTARLAILAGAQFIVSPSFNRETAKICNLYQIP-------YLPGCMTVTEIVTALEAGSEIVKLFP 137 (213)
T ss_pred CCCeEEeeeeCCCHHHHHHHHHcCCCEEECCCCCHHHHHHHHHcCCC-------EECCcCCHHHHHHHHHcCCCEEEECC
Confidence 579999 899999999999994 457788887776655 6774 55666778888888888755
Q ss_pred eeeecCCCCHHHHHHHHHHHHHcCeEeeecCCCceEEEeccccHHHHHHHhh
Q 020247 275 AHYYDEFPSRDVFEAACDYARDQSGLLWEDPKKMRLVVKAEIHMHMREFLRG 326 (329)
Q Consensus 275 g~Ly~~f~s~~~fe~v~~yA~~~g~llw~~~~kr~~~V~~~~h~~vr~f~k~ 326 (329)
+-.+ + .+|.+.+...+ +.-+.+.+.-=..+++.+|++.
T Consensus 138 a~~~----G-------~~~ik~l~~~~---p~ip~~atGGI~~~N~~~~l~a 175 (213)
T PRK06552 138 GSTL----G-------PSFIKAIKGPL---PQVNVMVTGGVNLDNVKDWFAA 175 (213)
T ss_pred cccC----C-------HHHHHHHhhhC---CCCEEEEECCCCHHHHHHHHHC
Confidence 3221 1 22233322121 2234444444445778888864
No 20
>COG1420 HrcA Transcriptional regulator of heat shock gene [Transcription]
Probab=54.44 E-value=9.9 Score=38.12 Aligned_cols=62 Identities=24% Similarity=0.423 Sum_probs=42.3
Q ss_pred HHHHHHHHHHHHHHcCCChHHHHHHHHHhcccccCccccCCCCCHHHHHHHHHHhhcCceeeecCCCccccccchhhh
Q 020247 82 LWYIVREYISNSQERGINQADLISFLLELSFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLAT 159 (329)
Q Consensus 82 ~W~lll~yl~~~e~~g~~~~e~L~fLf~Ls~~~~G~~Y~~~~lt~~q~~~L~~L~d~GLVy~~~~~~~~fy~pT~La~ 159 (329)
++.++-.|+++.| + .|+..+-+-|..+--+.|-++.+++|.++|++++.--.++| +||.++.
T Consensus 12 L~aIV~~Yi~t~e-----P---------VGSk~L~e~~~l~~SsATIRN~Ma~LE~~GlI~k~HtSsGR--vPT~~Gy 73 (346)
T COG1420 12 LRAIVEDYLATGE-----P---------VGSKTLSEKYNLDLSSATIRNEMADLEKLGLIEKPHTSSGR--VPTDKGY 73 (346)
T ss_pred HHHHHHHHHhcCC-----c---------cchHHHHHHhCCCCCchhHHHHHHHHHHCCCccCccccCCc--CCcHhHH
Confidence 4677888877643 1 12333334565555578999999999999999998655555 4666555
No 21
>COG3432 Predicted transcriptional regulator [Transcription]
Probab=50.12 E-value=11 Score=31.14 Aligned_cols=33 Identities=21% Similarity=0.281 Sum_probs=25.9
Q ss_pred CCcHHHHHHHHhCCCccCCCC----CCccchhchhhh
Q 020247 42 NFSSSMMKVFQRGLLSRRDKE----APRLTESGFQFL 74 (329)
Q Consensus 42 ~~s~~v~~lL~~~gL~~~~~~----~~~IT~~GfqFL 74 (329)
...+..++-|...||+....+ ...||++|..||
T Consensus 46 ~~~~~yi~~L~~~Gli~~~~~~~~~~y~lT~KG~~fl 82 (95)
T COG3432 46 KRAQKYIEMLVEKGLIIKQDNGRRKVYELTEKGKRFL 82 (95)
T ss_pred HHHHHHHHHHHhCCCEEeccCCccceEEEChhHHHHH
Confidence 356788999999997775433 489999999993
No 22
>PRK09333 30S ribosomal protein S19e; Provisional
Probab=50.01 E-value=12 Score=33.38 Aligned_cols=35 Identities=14% Similarity=0.243 Sum_probs=29.0
Q ss_pred CCCcHHHHHHHHhCCCccCCCCCCccchhchhhhc
Q 020247 41 TNFSSSMMKVFQRGLLSRRDKEAPRLTESGFQFLL 75 (329)
Q Consensus 41 ~~~s~~v~~lL~~~gL~~~~~~~~~IT~~GfqFLL 75 (329)
..+-.-+++-|...||++++.++..||++|=+||=
T Consensus 95 g~iiR~~LqqLE~~glVek~~~GR~lT~~G~~~LD 129 (150)
T PRK09333 95 GSIIRKILQQLEKAGLVEKTKKGRVITPKGRSLLD 129 (150)
T ss_pred cHHHHHHHHHHHHCCCeeeCCCCCEeCHHHHHHHH
Confidence 44567788999999999977677889999988863
No 23
>PF10711 DUF2513: Hypothetical protein (DUF2513); InterPro: IPR019650 The function of this family is not known.
Probab=49.13 E-value=13 Score=30.36 Aligned_cols=42 Identities=24% Similarity=0.342 Sum_probs=34.4
Q ss_pred HHHHHhCCCccCCCC----------CCccchhchhhhccChhhHHHHHHHHH
Q 020247 48 MKVFQRGLLSRRDKE----------APRLTESGFQFLLMDTNAQLWYIVREY 89 (329)
Q Consensus 48 ~~lL~~~gL~~~~~~----------~~~IT~~GfqFLL~d~~~Q~W~lll~y 89 (329)
+.+|..+||+..... -..||.+|.+||-.=++.-+|.=...-
T Consensus 41 l~lL~eagli~~~~~~~~~~~~~~~i~~LT~~GHdFLd~IRd~~vW~k~K~~ 92 (102)
T PF10711_consen 41 LKLLDEAGLIEGSVSGTMNGPYSFIIKRLTWSGHDFLDAIRDDTVWNKTKDK 92 (102)
T ss_pred HHHHHHCCCeeeccccccCCccchhhcccChhHHHHHHHhcCchHHHHHHHH
Confidence 678999999995321 248999999999999999999877644
No 24
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=48.88 E-value=15 Score=27.31 Aligned_cols=32 Identities=22% Similarity=0.380 Sum_probs=23.0
Q ss_pred CCHHH-HHHHHHHhhcCceeeecCCCccccccch
Q 020247 124 LSEIQ-KSMIKDFADLGLVKLQQGRKENWFIPTK 156 (329)
Q Consensus 124 lt~~q-~~~L~~L~d~GLVy~~~~~~~~fy~pT~ 156 (329)
++.+. ...|+.|.+.|+|....++...|. +.+
T Consensus 34 i~~~~v~~~L~~L~~~GlV~~~~~~~~~Y~-a~~ 66 (68)
T PF01978_consen 34 ISRSTVYRALKSLEEKGLVEREEGRPKVYR-AVP 66 (68)
T ss_dssp SSHHHHHHHHHHHHHTTSEEEEEECCEEEE-EE-
T ss_pred cCHHHHHHHHHHHHHCCCEEEEcCceEEEE-EeC
Confidence 34333 669999999999999887666665 543
No 25
>TIGR03853 matur_matur probable metal-binding protein. This protein family was identified by searching with a phylogenetic profile based on an anaerobic sulfatase-maturase enzyme, which contains multiple 4Fe-4S clusters. The linkages by phylogenetic profiling and by iron-sulfur cluster-related motifs together suggest this protein may be an accessory protein to certain maturases in sulfatase/maturase systems.
Probab=48.80 E-value=25 Score=28.19 Aligned_cols=27 Identities=41% Similarity=0.694 Sum_probs=21.9
Q ss_pred eCHHHHHHHHH--------------cCCCHHHHHHHHHhcC
Q 020247 215 ITKESLYNAFE--------------NGITAEQIISFLQQNA 241 (329)
Q Consensus 215 iTReSV~~Al~--------------~GITA~QII~fL~~hA 241 (329)
+||+|.++|+. .|.||+++|+||...-
T Consensus 18 ~t~~~L~~~i~~~FG~~arFhTCSa~~m~a~~Li~FL~~kg 58 (77)
T TIGR03853 18 YTRESLKAAIEQKFGEDARFHTCSAEGMTADELLQFLLKKG 58 (77)
T ss_pred cCHHHHHHHHHHHhCCCceEeecccccCCHHHHHHHHHHCC
Confidence 47788877774 6999999999998753
No 26
>PF06969 HemN_C: HemN C-terminal domain; InterPro: IPR010723 Proteins containing this domain are all oxygen-independent coproporphyrinogen-III oxidases (HemN). This enzyme catalyses the oxygen-independent conversion of coproporphyrinogen-III to protoporphyrinogen-IX [], one of the last steps in haem biosynthesis. The function of this domain is unclear, but comparison to other proteins containing a radical SAM domain suggest it may be a substrate binding domain.; GO: 0004109 coproporphyrinogen oxidase activity, 0006779 porphyrin-containing compound biosynthetic process, 0055114 oxidation-reduction process, 0005737 cytoplasm; PDB: 1OLT_A.
Probab=48.08 E-value=10 Score=27.89 Aligned_cols=27 Identities=30% Similarity=0.240 Sum_probs=21.5
Q ss_pred HHHHHHHHhCCCccCCCCCCccchhch
Q 020247 45 SSMMKVFQRGLLSRRDKEAPRLTESGF 71 (329)
Q Consensus 45 ~~v~~lL~~~gL~~~~~~~~~IT~~Gf 71 (329)
...++-|...||++.+++.+.+|++|+
T Consensus 39 ~~~l~~l~~~Gll~~~~~~l~lT~~G~ 65 (66)
T PF06969_consen 39 QKELEELQEDGLLEIDGGRLRLTEKGR 65 (66)
T ss_dssp HHHHHHHHHTTSEEE-SSEEEE-TTTG
T ss_pred HHHHHHHHHCCCEEEeCCEEEECcccC
Confidence 456778888999999999999999996
No 27
>COG1313 PflX Uncharacterized Fe-S protein PflX, homolog of pyruvate formate lyase activating proteins [General function prediction only]
Probab=48.03 E-value=23 Score=35.17 Aligned_cols=52 Identities=23% Similarity=0.312 Sum_probs=41.1
Q ss_pred HHHHHHHHHhcCCccccccCCCCChhHHHH----HHHHHH-hcCceeeeceeeecCCCCHHHHHHHHHHHHHcCe
Q 020247 230 AEQIISFLQQNAHPRVADRMPSVPENVCDQ----IRLWES-DLNRVEMTPAHYYDEFPSRDVFEAACDYARDQSG 299 (329)
Q Consensus 230 A~QII~fL~~hAHp~m~~~~~~iP~tV~dQ----I~lWe~-Er~Rl~~~~g~Ly~~f~s~~~fe~v~~yA~~~g~ 299 (329)
.+-|++|+..|.-- -++-||.+| -+-||. |-+ +..+.++|+.+.+||+..|.
T Consensus 273 TkpI~~wiae~~g~-------~~~vNiM~QY~P~ykA~eypeI~-----------R~lt~eE~e~a~~~a~~~gl 329 (335)
T COG1313 273 TKPILRWIAENLGN-------DVRVNIMFQYRPEYKAEEYPEIN-----------RRLTREEYEKALEYAEKLGL 329 (335)
T ss_pred cHHHHHHHHHhCCC-------CeeEEehhhccchhhhhhchhhc-----------ccCCHHHHHHHHHHHHHcCC
Confidence 35689999887621 577889999 457776 544 67889999999999999985
No 28
>COG2238 RPS19A Ribosomal protein S19E (S16A) [Translation, ribosomal structure and biogenesis]
Probab=47.99 E-value=13 Score=33.05 Aligned_cols=35 Identities=14% Similarity=0.251 Sum_probs=29.4
Q ss_pred CCCCcHHHHHHHHhCCCccCCCCCCccchhchhhh
Q 020247 40 PTNFSSSMMKVFQRGLLSRRDKEAPRLTESGFQFL 74 (329)
Q Consensus 40 ~~~~s~~v~~lL~~~gL~~~~~~~~~IT~~GfqFL 74 (329)
+..+...+++=|..+|++++..++..||++|-+||
T Consensus 94 sgsI~RkilqqLE~~G~V~k~~~GR~ltp~Grsll 128 (147)
T COG2238 94 SGSIIRKVLQQLEKAGLVEKTPKGRVLTPKGRSLL 128 (147)
T ss_pred CchHHHHHHHHHHHCCceeecCCCceeCccchhHH
Confidence 35577788899999999998767778999998876
No 29
>PF02244 Propep_M14: Carboxypeptidase activation peptide; InterPro: IPR003146 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. The peptidases are synthesised as inactive molecules, zymogens, with propeptides that must be removed by proteolytic cleavage to activate the enzyme. Structural studies of carboxypeptidases A and B reveal the propeptide to exist as a globular domain, followed by an extended alpha-helix; this shields the catalytic site, without specifically binding to it, while the substrate-binding site is blocked by making specific contacts [, ]. Members of this propeptide family are found in the metallocarboxypeptidases: A1, A2 [], A3, A4, A5, A6, U, insect gut carboxypeptidase and B [], and and are associated with peptidases belonging to MEROPS peptidase family M14A. Carboxypeptidases are found in abundance in pancreatic secretions. The pro-segment moiety (activation peptide) accounts for up to a quarter of the total length of the peptidase.; GO: 0004180 carboxypeptidase activity, 0006508 proteolysis; PDB: 3D68_C 3D67_B 3D66_A 1PBA_A 3GLJ_A 1NSA_A 1KWM_A 2BOA_B 1PYT_A 1JQG_A ....
Probab=47.31 E-value=77 Score=23.66 Aligned_cols=46 Identities=15% Similarity=0.351 Sum_probs=39.0
Q ss_pred CCHHHHHHHHHHHHHcCeEeeecCC----CceEEEeccccHHHHHHHhhc
Q 020247 282 PSRDVFEAACDYARDQSGLLWEDPK----KMRLVVKAEIHMHMREFLRGQ 327 (329)
Q Consensus 282 ~s~~~fe~v~~yA~~~g~llw~~~~----kr~~~V~~~~h~~vr~f~k~~ 327 (329)
.+.++.+.+.+.....++-.|+.+. .-.+.|+++..+.+.+++++.
T Consensus 6 ~t~~q~~~L~~L~~~~~~dfW~~~~~~~~~~dv~V~p~~~~~f~~~L~~~ 55 (74)
T PF02244_consen 6 KTEEQLELLQELEQSNELDFWKEPSSVGRPVDVMVPPEKLEEFEELLKEH 55 (74)
T ss_dssp SSHHHHHHHHHHHHHSTEEEEESSSSTTSEEEEEEEGGGHHHHHHHHHHT
T ss_pred CCHHHHHHHHHHhcccceeeecCCCCCCCeEEEEECHHHHHHHHHHHHHC
Confidence 3567888899999899999998887 247889999999999999864
No 30
>PF03428 RP-C: Replication protein C N-terminal domain; InterPro: IPR005090 Proteins in this group have homology with the RepC protein of Agrobacterium Ri and Ti plasmids []. They may be involved in plasmid replication and stabilisation functions.
Probab=46.20 E-value=83 Score=28.69 Aligned_cols=73 Identities=16% Similarity=0.352 Sum_probs=44.0
Q ss_pred hHHHHHHHHHHHHHHHcCCChH--HHHHHHHHhccc---ccCc---ccc--------CCCCCHHH-HHHHHHHhhcCcee
Q 020247 80 AQLWYIVREYISNSQERGINQA--DLISFLLELSFH---VAGE---AYN--------LNTLSEIQ-KSMIKDFADLGLVK 142 (329)
Q Consensus 80 ~Q~W~lll~yl~~~e~~g~~~~--e~L~fLf~Ls~~---~~G~---~Y~--------~~~lt~~q-~~~L~~L~d~GLVy 142 (329)
..=|.++...-+.....|++.. .+|..|+..... +.|. -|+ +.++|++. +..|..|.|.|||-
T Consensus 23 ~~k~~ll~~l~~a~~~lgl~~~~l~vL~aLls~~~~~d~~~~~~piVfpSN~~La~r~~G~s~~tlrR~l~~LveaGLI~ 102 (177)
T PF03428_consen 23 VTKWQLLRALKEARPALGLSDRALAVLDALLSFTPPDDWEPGRRPIVFPSNAQLAERLNGMSERTLRRHLARLVEAGLIV 102 (177)
T ss_pred CCHHHHHHHHHHHHHhcCCChhHHHHHHHHHHhCCcccccCCCCceeecCHHHHHHHHcCCCHHHHHHHHHHHHHCCCee
Confidence 3457777666555555677654 446655555421 1111 111 24677666 67999999999997
Q ss_pred ee-cCCCcccc
Q 020247 143 LQ-QGRKENWF 152 (329)
Q Consensus 143 ~~-~~~~~~fy 152 (329)
.+ +.+++||-
T Consensus 103 rrDS~NgkRy~ 113 (177)
T PF03428_consen 103 RRDSPNGKRYA 113 (177)
T ss_pred eccCCCCCccC
Confidence 75 45666665
No 31
>PF09639 YjcQ: YjcQ protein; InterPro: IPR018597 YjcQ is a protein of approx. 100 residues containing four alpha helices and three beta strands. It is found in bacteria and also in the Lactococcus phage Tuc2009. In bacteria it appears to be under the regulation of SigD RNA polymerase which is responsible for the expression of many genes encoding cell-surface proteins related to flagellar assembly, motility, chemotaxis and autolysis in the late exponential growth phase. The exact function of YjcQ is unknown []. However, it is thought to be the major head protein in viruses [] and is found in prophage in bacteria. ; PDB: 2HGC_A.
Probab=43.77 E-value=13 Score=29.85 Aligned_cols=31 Identities=19% Similarity=0.369 Sum_probs=20.9
Q ss_pred HHHHHHHhCCCcc----------CCCCCCccchhchhhhcc
Q 020247 46 SMMKVFQRGLLSR----------RDKEAPRLTESGFQFLLM 76 (329)
Q Consensus 46 ~v~~lL~~~gL~~----------~~~~~~~IT~~GfqFLL~ 76 (329)
.+++.|+..|++. .......||.+|.+||-.
T Consensus 29 ~il~~L~d~GyI~G~~~~~~~~~~~~~~~~IT~~Gi~YL~E 69 (88)
T PF09639_consen 29 DILRMLQDEGYIKGVSVVRYSPYVALSDPRITLKGIEYLEE 69 (88)
T ss_dssp HHHHHHHHHTSEE--EESSSSEE--SS--EE-HHHHHHHHH
T ss_pred HHHHHHHHCCCccceEEEeccceeecCCceEcHHHHHHHHH
Confidence 5678889999995 123477899999999864
No 32
>COG1412 Uncharacterized proteins of PilT N-term./Vapc superfamily [General function prediction only]
Probab=41.95 E-value=66 Score=28.25 Aligned_cols=18 Identities=39% Similarity=0.646 Sum_probs=14.3
Q ss_pred ccceEEEeeceeEEeecC
Q 020247 172 KEGFIVVETNFRMYAYST 189 (329)
Q Consensus 172 ~~g~IIVETNFrvYAYT~ 189 (329)
..-+|+|+|||=+|.|..
T Consensus 9 ~~~~VlvDTNfl~~~~q~ 26 (136)
T COG1412 9 KPYQVLVDTNFLLYPYQF 26 (136)
T ss_pred CceEEEecchHHHHHHHc
Confidence 345699999999888875
No 33
>PF04720 DUF506: Protein of unknown function (DUF506) ; InterPro: IPR006502 This family of uncharacterised plant proteins are defined by a region found toward the C terminus. This region is strongly conserved (greater than 30 % sequence identity between most pairs of members) but flanked by highly divergent regions including stretches of low-complexity sequence.
Probab=41.78 E-value=12 Score=35.37 Aligned_cols=66 Identities=23% Similarity=0.386 Sum_probs=49.0
Q ss_pred cccceEEEeeceeEEeecCChhHHH-HHHHhhhhhhccCceEEEEeCHHHHHHHHHcCCCHHHHHHHHHhcCCccccccC
Q 020247 171 RKEGFIVVETNFRMYAYSTSKLHCE-ILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRM 249 (329)
Q Consensus 171 ~~~g~IIVETNFrvYAYT~S~lqia-iL~lF~el~~r~PNlvvg~iTReSV~~Al~~GITA~QII~fL~~hAHp~m~~~~ 249 (329)
...-.+|||+||| +.+.|| -=.-+..+...+|...||...| + .||++.+-.-+.-.|+++.
T Consensus 135 ~~~~r~IVd~~fr------~~FeiArpt~~Y~~ll~~lP~vfVG~~~~--L----------~~iV~~~c~a~k~s~k~~g 196 (218)
T PF04720_consen 135 GKSERYIVDPDFR------SQFEIARPTPEYAALLAALPEVFVGTPER--L----------KQIVRLMCDAAKRSFKERG 196 (218)
T ss_pred CcceeEEEecchH------hCeeecCCCHHHHHHHHhCCCceEcCHHH--H----------HHHHHHHHHHHHHHHHHCC
Confidence 3556799999999 444442 2234566777899999995433 2 5789999988888898888
Q ss_pred CCCCh
Q 020247 250 PSVPE 254 (329)
Q Consensus 250 ~~iP~ 254 (329)
--|||
T Consensus 197 ~~lPP 201 (218)
T PF04720_consen 197 MHLPP 201 (218)
T ss_pred CCCCC
Confidence 88888
No 34
>PRK13824 replication initiation protein RepC; Provisional
Probab=40.31 E-value=1e+02 Score=31.56 Aligned_cols=68 Identities=12% Similarity=0.290 Sum_probs=43.8
Q ss_pred HHHHHHHHHHHHHHHcCCChHHH--HHHHHHhcccccCccc---------cC--------CCCCHHH-HHHHHHHhhcCc
Q 020247 81 QLWYIVREYISNSQERGINQADL--ISFLLELSFHVAGEAY---------NL--------NTLSEIQ-KSMIKDFADLGL 140 (329)
Q Consensus 81 Q~W~lll~yl~~~e~~g~~~~e~--L~fLf~Ls~~~~G~~Y---------~~--------~~lt~~q-~~~L~~L~d~GL 140 (329)
.=|.++..--+.....|++..++ |..|+... +..++ +. .+++++. +..|..|.|.||
T Consensus 36 ~Kw~l~r~l~~a~~~lGl~~~~l~vL~aLlsf~---p~~~~~~~~~~IVfpSN~~La~r~~Gms~~tlrRhla~LveaGL 112 (404)
T PRK13824 36 DKWKLFRDLCEARALLGVSDRALAVLNALLSFY---PETELSEEAGLVVFPSNAQLSLRAHGMAGATLRRHLAALVEAGL 112 (404)
T ss_pred CHHHHHHHHHHHHHhcCCChhHHHHHHHHHhhC---CcccccCCCCceechhHHHHHHHHcCCCHHHHHHHHHHHHHCCC
Confidence 45888888877666778876443 44444332 33222 22 3566666 679999999999
Q ss_pred eeee-cCCCccc
Q 020247 141 VKLQ-QGRKENW 151 (329)
Q Consensus 141 Vy~~-~~~~~~f 151 (329)
|-.+ +.+++||
T Consensus 113 I~rrDSpNGKRy 124 (404)
T PRK13824 113 IIRRDSPNGKRY 124 (404)
T ss_pred eEeecCCCCccc
Confidence 9665 3555665
No 35
>PRK11183 D-lactate dehydrogenase; Provisional
Probab=40.08 E-value=1.2e+02 Score=32.74 Aligned_cols=80 Identities=16% Similarity=0.223 Sum_probs=62.9
Q ss_pred EEeecCChhHHHHHHHhhhhhhccCceEEE--EeCHHHHHHHHHcCCCHHHHHHHHHhcCCccc----------cccCCC
Q 020247 184 MYAYSTSKLHCEILRLFSKVEYQLPNLIVG--AITKESLYNAFENGITAEQIISFLQQNAHPRV----------ADRMPS 251 (329)
Q Consensus 184 vYAYT~S~lqiaiL~lF~el~~r~PNlvvg--~iTReSV~~Al~~GITA~QII~fL~~hAHp~m----------~~~~~~ 251 (329)
.|+.|+++-... .+..++...|+++.++ .+.|+.+.-|-+.|=.-=-.|.+|-+..-|.| .++.|.
T Consensus 272 f~ig~n~~~~~~--~~rr~il~~~~~lP~a~Eym~r~~~d~~~~ygkd~~~~i~~~gt~~~p~~f~~k~~~d~~~~~~~~ 349 (564)
T PRK11183 272 FYIGTNDPAVLT--EIRRHILANFKNLPVAGEYMHRDAFDIAEKYGKDTFLMIDKLGTDKLPKLFALKGRVDAFLEKVPF 349 (564)
T ss_pred EEEeCCCHHHHH--HHHHHHHHhCCCCceeEeecCHHHHHHHHHhCCccEEehhhhCchhHHHHHhhHHHHHHHHHhcCC
Confidence 588888887762 3344556678888777 89999999999999766668888888888875 224599
Q ss_pred CChhHHHHHHHHHH
Q 020247 252 VPENVCDQIRLWES 265 (329)
Q Consensus 252 iP~tV~dQI~lWe~ 265 (329)
+|++++|.+..|-.
T Consensus 350 ~~~~~~d~~~q~~~ 363 (564)
T PRK11183 350 LPPHFTDRVMQALS 363 (564)
T ss_pred CCCCCcHHHHHHHH
Confidence 99999999998863
No 36
>PF10678 DUF2492: Protein of unknown function (DUF2492); InterPro: IPR019620 This entry describes a family of small cytosolic proteins, about 80 amino acids in length, in which the eight invariant residues include three His residues and two Cys residues. Two pairs of these invariant residues occur in motifs HxH (where x is A or G) and CxH, both of which suggest metal-binding activity. This protein family was identified by searching with a phylogenetic profile based on an anaerobic sulphatase-maturase enzyme, which contains multiple 4Fe-4S clusters. The linkages by phylogenetic profiling and by iron-sulphur cluster-related motifs together suggest this protein may be an accessory protein to certain maturases in sulphatase/maturase systems.
Probab=39.48 E-value=42 Score=26.90 Aligned_cols=26 Identities=38% Similarity=0.661 Sum_probs=21.7
Q ss_pred eCHHHHHHHHH--------------cCCCHHHHHHHHHhc
Q 020247 215 ITKESLYNAFE--------------NGITAEQIISFLQQN 240 (329)
Q Consensus 215 iTReSV~~Al~--------------~GITA~QII~fL~~h 240 (329)
+||+|+.+|+. .|.||+++|.||...
T Consensus 20 ~t~~~L~~ai~~~FG~~arFhTCSae~m~a~eLv~FL~~r 59 (78)
T PF10678_consen 20 YTKEELKAAIIEKFGEDARFHTCSAEGMTADELVDFLEER 59 (78)
T ss_pred cCHHHHHHHHHHHhCCCceEEecCCCCCCHHHHHHHHHHc
Confidence 57888877774 699999999999865
No 37
>smart00195 DSPc Dual specificity phosphatase, catalytic domain.
Probab=39.18 E-value=69 Score=26.43 Aligned_cols=51 Identities=12% Similarity=0.180 Sum_probs=36.0
Q ss_pred CceEEEE--eCHHHHHHHH----HcCCCHHHHHHHHHhcCCccccccCCCCC-hhHHHHHHHHHH
Q 020247 208 PNLIVGA--ITKESLYNAF----ENGITAEQIISFLQQNAHPRVADRMPSVP-ENVCDQIRLWES 265 (329)
Q Consensus 208 PNlvvg~--iTReSV~~Al----~~GITA~QII~fL~~hAHp~m~~~~~~iP-~tV~dQI~lWe~ 265 (329)
|-+|-+. ++|...--|. ..|+++++.++|+++ ++|. +.| +...+|++.||.
T Consensus 80 ~VlVHC~~G~~RS~~v~~~yl~~~~~~~~~~A~~~v~~-~R~~------~~p~~~~~~qL~~~e~ 137 (138)
T smart00195 80 KVLVHCQAGVSRSATLIIAYLMKYRNLSLNDAYDFVKD-RRPI------ISPNFGFLRQLIEYER 137 (138)
T ss_pred eEEEECCCCCchHHHHHHHHHHHHhCCCHHHHHHHHHH-HCCc------cCCCHhHHHHHHHHhh
Confidence 3344443 5787764443 579999999999975 4453 334 489999999995
No 38
>TIGR02425 decarb_PcaC 4-carboxymuconolactone decarboxylase. Members of this family are 4-carboxymuconolactone decarboxylase, which catalyzes the third step in the catabolism of protocatechuate (and therefore the fourth step in the catabolism of para-hydroxybenzoate, of 3-hydroxybenzoate, of vanillate, etc.). Most members of this family are encoded within protocatechuate catabolism operons. This protein is sometimes found as a fusion protein with other enzymes of the pathway, as in Rhodococcus opacus, Streptomyces avermitilis, and Caulobacter crescentus.
Probab=37.08 E-value=41 Score=28.66 Aligned_cols=25 Identities=20% Similarity=0.250 Sum_probs=21.0
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHhcC
Q 020247 217 KESLYNAFENGITAEQIISFLQQNA 241 (329)
Q Consensus 217 ReSV~~Al~~GITA~QII~fL~~hA 241 (329)
+.-++.|+++|+|.+||..-|..-+
T Consensus 76 ~~h~~~Al~~G~T~~ei~Evl~q~~ 100 (123)
T TIGR02425 76 AMHVRATANTGVTEDDIKEVLLHVA 100 (123)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHHH
Confidence 4568899999999999999877544
No 39
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=36.69 E-value=36 Score=27.30 Aligned_cols=35 Identities=26% Similarity=0.351 Sum_probs=25.0
Q ss_pred CHHHHHHHHHHhhcCceeeecCCCccccccchhhhh
Q 020247 125 SEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATN 160 (329)
Q Consensus 125 t~~q~~~L~~L~d~GLVy~~~~~~~~fy~pT~La~~ 160 (329)
+.+-++.+++|.++|||......+.-+. ||.-|..
T Consensus 37 ~aTIRN~M~~Le~lGlve~~p~~s~Gri-PT~~aYr 71 (78)
T PF03444_consen 37 PATIRNEMADLEELGLVESQPHPSGGRI-PTDKAYR 71 (78)
T ss_pred hHHHHHHHHHHHHCCCccCCCCCCCCCC-cCHHHHH
Confidence 5788999999999999975333233444 8876543
No 40
>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR. This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.
Probab=35.94 E-value=37 Score=28.80 Aligned_cols=53 Identities=19% Similarity=0.334 Sum_probs=33.5
Q ss_pred HHHHHHHhcccccCccccCCCCCH-------HHHHHHHHHhhcCceeeecCCCccccccch
Q 020247 103 LISFLLELSFHVAGEAYNLNTLSE-------IQKSMIKDFADLGLVKLQQGRKENWFIPTK 156 (329)
Q Consensus 103 ~L~fLf~Ls~~~~G~~Y~~~~lt~-------~q~~~L~~L~d~GLVy~~~~~~~~fy~pT~ 156 (329)
.++.+..|....-+...+.+.+++ .-..+|+.|++-|||...++.++-|. |++
T Consensus 10 Al~~l~~La~~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~~~glv~s~~G~~Ggy~-l~~ 69 (135)
T TIGR02010 10 AVTAMLDLALNAETGPVTLADISERQGISLSYLEQLFAKLRKAGLVKSVRGPGGGYQ-LGR 69 (135)
T ss_pred HHHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEeCCCCCEe-ccC
Confidence 355555665544344555544332 22669999999999987666556677 555
No 41
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=34.27 E-value=49 Score=25.14 Aligned_cols=57 Identities=19% Similarity=0.411 Sum_probs=35.0
Q ss_pred ccChhhHHHHHHHHHHHHHHHcCCCh--HHHHHHHHHhcccccCccccCCCCCHHHHHHHHHHhhcCceeeecCC
Q 020247 75 LMDTNAQLWYIVREYISNSQERGINQ--ADLISFLLELSFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGR 147 (329)
Q Consensus 75 L~d~~~Q~W~lll~yl~~~e~~g~~~--~e~L~fLf~Ls~~~~G~~Y~~~~lt~~q~~~L~~L~d~GLVy~~~~~ 147 (329)
|-+++.++..++..| .++.|..+ .|+-. .+.+. -+.+-...|..|.+-|+|-...+.
T Consensus 4 LT~rQ~~vL~~I~~~---~~~~G~~Pt~rEIa~------------~~g~~-S~~tv~~~L~~Le~kG~I~r~~~~ 62 (65)
T PF01726_consen 4 LTERQKEVLEFIREY---IEENGYPPTVREIAE------------ALGLK-STSTVQRHLKALERKGYIRRDPGK 62 (65)
T ss_dssp --HHHHHHHHHHHHH---HHHHSS---HHHHHH------------HHTSS-SHHHHHHHHHHHHHTTSEEEGCCS
T ss_pred CCHHHHHHHHHHHHH---HHHcCCCCCHHHHHH------------HhCCC-ChHHHHHHHHHHHHCcCccCCCCC
Confidence 446778888888888 44556543 33322 22222 145667799999999999766543
No 42
>PRK03911 heat-inducible transcription repressor; Provisional
Probab=33.20 E-value=28 Score=33.78 Aligned_cols=47 Identities=21% Similarity=0.193 Sum_probs=34.8
Q ss_pred cccccCccccCCCCCHHHHHHHHHHhhcCceeeecCCCccccccchhhh
Q 020247 111 SFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLAT 159 (329)
Q Consensus 111 s~~~~G~~Y~~~~lt~~q~~~L~~L~d~GLVy~~~~~~~~fy~pT~La~ 159 (329)
|+.++.+.|.++--+.|-++.+++|.+.|++.++-..++| +||..+.
T Consensus 24 GSk~L~~~~~l~~SsATIRn~m~~LE~~G~L~qpHtSsGR--IPT~~gy 70 (260)
T PRK03911 24 GSNELKSLMNLKISAATIRNYFKKLSDEGLLTQLHISGGR--IPTIKAM 70 (260)
T ss_pred CHHHHHHHcCCCCCcHHHHHHHHHHHHCcCccCCcCCCCc--CCCHHHH
Confidence 3444455677766689999999999999999998655555 4666555
No 43
>PTZ00095 40S ribosomal protein S19; Provisional
Probab=33.02 E-value=30 Score=31.59 Aligned_cols=36 Identities=17% Similarity=0.217 Sum_probs=28.3
Q ss_pred CCCCCcHHHHHHHHhCCCccCCC--CCCccchhchhhh
Q 020247 39 RPTNFSSSMMKVFQRGLLSRRDK--EAPRLTESGFQFL 74 (329)
Q Consensus 39 ~~~~~s~~v~~lL~~~gL~~~~~--~~~~IT~~GfqFL 74 (329)
++..+-..+++=|...||++.+. ++..||++|=+||
T Consensus 117 aSg~iiR~~LQqLE~~glVek~~~~~GR~lT~~Gr~~L 154 (169)
T PTZ00095 117 ASGKILRWICQQLEKLGLVEQGPKKKGRRLTRKGCNFA 154 (169)
T ss_pred CchHHHHHHHHHHHHCCCEEecCCCCCCEECHhHHHHH
Confidence 33456677888899999999662 5779999998876
No 44
>KOG4175 consensus Tryptophan synthase alpha chain [Amino acid transport and metabolism]
Probab=32.84 E-value=1.8e+02 Score=27.82 Aligned_cols=77 Identities=21% Similarity=0.236 Sum_probs=49.9
Q ss_pred HHHHHHHHcCCCHHHHHHHHHhcCCcc--------ccccCCCCChhHHHHHHHHHHhcCceeeeceeeecCCCCHHHHHH
Q 020247 218 ESLYNAFENGITAEQIISFLQQNAHPR--------VADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEA 289 (329)
Q Consensus 218 eSV~~Al~~GITA~QII~fL~~hAHp~--------m~~~~~~iP~tV~dQI~lWe~Er~Rl~~~~g~Ly~~f~s~~~fe~ 289 (329)
.+-+.|+.+|+|-.+||+-++. |.|+ |.=..|++---+..-|.-=. + .=.+|++.-|.+ .++.+.
T Consensus 67 ~~n~~aL~ng~tl~~i~emvk~-ar~~gvt~PIiLmgYYNPIl~yG~e~~iq~ak-~----aGanGfiivDlP-pEEa~~ 139 (268)
T KOG4175|consen 67 AANRRALLNGTTLNSIIEMVKE-ARPQGVTCPIILMGYYNPILRYGVENYIQVAK-N----AGANGFIIVDLP-PEEAET 139 (268)
T ss_pred hhHHHHHHcCCcHHHHHHHHHH-hcccCcccceeeeecccHHHhhhHHHHHHHHH-h----cCCCceEeccCC-hHHHHH
Confidence 4568999999999999999875 5554 22223444443433333211 1 124667765554 688899
Q ss_pred HHHHHHHcCeEe
Q 020247 290 ACDYARDQSGLL 301 (329)
Q Consensus 290 v~~yA~~~g~ll 301 (329)
++++|++.|+-+
T Consensus 140 ~Rne~~k~gisl 151 (268)
T KOG4175|consen 140 LRNEARKHGISL 151 (268)
T ss_pred HHHHHHhcCceE
Confidence 999999999643
No 45
>PF09713 A_thal_3526: Plant protein 1589 of unknown function (A_thal_3526); InterPro: IPR006476 This plant-specific family of proteins are defined by an uncharacterised region 57 residues in length. It is found toward the N terminus of most proteins that contain it. Examples include at least several proteins from Arabidopsis thaliana (Mouse-ear cress) and Oryza sativa (Rice). The function of the proteins are unknown.
Probab=30.84 E-value=73 Score=23.84 Aligned_cols=24 Identities=17% Similarity=0.225 Sum_probs=21.3
Q ss_pred HHHHHHHHcCCCHHHHHHHHHhcC
Q 020247 218 ESLYNAFENGITAEQIISFLQQNA 241 (329)
Q Consensus 218 eSV~~Al~~GITA~QII~fL~~hA 241 (329)
.-|.+.+....|-++++..|..||
T Consensus 3 ~lIErCl~~yMsk~E~v~~L~~~a 26 (54)
T PF09713_consen 3 NLIERCLQLYMSKEECVRALQKQA 26 (54)
T ss_pred hHHHHHHHHcCCHHHHHHHHHHHc
Confidence 347788999999999999999988
No 46
>TIGR03147 cyt_nit_nrfF cytochrome c nitrite reductase, accessory protein NrfF.
Probab=30.31 E-value=95 Score=26.99 Aligned_cols=39 Identities=21% Similarity=0.288 Sum_probs=28.9
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHhcCCccccccCCCCChh
Q 020247 217 KESLYNAFENGITAEQIISFLQQNAHPRVADRMPSVPEN 255 (329)
Q Consensus 217 ReSV~~Al~~GITA~QII~fL~~hAHp~m~~~~~~iP~t 255 (329)
|.-|++-+..|-|-+||++|+...-=....-++|.=|.|
T Consensus 63 R~~Vr~~i~~G~Sd~eI~~~~v~RYG~~Vly~Pp~~~~t 101 (126)
T TIGR03147 63 RHEVYSMVNEGKSNQQIIDFMTARFGDFVLYNPPFKWQT 101 (126)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHhcCCeEEecCCCCcch
Confidence 778999999999999999999987655444444433333
No 47
>PF03918 CcmH: Cytochrome C biogenesis protein; InterPro: IPR005616 Members of this family include NrfF, CcmH, CycL, Ccl2.; PDB: 2KW0_A 2HL7_A.
Probab=30.21 E-value=48 Score=29.32 Aligned_cols=31 Identities=16% Similarity=0.288 Sum_probs=23.4
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHhcCCccccc
Q 020247 217 KESLYNAFENGITAEQIISFLQQNAHPRVAD 247 (329)
Q Consensus 217 ReSV~~Al~~GITA~QII~fL~~hAHp~m~~ 247 (329)
|+-|++-+..|-|.+||++|+.++-=+...-
T Consensus 63 R~~I~~~l~~G~s~~eI~~~~v~rYG~~Vl~ 93 (148)
T PF03918_consen 63 RREIREMLAEGKSDEEIIDYFVERYGEFVLY 93 (148)
T ss_dssp HHHHHHHHHHT--HHHHHHHHHHHHTTT-EE
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHhcCcceee
Confidence 7789999999999999999999876555443
No 48
>PF14338 Mrr_N: Mrr N-terminal domain
Probab=29.99 E-value=43 Score=26.59 Aligned_cols=31 Identities=23% Similarity=0.207 Sum_probs=24.8
Q ss_pred HHHHHHhCCCccCC-CCCCccchhchhhhccC
Q 020247 47 MMKVFQRGLLSRRD-KEAPRLTESGFQFLLMD 77 (329)
Q Consensus 47 v~~lL~~~gL~~~~-~~~~~IT~~GfqFLL~d 77 (329)
.+.-|..+|++++. .+...||++|-++|...
T Consensus 60 a~~~L~~aGli~~~~rG~~~iT~~G~~~l~~~ 91 (92)
T PF14338_consen 60 ARSYLKKAGLIERPKRGIWRITEKGRKALAEH 91 (92)
T ss_pred HHHHHHHCCCccCCCCCceEECHhHHHHHhhC
Confidence 35678999999974 45789999999988653
No 49
>PF09330 Lact-deh-memb: D-lactate dehydrogenase, membrane binding; InterPro: IPR015409 Members of this entry are predominantly found in prokaryotic D-lactate dehydrogenase, forming the cap-membrane-binding domain, which consists of a large seven-stranded antiparallel beta-sheet flanked on both sides by alpha-helices. They allow for membrane association []. ; GO: 0050660 flavin adenine dinucleotide binding, 0055085 transmembrane transport; PDB: 1F0X_A.
Probab=29.94 E-value=2e+02 Score=28.48 Aligned_cols=119 Identities=18% Similarity=0.218 Sum_probs=41.8
Q ss_pred EeecCChhHHHHHHHhhhhhhccCceEEE--EeCHHHHHHHHHcCCCHHHHHHHHHhcCCccccc----------cCCCC
Q 020247 185 YAYSTSKLHCEILRLFSKVEYQLPNLIVG--AITKESLYNAFENGITAEQIISFLQQNAHPRVAD----------RMPSV 252 (329)
Q Consensus 185 YAYT~S~lqiaiL~lF~el~~r~PNlvvg--~iTReSV~~Al~~GITA~QII~fL~~hAHp~m~~----------~~~~i 252 (329)
|.=||+|-.+.-|+-- +...|++|-|. =+-|+.+.-|-+.|=.-=.+|.+|-+..-|.|-. +.|.+
T Consensus 3 YIGTNd~~~L~~lRR~--iL~~f~~LPisgEYmHRdafdia~~YGKDtfl~I~~lGt~~lP~lFa~K~~~D~~~~k~~~l 80 (291)
T PF09330_consen 3 YIGTNDPAVLTDLRRH--ILSNFKNLPISGEYMHRDAFDIAEKYGKDTFLMIKKLGTDRLPRLFALKARIDALLEKLPFL 80 (291)
T ss_dssp EEEES-HHHHHHHHHH--HHHH-SS--SEEEEEEHHHHHHH---------------------------------------
T ss_pred EeccCCHHHHHHHHHH--HHhCCccCChhhhhhhhHHHHHHHHhcchHHHHHHHhCchhHHHHHHHHHHHHHHHHhcCCC
Confidence 5667787776555443 35557777555 7999999999999999999999999999998632 34999
Q ss_pred ChhHHHHHHHHHHhcCceeeeceeeecCCCCHHHHHHHHHHHHHcCeEeeecCCCceEEEeccccHHHHHHHhh
Q 020247 253 PENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEAACDYARDQSGLLWEDPKKMRLVVKAEIHMHMREFLRG 326 (329)
Q Consensus 253 P~tV~dQI~lWe~Er~Rl~~~~g~Ly~~f~s~~~fe~v~~yA~~~g~llw~~~~kr~~~V~~~~h~~vr~f~k~ 326 (329)
|++++|.+..|-. +..-...=..+.+|-+..-- .-++-|+.+|.++.++|+++
T Consensus 81 p~~lsDr~lQ~~s--------------~l~P~hLP~Rm~~yr~ryeH-------HLilkm~~~gi~ea~~~L~~ 133 (291)
T PF09330_consen 81 PPNLSDRVLQALS--------------NLLPNHLPKRMRDYRDRYEH-------HLILKMSGDGIEEARAYLKE 133 (291)
T ss_dssp -----------------------------------HHHHHHHHH-SE-------EEEEEE-TTHHHHHHHHHHH
T ss_pred CCCccHHHHHHHH--------------hhChhhcCHHHHHHHHhhhh-------heeeeecCCcHHHHHHHHHH
Confidence 9999999987752 22233444556666665332 11245777778888888775
No 50
>PF09821 AAA_assoc_C: C-terminal AAA-associated domain; InterPro: IPR018632 Members of this family are found in various prokaryotic ABC transporters, predominantly involved in nitrate, sulphonate and bicarbonate translocation.
Probab=29.81 E-value=45 Score=28.45 Aligned_cols=36 Identities=17% Similarity=0.183 Sum_probs=31.3
Q ss_pred HHHHHHHhCCCccCCCCCCccchhchhhhccChhhH
Q 020247 46 SMMKVFQRGLLSRRDKEAPRLTESGFQFLLMDTNAQ 81 (329)
Q Consensus 46 ~v~~lL~~~gL~~~~~~~~~IT~~GfqFLL~d~~~Q 81 (329)
.+++.++-.|+++..++.+.+|+.|=.|.-.|...+
T Consensus 16 p~~eAaelLgf~~~~~Gdi~LT~~G~~f~~a~~~~r 51 (120)
T PF09821_consen 16 PIVEAAELLGFAEVEEGDIRLTPLGRRFAEADIDER 51 (120)
T ss_pred HHHHHHHHcCCeeecCCcEEeccchHHHHHCChHHH
Confidence 467788999999988899999999999998888554
No 51
>COG0563 Adk Adenylate kinase and related kinases [Nucleotide transport and metabolism]
Probab=29.68 E-value=33 Score=30.85 Aligned_cols=79 Identities=16% Similarity=0.275 Sum_probs=54.7
Q ss_pred hccCceEEEEeCHHHHHHHHHcCCCHHHHHHHHHhcCCccccccCCCCChhHHHHHH-HHHHhcCceeeeceeeecCCCC
Q 020247 205 YQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRMPSVPENVCDQIR-LWESDLNRVEMTPAHYYDEFPS 283 (329)
Q Consensus 205 ~r~PNlvvg~iTReSV~~Al~~GITA~QII~fL~~hAHp~m~~~~~~iP~tV~dQI~-lWe~Er~Rl~~~~g~Ly~~f~s 283 (329)
+.+|++..|-+=|+.+.++-..|..+++ |+.... ++|..++.++- -|=.+.+ . ..+++|..|+.
T Consensus 24 ~~i~hlstgd~~r~~~~~~t~lg~~~k~---~i~~g~---------lv~d~i~~~~v~~rl~~~d--~-~~~~I~dg~PR 88 (178)
T COG0563 24 LGLPHLDTGDILRAAIAERTELGEEIKK---YIDKGE---------LVPDEIVNGLVKERLDEAD--C-KAGFILDGFPR 88 (178)
T ss_pred hCCcEEcHhHHhHhhhccCChHHHHHHH---HHHcCC---------ccchHHHHHHHHHHHHhhc--c-cCeEEEeCCCC
Confidence 6689999998888888777666665555 544432 89999986644 4443331 1 12899999998
Q ss_pred H-HHHHHHHHHHHHcC
Q 020247 284 R-DVFEAACDYARDQS 298 (329)
Q Consensus 284 ~-~~fe~v~~yA~~~g 298 (329)
. ..++.+.++-++.|
T Consensus 89 ~~~qa~~l~r~l~~~g 104 (178)
T COG0563 89 TLCQARALKRLLKELG 104 (178)
T ss_pred cHHHHHHHHHHHHHcC
Confidence 5 66777777777755
No 52
>PF13833 EF-hand_8: EF-hand domain pair; PDB: 3KF9_A 1TTX_A 1WLZ_A 1ALV_A 1NX3_A 1ALW_A 1NX2_A 1NX1_A 1NX0_A 1DF0_A ....
Probab=29.60 E-value=63 Score=22.41 Aligned_cols=21 Identities=33% Similarity=0.705 Sum_probs=16.2
Q ss_pred EEeCHHHHHHHHHc-C---CCHHHH
Q 020247 213 GAITKESLYNAFEN-G---ITAEQI 233 (329)
Q Consensus 213 g~iTReSV~~Al~~-G---ITA~QI 233 (329)
|.||++.++.|+.. | +|.+++
T Consensus 3 G~i~~~~~~~~l~~~g~~~~s~~e~ 27 (54)
T PF13833_consen 3 GKITREEFRRALSKLGIKDLSEEEV 27 (54)
T ss_dssp SEEEHHHHHHHHHHTTSSSSCHHHH
T ss_pred CEECHHHHHHHHHHhCCCCCCHHHH
Confidence 78999999999965 5 556653
No 53
>PF01316 Arg_repressor: Arginine repressor, DNA binding domain; InterPro: IPR020900 The arginine dihydrolase (AD) pathway is found in many prokaryotes and some primitive eukaryotes, an example of the latter being Giardia lamblia (Giardia intestinalis) []. The three-enzyme anaerobic pathway breaks down L-arginine to form 1 mol of ATP, carbon dioxide and ammonia. In simpler bacteria, the first enzyme, arginine deiminase, can account for up to 10% of total cell protein []. Most prokaryotic arginine deiminase pathways are under the control of a repressor gene, termed ArgR []. This is a negative regulator, and will only release the arginine deiminase operon for expression in the presence of arginine []. The crystal structure of apo-ArgR from Bacillus stearothermophilus has been determined to 2.5A by means of X-ray crystallography []. The protein exists as a hexamer of identical subunits, and is shown to have six DNA-binding domains, clustered around a central oligomeric core when bound to arginine. It predominantly interacts with A.T residues in ARG boxes. This hexameric protein binds DNA at its N terminus to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbour-joining tree, some of these paralogous sequences show long branches and differ significantly from the well-conserved C-terminal region. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0006525 arginine metabolic process; PDB: 1AOY_A 3V4G_A 3LAJ_D 3FHZ_A 3LAP_B 3ERE_D 2P5L_C 1F9N_D 2P5K_A 1B4A_A ....
Probab=28.42 E-value=70 Score=24.87 Aligned_cols=29 Identities=24% Similarity=0.510 Sum_probs=21.4
Q ss_pred CCHHHHHHHHHHhhcCceeeecCCCcccc
Q 020247 124 LSEIQKSMIKDFADLGLVKLQQGRKENWF 152 (329)
Q Consensus 124 lt~~q~~~L~~L~d~GLVy~~~~~~~~fy 152 (329)
.+-+|-++=+||+++|+|..+..++...|
T Consensus 34 i~vTQaTiSRDLkeL~~vKv~~~~g~~~Y 62 (70)
T PF01316_consen 34 IEVTQATISRDLKELGAVKVPDGNGKYRY 62 (70)
T ss_dssp -T--HHHHHHHHHHHT-EEEECTTSSEEE
T ss_pred CCcchhHHHHHHHHcCcEEeeCCCCCEEE
Confidence 34688899999999999999977666666
No 54
>PF04023 FeoA: FeoA domain; InterPro: IPR007167 This entry represents the core domain of the ferrous iron (Fe2+) transport protein FeoA found in bacteria. This domain also occurs at the C terminus in related proteins. The transporter Feo is composed of three proteins: FeoA a small, soluble SH3-domain protein probably located in the cytosol; FeoB, a large protein with a cytosolic N-terminal G-protein domain and a C-terminal integral inner-membrane domain containing two 'Gate' motifs which likely functions as the Fe2+ permease; and FeoC, a small protein apparently functioning as an [Fe-S]-dependent transcriptional repressor [, ]. Feo allows the bacterial cell to acquire iron from its environment. ; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 1G3T_A 1C0W_B 1BI3_A 1QVP_A 1BI1_A 1BYM_A 2QQB_A ....
Probab=28.39 E-value=18 Score=27.06 Aligned_cols=35 Identities=29% Similarity=0.370 Sum_probs=28.1
Q ss_pred HhcccccCccccCCCCCHHHHHHHHHHhhcCceee
Q 020247 109 ELSFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKL 143 (329)
Q Consensus 109 ~Ls~~~~G~~Y~~~~lt~~q~~~L~~L~d~GLVy~ 143 (329)
.|+.+..|+.+.+..+.+....+++.|.++|+.-.
T Consensus 2 ~L~~~~~g~~~~I~~i~~~d~~~~~~L~~lGl~~G 36 (74)
T PF04023_consen 2 PLSELPPGERARIVRISDEDPELLRRLADLGLTPG 36 (74)
T ss_dssp BGGGSSTTEEEEEEEESTSSHHHHHHHHHCT-STT
T ss_pred ChhHCCCCCEEEEEEEECCCHHHHHHHHHCCCCCC
Confidence 37778899999998887655779999999999844
No 55
>cd00115 LMWPc Substituted updates: Aug 22, 2001
Probab=28.26 E-value=35 Score=28.81 Aligned_cols=67 Identities=15% Similarity=0.197 Sum_probs=40.4
Q ss_pred cccCCeeeeeeccccCcccee-cceeccCCCCCCCCCCCCCcHHHHHHHHhCCCccCCCCCCccchhc
Q 020247 4 LCQGNQCLLVLLQGFQPWRTL-RPMPLDNGSSTQAERPTNFSSSMMKVFQRGLLSRRDKEAPRLTESG 70 (329)
Q Consensus 4 ~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~s~~v~~lL~~~gL~~~~~~~~~IT~~G 70 (329)
+|.||.|--.+-.+.-+-..- .++-+...+..+...+..+++.+.++|...|+=-.+..+..+|..-
T Consensus 6 vc~~N~~RS~mAEai~~~~~~~~~~~v~SaG~~~~~~g~~~~~~a~~~l~~~Gid~s~h~s~~l~~~~ 73 (141)
T cd00115 6 VCTGNICRSPMAEAIFRHLAPKLDIEVDSAGTSGWHVGGRPDPRAIAVLAEHGIDISGHRARQLTEDD 73 (141)
T ss_pred EecChhhhhHHHHHHHHHHhhhCCEEEECCCCCCccCCCCCCHHHHHHHHHcCCCcccCeeeeCCHHH
Confidence 699999976655554332211 1455533333222234679999999999999854444455666543
No 56
>PRK10144 formate-dependent nitrite reductase complex subunit NrfF; Provisional
Probab=28.10 E-value=1.1e+02 Score=26.61 Aligned_cols=39 Identities=15% Similarity=0.285 Sum_probs=28.8
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHhcCCccccccCCCCChh
Q 020247 217 KESLYNAFENGITAEQIISFLQQNAHPRVADRMPSVPEN 255 (329)
Q Consensus 217 ReSV~~Al~~GITA~QII~fL~~hAHp~m~~~~~~iP~t 255 (329)
|.-|++-+..|-|-+||++|+...-=....-++|.=|.|
T Consensus 63 R~~Vr~~i~~G~sd~eI~~~~v~RYG~~Vl~~Pp~~~~t 101 (126)
T PRK10144 63 RHQVYSMVAEGKSEVEIIGWMTERYGDFVRYNPPLTGQT 101 (126)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHhcCCeEEecCCCCcch
Confidence 778999999999999999999987654444344433333
No 57
>PF12637 TSCPD: TSCPD domain; InterPro: IPR024434 The domain is found in isolation in many proteins where it has a conserved C-terminal motif TSCPD, after which the domain is named. Most copies of the domain possess 4 conserved cysteines that may be part of an Iron-sulphur cluster. This domain is found at the C terminus of some ribonucleoside-diphosphate reductase enzymes.
Probab=28.01 E-value=1e+02 Score=24.98 Aligned_cols=54 Identities=19% Similarity=0.087 Sum_probs=35.0
Q ss_pred HHHHHHhhhhhhccCceEEEEeCHHHHHHHHHcCCCHHHHHHHHHhcCCccccccCCCCChhHHHHHHHH
Q 020247 194 CEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRMPSVPENVCDQIRLW 263 (329)
Q Consensus 194 iaiL~lF~el~~r~PNlvvg~iTReSV~~Al~~GITA~QII~fL~~hAHp~m~~~~~~iP~tV~dQI~lW 263 (329)
-+.+.-++++.+ -||++|++++.||+=|+.---+.-....+....++.|||-.+
T Consensus 37 ~~~~~ai~rliS----------------~~Lr~G~~~~~ii~~L~gi~~~~~~~~~~~~~~S~~D~Ia~~ 90 (95)
T PF12637_consen 37 SGNLEAIARLIS----------------LALRSGVPPEEIIDQLRGIRCGPSGTVGGSRVTSCPDAIAKA 90 (95)
T ss_pred hHHHHHHHHHHH----------------HHHHcCCCHHHHHHHhcCCCCCCCCccCCCccCcHHHHHHHH
Confidence 466667777666 899999999999999986543321111123334577777543
No 58
>PF00782 DSPc: Dual specificity phosphatase, catalytic domain; InterPro: IPR000340 Protein tyrosine (pTyr) phosphorylation is a common post-translational modification which can create novel recognition motifs for protein interactions and cellular localisation, affect protein stability, and regulate enzyme activity. Consequently, maintaining an appropriate level of protein tyrosine phosphorylation is essential for many cellular functions. Tyrosine-specific protein phosphatases (PTPase; 3.1.3.48 from EC) catalyse the removal of a phosphate group attached to a tyrosine residue, using a cysteinyl-phosphate enzyme intermediate. These enzymes are key regulatory components in signal transduction pathways (such as the MAP kinase pathway) and cell cycle control, and are important in the control of cell growth, proliferation, differentiation and transformation [, ]. The PTP superfamily can be divided into four subfamilies []: (1) pTyr-specific phosphatases (2) dual specificity phosphatases (dTyr and dSer/dThr) (3) Cdc25 phosphatases (dTyr and/or dThr) (4) LMW (low molecular weight) phosphatases Based on their cellular localisation, PTPases are also classified as: Receptor-like, which are transmembrane receptors that contain PTPase domains [] Non-receptor (intracellular) PTPases [] All PTPases carry the highly conserved active site motif C(X)5R (PTP signature motif), employ a common catalytic mechanism, and share a similar core structure made of a central parallel beta-sheet with flanking alpha-helices containing a beta-loop-alpha-loop that encompasses the PTP signature motif []. Functional diversity between PTPases is endowed by regulatory domains and subunits. This entry represents dual specificity protein-tyrosine phosphatases. Ser/Thr and Tyr dual specificity phosphatases are a group of enzymes with both Ser/Thr (3.1.3.16 from EC) and tyrosine specific protein phosphatase (3.1.3.48 from EC) activity able to remove both the serine/threonine or tyrosine-bound phosphate group from a wide range of phosphoproteins, including a number of enzymes which have been phosphorylated under the action of a kinase. Dual specificity protein phosphatases (DSPs) regulate mitogenic signal transduction and control the cell cycle. The crystal structure of a human DSP, vaccinia H1-related phosphatase (or VHR), has been determined at 2.1 angstrom resolution []. A shallow active site pocket in VHR allows for the hydrolysis of phosphorylated serine, threonine, or tyrosine protein residues, whereas the deeper active site of protein tyrosine phosphatases (PTPs) restricts substrate specificity to only phosphotyrosine. Positively charged crevices near the active site may explain the enzyme's preference for substrates with two phosphorylated residues. The VHR structure defines a conserved structural scaffold for both DSPs and PTPs. A "recognition region" connecting helix alpha1 to strand beta1, may determine differences in substrate specificity between VHR, the PTPs, and other DSPs. These proteins may also have inactive phosphatase domains, and dependent on the domain composition this loss of catalytic activity has different effects on protein function. Inactive single domain phosphatases can still specifically bind substrates, and protect again dephosphorylation, while the inactive domains of tandem phosphatases can be further subdivided into two classes. Those which bind phosphorylated tyrosine residues may recruit multi-phosphorylated substrates for the adjacent active domains and are more conserved, while the other class have accumulated several variable amino acid substitutions and have a complete loss of tyrosine binding capability. The second class shows a release of evolutionary constraint for the sites around the catalytic centre, which emphasises a difference in function from the first group. There is a region of higher conservation common to both classes, suggesting a new regulatory centre [].; GO: 0008138 protein tyrosine/serine/threonine phosphatase activity, 0006470 protein dephosphorylation; PDB: 2G6Z_A 1MKP_A 1YZ4_A 2P4D_A 1M3G_A 1ZZW_A 2OUD_A 2HXP_A 3LJ8_A 1OHD_A ....
Probab=26.70 E-value=1.3e+02 Score=24.53 Aligned_cols=44 Identities=20% Similarity=0.433 Sum_probs=35.2
Q ss_pred eCHHHHHHHH----HcCCCHHHHHHHHHhcCCccccccCCCCC-hhHHHHHHHHHH
Q 020247 215 ITKESLYNAF----ENGITAEQIISFLQQNAHPRVADRMPSVP-ENVCDQIRLWES 265 (329)
Q Consensus 215 iTReSV~~Al----~~GITA~QII~fL~~hAHp~m~~~~~~iP-~tV~dQI~lWe~ 265 (329)
++|...--|. ..|+|.++-++++++.- |. +.| +...+|++.||.
T Consensus 84 ~~RS~~v~~ayLm~~~~~~~~~A~~~v~~~r-p~------~~~~~~~~~~L~~~e~ 132 (133)
T PF00782_consen 84 LSRSGAVAAAYLMKKNGMSLEEAIEYVRSRR-PQ------INPNPSFIRQLYEYEK 132 (133)
T ss_dssp SSHHHHHHHHHHHHHHTSSHHHHHHHHHHHS-TT------STHHHHHHHHHHHHHH
T ss_pred cccchHHHHHHHHHHcCCCHHHHHHHHHHHC-CC------CCCCHHHHHHHHHhhc
Confidence 7898875554 58999999999998865 64 445 479999999996
No 59
>PLN02459 probable adenylate kinase
Probab=26.61 E-value=1.3e+02 Score=29.17 Aligned_cols=69 Identities=17% Similarity=0.257 Sum_probs=46.7
Q ss_pred hhccCceEEEEeCHHHHHHHHHcCCCHHHHHHHHHhcCCccccccCCCCChhHHHHHHHHHHhcCceeeeceeeecCCCC
Q 020247 204 EYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPS 283 (329)
Q Consensus 204 ~~r~PNlvvg~iTReSV~~Al~~GITA~QII~fL~~hAHp~m~~~~~~iP~tV~dQI~lWe~Er~Rl~~~~g~Ly~~f~s 283 (329)
.+.++.+.+|.|=|+.|..--..| .+|-+|+.+ +..||..++-++-..+.....-.-..|++++.|+-
T Consensus 52 ~~~~~~is~gdllR~ei~~~t~lg---~~i~~~~~~---------G~lVPdeiv~~ll~~~l~~~~~~~~~g~iLDGFPR 119 (261)
T PLN02459 52 LLGVPHIATGDLVREEIKSSGPLG---AQLKEIVNQ---------GKLVPDEIIFSLLSKRLEAGEEEGESGFILDGFPR 119 (261)
T ss_pred HhCCcEEeCcHHHHHHHhccchhH---HHHHHHHHc---------CCccCHHHHHHHHHHHHhcccccCCceEEEeCCCC
Confidence 457899999988888775433322 455556554 34788888888777666543223467888888887
Q ss_pred H
Q 020247 284 R 284 (329)
Q Consensus 284 ~ 284 (329)
.
T Consensus 120 t 120 (261)
T PLN02459 120 T 120 (261)
T ss_pred C
Confidence 5
No 60
>PF00085 Thioredoxin: Thioredoxin; InterPro: IPR013766 Thioredoxins [, , , ] are small disulphide-containing redox proteins that have been found in all the kingdoms of living organisms. Thioredoxin serves as a general protein disulphide oxidoreductase. It interacts with a broad range of proteins by a redox mechanism based on reversible oxidation of two cysteine thiol groups to a disulphide, accompanied by the transfer of two electrons and two protons. The net result is the covalent interconversion of a disulphide and a dithiol. In the NADPH-dependent protein disulphide reduction, thioredoxin reductase (TR) catalyses the reduction of oxidised thioredoxin (trx) by NADPH using FAD and its redox-active disulphide; reduced thioredoxin then directly reduces the disulphide in the substrate protein []. Thioredoxin is present in prokaryotes and eukaryotes and the sequence around the redox-active disulphide bond is well conserved. All thioredoxins contain a cis-proline located in a loop preceding beta-strand 4, which makes contact with the active site cysteines, and is important for stability and function []. Thioredoxin belongs to a structural family that includes glutaredoxin, glutathione peroxidase, bacterial protein disulphide isomerase DsbA, and the N-terminal domain of glutathione transferase []. Thioredoxins have a beta-alpha unit preceding the motif common to all these proteins. A number of eukaryotic proteins contain domains evolutionary related to thioredoxin, most of them are protein disulphide isomerases (PDI). PDI (5.3.4.1 from EC) [, , ] is an endoplasmic reticulum multi-functional enzyme that catalyses the formation and rearrangement of disulphide bonds during protein folding []. All PDI contains two or three (ERp72) copies of the thioredoxin domain, each of which contributes to disulphide isomerase activity, but which are functionally non-equivalent []. Moreover, PDI exhibits chaperone-like activity towards proteins that contain no disulphide bonds, i.e. behaving independently of its disulphide isomerase activity []. The various forms of PDI which are currently known are: PDI major isozyme; a multifunctional protein that also function as the beta subunit of prolyl 4-hydroxylase (1.14.11.2 from EC), as a component of oligosaccharyl transferase (2.4.1.119 from EC), as thyroxine deiodinase (3.8.1.4 from EC), as glutathione-insulin transhydrogenase (1.8.4.2 from EC) and as a thyroid hormone-binding protein ERp60 (ER-60; 58 Kd microsomal protein). ERp60 was originally thought to be a phosphoinositide-specific phospholipase C isozyme and later to be a protease. ERp72. ERp5. Bacterial proteins that act as thiol:disulphide interchange proteins that allows disulphide bond formation in some periplasmic proteins also contain a thioredoxin domain. These proteins include: Escherichia coli DsbA (or PrfA) and its orthologs in Vibrio cholerae (TtcpG) and Haemophilus influenzae (Por). E. coli DsbC (or XpRA) and its orthologues in Erwinia chrysanthemi and H. influenzae. E. coli DsbD (or DipZ) and its H. influenzae orthologue. E. coli DsbE (or CcmG) and orthologues in H. influenzae. Rhodobacter capsulatus (Rhodopseudomonas capsulata) (HelX), Rhiziobiacae (CycY and TlpA). This entry represents the thioredoxin domain.; GO: 0045454 cell redox homeostasis; PDB: 3ED3_B 1EP7_A 1EP8_B 1TOF_A 2OE3_B 2OE1_B 2OE0_B 1V98_A 3H79_A 3CXG_A ....
Probab=26.47 E-value=1.4e+02 Score=22.51 Aligned_cols=37 Identities=14% Similarity=0.263 Sum_probs=24.4
Q ss_pred EEeecCChhHH-HHHHHhhhhhhccC-ceEEEEeCHHHH
Q 020247 184 MYAYSTSKLHC-EILRLFSKVEYQLP-NLIVGAITKESL 220 (329)
Q Consensus 184 vYAYT~S~lqi-aiL~lF~el~~r~P-Nlvvg~iTReSV 220 (329)
||-|++.--+. ++...|.++...++ ++.++.+.-+.-
T Consensus 22 v~f~~~~C~~C~~~~~~~~~~~~~~~~~v~~~~vd~~~~ 60 (103)
T PF00085_consen 22 VYFYAPWCPPCKAFKPILEKLAKEYKDNVKFAKVDCDEN 60 (103)
T ss_dssp EEEESTTSHHHHHHHHHHHHHHHHTTTTSEEEEEETTTS
T ss_pred EEEeCCCCCccccccceecccccccccccccchhhhhcc
Confidence 34455554444 66678888888787 788887766543
No 61
>PF01216 Calsequestrin: Calsequestrin; InterPro: IPR001393 Calsequestrin is the principal calcium-binding protein present in the sarcoplasmic reticulum of cardiac and skeletal muscle []. It is a highly acidic protein that is able to bind over 40 calcium ions and acts as an internal calcium store in muscle. Sequence analysis has suggested that calcium is not bound in distinct pockets via EF-hand motifs, but rather via presentation of a charged protein surface. Two forms of calsequestrin have been identified. The cardiac form is present in cardiac and slow skeletal muscle and the fast skeletal form is found in fast skeletal muscle. The release of calsequestrin-bound calcium (through a a calcium release channel) triggers muscle contraction. The active protein is not highly structured, more than 50% of it adopting a random coil conformation []. When calcium binds there is a structural change whereby the alpha-helical content of the protein increases from 3 to 11% []. Both forms of calsequestrin are phosphorylated by casein kinase II, but the cardiac form is phosphorylated more rapidly and to a higher degree [].; GO: 0005509 calcium ion binding; PDB: 1SJI_B 2VAF_A 3UOM_C 1A8Y_A 3TRQ_A 3TRP_A 3US3_A.
Probab=25.41 E-value=1.7e+02 Score=29.97 Aligned_cols=135 Identities=16% Similarity=0.309 Sum_probs=74.1
Q ss_pred EeeceeEEeecCChhHHHHHHHhhhhhhcc-CceEEEEeCHHHHHHHHHc---------------------CCCHHHHHH
Q 020247 178 VETNFRMYAYSTSKLHCEILRLFSKVEYQL-PNLIVGAITKESLYNAFEN---------------------GITAEQIIS 235 (329)
Q Consensus 178 VETNFrvYAYT~S~lqiaiL~lF~el~~r~-PNlvvg~iTReSV~~Al~~---------------------GITA~QII~ 235 (329)
+|-.=||.-|=.|.--- =+.-|.+-.-.| |-+-.+...-..|.+.+.. -.|-++|..
T Consensus 163 ied~~klIGyFk~~~s~-~yk~FeeAAe~F~p~IkFfAtfd~~vAk~L~lK~nev~fyepF~~~pi~ip~~p~~e~e~~~ 241 (383)
T PF01216_consen 163 IEDDIKLIGYFKSEDSE-HYKEFEEAAEHFQPYIKFFATFDKKVAKKLGLKLNEVDFYEPFMDEPITIPGKPYTEEELVE 241 (383)
T ss_dssp --SS-EEEEE-SSTTSH-HHHHHHHHHHHCTTTSEEEEE-SHHHHHHHT-STT-EEEE-TTSSSEEEESSSS--HHHHHH
T ss_pred cccceeEEEEeCCCCcH-HHHHHHHHHHhhcCceeEEEEecchhhhhcCccccceeeeccccCCCccCCCCCCCHHHHHH
Confidence 34344555554431111 234555666566 5555555555566555532 236689999
Q ss_pred HHHhcCCccccccCCCCChhHHHHHHHHHHhcCceeeeceeeecCCCCH---HHHHHHHHHHHHcCeEeeecCCCceEEE
Q 020247 236 FLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSR---DVFEAACDYARDQSGLLWEDPKKMRLVV 312 (329)
Q Consensus 236 fL~~hAHp~m~~~~~~iP~tV~dQI~lWe~Er~Rl~~~~g~Ly~~f~s~---~~fe~v~~yA~~~g~llw~~~~kr~~~V 312 (329)
|++.|-.|.|+|-. |. |=...||...+-+ +-+-|.+=.+. +-++.+.+-|++.. .++.--.+-|
T Consensus 242 fi~~h~rptlrkl~---~~---~m~e~Wedd~~g~---hIvaFaee~dpdG~efleilk~va~~nt----~np~LsivwI 308 (383)
T PF01216_consen 242 FIEEHKRPTLRKLR---PE---DMFETWEDDIDGI---HIVAFAEEEDPDGFEFLEILKQVARDNT----DNPDLSIVWI 308 (383)
T ss_dssp HHHHT-S-SEEE-----GG---GHHHHHHSSSSSE---EEEEE--TTSHHHHHHHHHHHHHHHHCT----T-TT--EEEE
T ss_pred HHHHhchhHhhhCC---hh---hhhhhhcccCCCc---eEEEEecCCCCchHHHHHHHHHHHHhcC----cCCceeEEEE
Confidence 99999999999843 34 3467899765422 22334443333 44577888898877 5666556668
Q ss_pred eccccHHHHHHHhh
Q 020247 313 KAEIHMHMREFLRG 326 (329)
Q Consensus 313 ~~~~h~~vr~f~k~ 326 (329)
.++.-.-+..||.+
T Consensus 309 DPD~fPllv~yWE~ 322 (383)
T PF01216_consen 309 DPDDFPLLVPYWEK 322 (383)
T ss_dssp -GGG-HHHHHHHHH
T ss_pred CCCCCchhHHHHHh
Confidence 99999999999976
No 62
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=25.03 E-value=95 Score=24.85 Aligned_cols=53 Identities=13% Similarity=0.278 Sum_probs=31.4
Q ss_pred ccChhhHHHHHHHHHHHHHHHcCCChHHHHHHHHHhcccccCccccCCCCCHHH-HHHHHHHhhcCceeee
Q 020247 75 LMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGEAYNLNTLSEIQ-KSMIKDFADLGLVKLQ 144 (329)
Q Consensus 75 L~d~~~Q~W~lll~yl~~~e~~g~~~~e~L~fLf~Ls~~~~G~~Y~~~~lt~~q-~~~L~~L~d~GLVy~~ 144 (329)
+.+...+|..++.. ....+.|+...++..-| ++++.+ +..+++|.+.|.||.-
T Consensus 45 ~~~~~~~Vl~~i~~--~~~~~~Gv~v~~I~~~l---------------~~~~~~v~~al~~L~~eG~IYsT 98 (102)
T PF08784_consen 45 LSPLQDKVLNFIKQ--QPNSEEGVHVDEIAQQL---------------GMSENEVRKALDFLSNEGHIYST 98 (102)
T ss_dssp S-HHHHHHHHHHHC------TTTEEHHHHHHHS---------------TS-HHHHHHHHHHHHHTTSEEES
T ss_pred CCHHHHHHHHHHHh--cCCCCCcccHHHHHHHh---------------CcCHHHHHHHHHHHHhCCeEecc
Confidence 44555666655555 11233477777776533 234444 6799999999999964
No 63
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=24.94 E-value=61 Score=28.19 Aligned_cols=21 Identities=14% Similarity=0.257 Sum_probs=17.3
Q ss_pred HHHHHHHHHHhhcCceeeecC
Q 020247 126 EIQKSMIKDFADLGLVKLQQG 146 (329)
Q Consensus 126 ~~q~~~L~~L~d~GLVy~~~~ 146 (329)
.+-...|+.|.+.|||+..+.
T Consensus 57 Stv~rsl~~L~~~GlV~Rek~ 77 (126)
T COG3355 57 STVYRSLQNLLEAGLVEREKV 77 (126)
T ss_pred HHHHHHHHHHHHcCCeeeeee
Confidence 345678999999999998874
No 64
>PLN02674 adenylate kinase
Probab=24.91 E-value=3.4e+02 Score=25.80 Aligned_cols=81 Identities=15% Similarity=0.106 Sum_probs=54.4
Q ss_pred hhccCceEEEEeCHHHHHHHHHcCCCHHHHHHHHHhcCCccccccCCCCChhHHHHHHHHHHhcCceeeeceeeecCCCC
Q 020247 204 EYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPS 283 (329)
Q Consensus 204 ~~r~PNlvvg~iTReSV~~Al~~GITA~QII~fL~~hAHp~m~~~~~~iP~tV~dQI~lWe~Er~Rl~~~~g~Ly~~f~s 283 (329)
.+-++.+.+|.+=|+.|+..=..| .+|-+++.+ +..+|..++.++-..+.... ....|++++.|+-
T Consensus 54 ~~~~~his~GdllR~~i~~~s~~g---~~i~~~~~~---------G~lvpd~iv~~lv~~~l~~~--~~~~g~ilDGfPR 119 (244)
T PLN02674 54 EYCLCHLATGDMLRAAVAAKTPLG---IKAKEAMDK---------GELVSDDLVVGIIDEAMKKP--SCQKGFILDGFPR 119 (244)
T ss_pred HcCCcEEchhHHHHHHHhccChhh---HHHHHHHHc---------CCccCHHHHHHHHHHHHhCc--CcCCcEEEeCCCC
Confidence 556899999987777765444444 344444443 44899999999887776543 3458999999997
Q ss_pred H-HHHHHHHHHHHHcC
Q 020247 284 R-DVFEAACDYARDQS 298 (329)
Q Consensus 284 ~-~~fe~v~~yA~~~g 298 (329)
. +..+.+.+.....|
T Consensus 120 t~~Qa~~l~~~l~~~~ 135 (244)
T PLN02674 120 TVVQAQKLDEMLAKQG 135 (244)
T ss_pred CHHHHHHHHHHHHhcC
Confidence 5 44555555555555
No 65
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=24.83 E-value=3.2e+02 Score=21.00 Aligned_cols=62 Identities=18% Similarity=0.160 Sum_probs=38.5
Q ss_pred HHHHHHHHhCCCccCCC-CCCccchhchhhhccChhhHHHHHHHHHHHHHH-HcCCChHHHHHHHHHhc
Q 020247 45 SSMMKVFQRGLLSRRDK-EAPRLTESGFQFLLMDTNAQLWYIVREYISNSQ-ERGINQADLISFLLELS 111 (329)
Q Consensus 45 ~~v~~lL~~~gL~~~~~-~~~~IT~~GfqFLL~d~~~Q~W~lll~yl~~~e-~~g~~~~e~L~fLf~Ls 111 (329)
...++-|...||+.... ....+|++|-+.. .++......+-..+. ..|.+..++-.++..|.
T Consensus 17 s~~l~~L~~~glI~r~~~~~~~lT~~g~~~~-----~~~~~~~~~~~~~l~~~~~~~~~e~~~l~~~l~ 80 (96)
T smart00529 17 TQMLKKLEKDGLVEYEPYRGITLTEKGRRLA-----RRLLRKHRLLERFLVDVLGVDEEEVHEEAERLE 80 (96)
T ss_pred HHHHHHHHHCCCEEEcCCCceEechhHHHHH-----HHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHH
Confidence 44567778889999754 4789999998764 222222222222222 24777777777666665
No 66
>PF05184 SapB_1: Saposin-like type B, region 1; InterPro: IPR007856 Synonym(s):cerebroside sulphate activator, CSAct Saposin B is a small non-enzymatic glycoprotein required for the breakdown of cerebroside sulphates (sulphatides) in lysosomes. Saposin B contains three intramolecular disulphide bridges, exists as a dimer and is remarkably heat, protease, and pH stable. The crystal structure of human saposin B reveals an unusual shell-like dimer consisting of a monolayer of alpha-helices enclosing a large hydrophobic cavity. Although the secondary structure of saposin B is similar to that of the known monomeric members of the saposin-like superfamily, the helices are repacked into a different tertiary arrangement to form the homodimer. A comparison of the two forms of the saposin B dimer suggests that extraction of target lipids from membranes involves a conformational change that facilitates access to the inner cavity [].; GO: 0006629 lipid metabolic process; PDB: 1N69_C 1QDM_C 4DDJ_A 2DOB_A 1OF9_A 2Z9A_A 1M12_A 2GTG_A 1SN6_A 2QYP_B ....
Probab=24.40 E-value=74 Score=20.83 Aligned_cols=21 Identities=24% Similarity=0.317 Sum_probs=18.5
Q ss_pred HHHHHHHcCCCHHHHHHHHHh
Q 020247 219 SLYNAFENGITAEQIISFLQQ 239 (329)
Q Consensus 219 SV~~Al~~GITA~QII~fL~~ 239 (329)
-++..+.++.|-++|+++|..
T Consensus 13 ~i~~~l~~~~t~~~I~~~l~~ 33 (39)
T PF05184_consen 13 EIEKLLKNNKTEEEIKKALEK 33 (39)
T ss_dssp HHHHHHHSTCHHHHHHHHHHH
T ss_pred HHHHHHHcCccHHHHHHHHHH
Confidence 467889999999999999985
No 67
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=24.35 E-value=24 Score=34.05 Aligned_cols=39 Identities=15% Similarity=0.242 Sum_probs=27.3
Q ss_pred CCCcHHHHHHHHhCCCccCCC-CCCccchhchhhhccChhh
Q 020247 41 TNFSSSMMKVFQRGLLSRRDK-EAPRLTESGFQFLLMDTNA 80 (329)
Q Consensus 41 ~~~s~~v~~lL~~~gL~~~~~-~~~~IT~~GfqFLL~d~~~ 80 (329)
+.+|.-+++ |-..||++..+ +..+||.+|++||+.....
T Consensus 40 QaVsehiK~-Lv~eG~i~~~gR~~Y~iTkkG~e~l~~~~~d 79 (260)
T COG1497 40 QAVSEHIKE-LVKEGLIEKEGRGEYEITKKGAEWLLEQLSD 79 (260)
T ss_pred HHHHHHHHH-HHhccceeecCCeeEEEehhHHHHHHHHHHH
Confidence 445555555 46778888654 3678999999999855443
No 68
>PRK13808 adenylate kinase; Provisional
Probab=23.51 E-value=2.2e+02 Score=28.53 Aligned_cols=78 Identities=18% Similarity=0.204 Sum_probs=48.2
Q ss_pred hhccCceEEEEeCHHHHHHHHHcCCCHHH-HHHHHHhcCCccccccCCCCChhHHHHHHHHHHhcCceeeeceeeecCCC
Q 020247 204 EYQLPNLIVGAITKESLYNAFENGITAEQ-IISFLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFP 282 (329)
Q Consensus 204 ~~r~PNlvvg~iTReSV~~Al~~GITA~Q-II~fL~~hAHp~m~~~~~~iP~tV~dQI~lWe~Er~Rl~~~~g~Ly~~f~ 282 (329)
.|.++.+.+|.|=|+-|. .|..... |-+++. ....+|..++.+|-.++++... ...|++++.|+
T Consensus 23 ~ygl~~is~gdlLR~~i~----~~s~~g~~~~~~~~---------~G~lVPdeiv~~li~e~l~~~~--~~~G~ILDGFP 87 (333)
T PRK13808 23 QYGIVQLSTGDMLRAAVA----AGTPVGLKAKDIMA---------SGGLVPDEVVVGIISDRIEQPD--AANGFILDGFP 87 (333)
T ss_pred HhCCceecccHHHHHHhh----cCChhhHHHHHHHH---------cCCCCCHHHHHHHHHHHHhccc--ccCCEEEeCCC
Confidence 356777777765555553 4443332 222322 2458999999999888876543 36799999999
Q ss_pred CH-HHHHHHHHHHHH
Q 020247 283 SR-DVFEAACDYARD 296 (329)
Q Consensus 283 s~-~~fe~v~~yA~~ 296 (329)
.. ++.+.+-....+
T Consensus 88 Rt~~QA~~L~~ll~~ 102 (333)
T PRK13808 88 RTVPQAEALDALLKD 102 (333)
T ss_pred CCHHHHHHHHHHHHh
Confidence 76 444444444443
No 69
>PRK14526 adenylate kinase; Provisional
Probab=22.93 E-value=1.6e+02 Score=27.11 Aligned_cols=74 Identities=16% Similarity=0.276 Sum_probs=45.3
Q ss_pred ccCceEEEEeCHHHHHHHHHcCCCHHHHHHHHHhcCCccccccCCCCChhHHHHHHHHHHhcCceeeeceeeecCCC-CH
Q 020247 206 QLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFP-SR 284 (329)
Q Consensus 206 r~PNlvvg~iTReSV~~Al~~GITA~QII~fL~~hAHp~m~~~~~~iP~tV~dQI~lWe~Er~Rl~~~~g~Ly~~f~-s~ 284 (329)
.++.+.+|.+-|+.+...-..| .+|-.++... ..+|..++.++-....+. .....|++++.|+ +.
T Consensus 25 ~~~~is~G~llr~~~~~~t~~g---~~i~~~~~~g---------~lvpd~~~~~lv~~~l~~--~~~~~g~ilDGfPR~~ 90 (211)
T PRK14526 25 NYYHISTGDLFRENILNSTPLG---KEIKQIVENG---------QLVPDSITIKIVEDKINT--IKNNDNFILDGFPRNI 90 (211)
T ss_pred CCceeecChHHHHhcccCChhh---HHHHHHHHcC---------ccCChHHHHHHHHHHHhc--ccccCcEEEECCCCCH
Confidence 4777888888776665433322 4455555543 378888886665544432 2346789999995 44
Q ss_pred HHHHHHHHH
Q 020247 285 DVFEAACDY 293 (329)
Q Consensus 285 ~~fe~v~~y 293 (329)
++.+.+.++
T Consensus 91 ~Qa~~l~~~ 99 (211)
T PRK14526 91 NQAKALDKF 99 (211)
T ss_pred HHHHHHHHh
Confidence 555555444
No 70
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=22.31 E-value=85 Score=27.95 Aligned_cols=53 Identities=19% Similarity=0.330 Sum_probs=34.8
Q ss_pred HHHHHHHhcccccCccccCCCCCHHH-------HHHHHHHhhcCceeeecCCCccccccch
Q 020247 103 LISFLLELSFHVAGEAYNLNTLSEIQ-------KSMIKDFADLGLVKLQQGRKENWFIPTK 156 (329)
Q Consensus 103 ~L~fLf~Ls~~~~G~~Y~~~~lt~~q-------~~~L~~L~d~GLVy~~~~~~~~fy~pT~ 156 (329)
.|..++.|.+..-+...+.+.+++.+ ..+|+.|++-|||.-.++..+-|. |.+
T Consensus 10 Al~~l~~lA~~~~~~~vs~~eIA~~~~ip~~~l~kIl~~L~~aGLv~s~rG~~GGy~-Lar 69 (164)
T PRK10857 10 AVTAMLDVALNSEAGPVPLADISERQGISLSYLEQLFSRLRKNGLVSSVRGPGGGYL-LGK 69 (164)
T ss_pred HHHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeCCCCCCCee-ccC
Confidence 45566666655555555655443332 569999999999988666666666 544
No 71
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=21.84 E-value=91 Score=24.08 Aligned_cols=25 Identities=16% Similarity=0.462 Sum_probs=20.3
Q ss_pred HHHHHHHHhhcCceeeecCCCcccc
Q 020247 128 QKSMIKDFADLGLVKLQQGRKENWF 152 (329)
Q Consensus 128 q~~~L~~L~d~GLVy~~~~~~~~fy 152 (329)
-..+++.|.+-|||...++..+-|+
T Consensus 42 l~kil~~L~~~Gli~s~~G~~GGy~ 66 (83)
T PF02082_consen 42 LRKILQKLKKAGLIESSRGRGGGYR 66 (83)
T ss_dssp HHHHHHHHHHTTSEEEETSTTSEEE
T ss_pred HHHHHHHHhhCCeeEecCCCCCcee
Confidence 3679999999999988877656666
No 72
>PRK11235 bifunctional antitoxin/transcriptional repressor RelB; Provisional
Probab=21.10 E-value=2.5e+02 Score=22.48 Aligned_cols=45 Identities=11% Similarity=0.263 Sum_probs=39.0
Q ss_pred HHHcCCChHHHHHHHHHhcccccCccccCCCCCHHHHHHHHHHhh
Q 020247 93 SQERGINQADLISFLLELSFHVAGEAYNLNTLSEIQKSMIKDFAD 137 (329)
Q Consensus 93 ~e~~g~~~~e~L~fLf~Ls~~~~G~~Y~~~~lt~~q~~~L~~L~d 137 (329)
+++.|++..+++..++.=...+-|-+|+...+|+.++.+|.--++
T Consensus 20 l~~lGls~S~Ai~~fl~qi~~~~~iPF~~~~~s~ed~~~l~~~re 64 (80)
T PRK11235 20 LEKLGVTPSEALRLLLQYVAENGRLPFKTVLLSDEDAALLETVRE 64 (80)
T ss_pred HHHhCCCHHHHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHH
Confidence 567799999999999988888889899999999999998887443
No 73
>PF01090 Ribosomal_S19e: Ribosomal protein S19e; InterPro: IPR001266 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family includes a number of eukaryotic and archaebacterial ribosomal proteins; mammalian S19, Drosophila S19, Ascaris lumbricoides S19g (ALEP-1) and S19s, yeast YS16 (RP55A and RP55B), Aspergillus S16 and Haloarcula marismortui HS12.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZ6_S 3U5G_T 3U5C_T 3O30_M 3O2Z_M 3IZB_S 2XZN_T 2XZM_T 2V7F_A.
Probab=21.10 E-value=21 Score=31.56 Aligned_cols=34 Identities=24% Similarity=0.347 Sum_probs=26.1
Q ss_pred CCCcHHHHHHHHhCCCccCC-CCCCccchhchhhh
Q 020247 41 TNFSSSMMKVFQRGLLSRRD-KEAPRLTESGFQFL 74 (329)
Q Consensus 41 ~~~s~~v~~lL~~~gL~~~~-~~~~~IT~~GfqFL 74 (329)
..+-..+++=|...||++.+ +++..||++|-++|
T Consensus 94 g~iiR~~LqqLE~~glv~k~~~~GR~lT~~G~~~l 128 (139)
T PF01090_consen 94 GSIIRKILQQLEKAGLVEKDPKGGRRLTPKGQRDL 128 (139)
T ss_dssp HHHHHHHHHHHHHTTSEEEETTTEEEE-HHHHHHH
T ss_pred cHHHHHHHHHHHHCCCEEecCCCCCEECHHHHHHH
Confidence 34556778888999999976 55678999998876
No 74
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator). This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.
Probab=20.61 E-value=1e+02 Score=25.37 Aligned_cols=29 Identities=14% Similarity=0.302 Sum_probs=20.7
Q ss_pred HHHHHHHHHhhcCceeeecCCCccccccch
Q 020247 127 IQKSMIKDFADLGLVKLQQGRKENWFIPTK 156 (329)
Q Consensus 127 ~q~~~L~~L~d~GLVy~~~~~~~~fy~pT~ 156 (329)
+-.++|+.|.+.|+|....+..+.|. |++
T Consensus 41 ~v~~il~~L~~~gli~~~~g~~ggy~-l~~ 69 (132)
T TIGR00738 41 YLEKILRTLRRAGLVESVRGPGGGYR-LAR 69 (132)
T ss_pred HHHHHHHHHHHCCcEEeccCCCCCcc-CCC
Confidence 34679999999999976544445566 544
No 75
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=20.53 E-value=1.1e+02 Score=26.08 Aligned_cols=50 Identities=12% Similarity=0.196 Sum_probs=33.4
Q ss_pred HHHHHHHhcccccCccccCCCCC-------HHHHHHHHHHhhcCceeeecCCCcccc
Q 020247 103 LISFLLELSFHVAGEAYNLNTLS-------EIQKSMIKDFADLGLVKLQQGRKENWF 152 (329)
Q Consensus 103 ~L~fLf~Ls~~~~G~~Y~~~~lt-------~~q~~~L~~L~d~GLVy~~~~~~~~fy 152 (329)
.+..+..++....|+..+.+.+. ..-+..|+.|+.-|||...++.++.|.
T Consensus 10 Al~~~i~la~~~~g~~~s~~~ia~~~~is~~~vrk~l~~L~~~Glv~s~~G~~GG~~ 66 (141)
T PRK11014 10 GLRALIYMASLPEGRMTSISEVTEVYGVSRNHMVKIINQLSRAGYVTAVRGKNGGIR 66 (141)
T ss_pred HHHHHHHHhcCCCCCccCHHHHHHHHCcCHHHHHHHHHHHHhCCEEEEecCCCCCee
Confidence 35555566666666544443332 333779999999999998887666665
No 76
>PRK00279 adk adenylate kinase; Reviewed
Probab=20.10 E-value=6.3e+02 Score=22.56 Aligned_cols=101 Identities=11% Similarity=0.159 Sum_probs=56.6
Q ss_pred hhccCceEEEEeCHHHHHHHHHcCCCHHHHHHHHHhcCCccccccCCCCChhHHHHHHHHHHhcCceeeeceeeecCCCC
Q 020247 204 EYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPS 283 (329)
Q Consensus 204 ~~r~PNlvvg~iTReSV~~Al~~GITA~QII~fL~~hAHp~m~~~~~~iP~tV~dQI~lWe~Er~Rl~~~~g~Ly~~f~s 283 (329)
.+-++.+.+|-+-|+.+...- -.+.+|-.++.. ...+|.+++..+-.-..... ....|++++.|+.
T Consensus 23 ~~~~~~is~~dl~r~~~~~~~---~~~~~~~~~~~~---------g~~~p~~~~~~~i~~~l~~~--~~~~g~VlDGfPr 88 (215)
T PRK00279 23 KYGIPHISTGDMLRAAVKAGT---ELGKEAKSYMDA---------GELVPDEIVIGLVKERLAQP--DCKNGFLLDGFPR 88 (215)
T ss_pred HhCCcEEECCccHHHHHhccc---hHHHHHHHHHHc---------CCcCCHHHHHHHHHHHHhcc--CccCCEEEecCCC
Confidence 345788888888777665422 223445555543 23788888766554443322 2345899999966
Q ss_pred H-HHHHHHHHHHHHcCeEeeecCCCceEEEeccccHHHHHH
Q 020247 284 R-DVFEAACDYARDQSGLLWEDPKKMRLVVKAEIHMHMREF 323 (329)
Q Consensus 284 ~-~~fe~v~~yA~~~g~llw~~~~kr~~~V~~~~h~~vr~f 323 (329)
. ++.+.+.++.++.|+ .....+++......-++..
T Consensus 89 ~~~qa~~l~~~l~~~~~-----~~~~vi~l~~~~~~~~~Rl 124 (215)
T PRK00279 89 TIPQAEALDEMLKELGI-----KLDAVIEIDVPDEELVERL 124 (215)
T ss_pred CHHHHHHHHHHHHHcCC-----CCCEEEEEECCHHHHHHHH
Confidence 4 555666566565552 2233455555533333333
Done!