Query 029030
Match_columns 200
No_of_seqs 110 out of 187
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 06:22:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029030.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029030hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR00625 tfb2 Transcription f 100.0 9.7E-81 2.1E-85 577.9 21.1 198 1-200 244-448 (448)
2 KOG3471 RNA polymerase II tran 100.0 1.1E-80 2.4E-85 569.2 14.2 198 1-200 256-463 (465)
3 COG5144 TFB2 RNA polymerase II 100.0 3.3E-71 7.2E-76 496.9 9.5 197 1-199 243-445 (447)
4 PF03849 Tfb2: Transcription f 100.0 1.8E-49 4E-54 361.4 11.6 112 1-114 244-366 (366)
5 PF13625 Helicase_C_3: Helicas 99.7 4.3E-17 9.2E-22 128.3 12.3 118 47-172 2-121 (129)
6 TIGR00603 rad25 DNA repair hel 97.7 0.00043 9.4E-09 69.2 11.8 106 44-164 22-132 (732)
7 PF08671 SinI: Anti-repressor 94.0 0.053 1.1E-06 33.6 2.5 22 90-111 8-29 (30)
8 PRK06015 keto-hydroxyglutarate 88.0 4.4 9.5E-05 34.8 8.9 125 44-197 28-164 (201)
9 TIGR01615 A_thal_3542 uncharac 86.6 0.34 7.5E-06 39.4 1.3 65 43-125 47-112 (131)
10 PRK05718 keto-hydroxyglutarate 84.3 12 0.00026 32.3 9.7 125 44-197 39-175 (212)
11 TIGR01182 eda Entner-Doudoroff 82.3 15 0.00032 31.7 9.5 124 45-197 33-168 (204)
12 PRK07114 keto-hydroxyglutarate 81.3 27 0.00059 30.4 10.9 125 44-197 39-180 (222)
13 KOG1123 RNA polymerase II tran 79.8 3.8 8.2E-05 40.8 5.5 86 43-143 81-169 (776)
14 PF01081 Aldolase: KDPG and KH 72.0 9 0.00019 32.8 5.2 125 44-197 32-168 (196)
15 COG1313 PflX Uncharacterized F 71.6 5.7 0.00012 36.8 4.1 52 101-170 273-329 (335)
16 PRK06552 keto-hydroxyglutarate 66.7 70 0.0015 27.5 9.7 125 43-197 36-175 (213)
17 PRK14529 adenylate kinase; Pro 66.1 38 0.00083 29.3 8.0 80 75-169 23-103 (223)
18 PF00406 ADK: Adenylate kinase 64.1 15 0.00033 28.6 4.8 81 75-169 19-100 (151)
19 PF02244 Propep_M14: Carboxype 63.2 36 0.00078 23.5 6.1 46 153-198 6-55 (74)
20 PF04720 DUF506: Protein of un 61.6 3.8 8.2E-05 35.9 1.0 66 42-125 135-201 (218)
21 TIGR03853 matur_matur probable 57.9 14 0.0003 27.6 3.3 27 86-112 18-58 (77)
22 KOG4175 Tryptophan synthase al 53.2 62 0.0013 28.9 7.0 78 88-172 66-151 (268)
23 TIGR00262 trpA tryptophan synt 50.8 1.7E+02 0.0037 25.6 9.6 26 86-111 56-81 (256)
24 TIGR02425 decarb_PcaC 4-carbox 49.4 22 0.00048 28.0 3.4 25 88-112 76-100 (123)
25 smart00195 DSPc Dual specifici 49.1 44 0.00096 25.4 5.0 52 79-136 80-137 (138)
26 PF10678 DUF2492: Protein of u 47.7 29 0.00063 25.9 3.6 27 86-112 20-60 (78)
27 PF03918 CcmH: Cytochrome C bi 41.0 26 0.00057 28.7 2.8 30 88-117 63-92 (148)
28 PF00085 Thioredoxin: Thioredo 41.0 71 0.0015 22.2 4.7 37 55-91 22-60 (103)
29 PF12637 TSCPD: TSCPD domain; 40.0 58 0.0013 24.4 4.3 54 65-134 37-90 (95)
30 PF01216 Calsequestrin: Calseq 39.9 80 0.0017 30.0 6.0 134 50-197 164-322 (383)
31 PF13833 EF-hand_8: EF-hand do 38.8 41 0.00089 21.5 3.0 20 84-103 3-26 (54)
32 PF09713 A_thal_3526: Plant pr 38.6 47 0.001 23.1 3.3 24 89-112 3-26 (54)
33 COG1412 Uncharacterized protei 38.6 75 0.0016 25.9 5.0 18 43-60 9-26 (136)
34 PRK13808 adenylate kinase; Pro 37.8 99 0.0021 28.6 6.2 77 75-166 23-101 (333)
35 TIGR03147 cyt_nit_nrfF cytochr 36.0 75 0.0016 25.7 4.6 29 88-116 63-91 (126)
36 PF09170 STN1_2: CST, Suppress 35.4 12 0.00025 31.9 -0.2 25 2-27 111-135 (174)
37 PLN02674 adenylate kinase 34.6 1.6E+02 0.0034 26.0 6.8 81 75-169 54-135 (244)
38 PF05184 SapB_1: Saposin-like 34.2 43 0.00093 20.3 2.3 21 90-110 13-33 (39)
39 PRK10144 formate-dependent nit 33.4 88 0.0019 25.3 4.6 29 88-116 63-91 (126)
40 COG0563 Adk Adenylate kinase a 33.0 27 0.00059 29.0 1.7 79 76-169 24-104 (178)
41 PLN02459 probable adenylate ki 32.8 1.8E+02 0.0039 26.0 6.9 69 75-155 52-120 (261)
42 KOG2036 Predicted P-loop ATPas 31.9 37 0.0008 35.2 2.6 58 58-132 529-605 (1011)
43 PF13496 DUF4120: Domain of un 29.0 45 0.00098 25.6 2.1 16 155-170 5-20 (95)
44 PRK12928 lipoyl synthase; Prov 28.6 4.3E+02 0.0093 23.7 10.3 114 66-183 124-251 (290)
45 PF03444 HrcA_DNA-bdg: Winged 28.6 24 0.00053 26.3 0.6 29 2-32 44-72 (78)
46 PF00782 DSPc: Dual specificit 28.5 66 0.0014 24.1 3.0 44 86-136 84-132 (133)
47 PRK14526 adenylate kinase; Pro 28.0 1.3E+02 0.0027 25.6 4.9 74 77-164 25-99 (211)
48 PF14133 DUF4300: Domain of un 27.7 63 0.0014 28.9 3.1 30 85-114 9-39 (250)
49 TIGR01470 cysG_Nterm siroheme 27.0 2.6E+02 0.0057 23.6 6.7 78 98-182 18-109 (205)
50 PRK08508 biotin synthase; Prov 27.0 3.5E+02 0.0077 23.7 7.7 99 66-170 76-180 (279)
51 cd00127 DSPc Dual specificity 26.8 1.1E+02 0.0024 22.9 4.0 44 86-135 92-139 (139)
52 PF01978 TrmB: Sugar-specific 26.6 21 0.00045 24.5 -0.1 23 2-26 43-65 (68)
53 PRK00279 adk adenylate kinase; 26.6 3.3E+02 0.0072 22.4 7.2 80 76-169 24-104 (215)
54 PRK14089 ipid-A-disaccharide s 26.3 41 0.00089 31.0 1.8 54 57-110 260-315 (347)
55 PRK13761 hypothetical protein; 25.1 33 0.00071 30.7 0.8 19 85-103 12-30 (248)
56 PF00482 T2SF: Type II secreti 24.7 68 0.0015 22.8 2.4 29 90-118 4-33 (124)
57 PF00508 PPV_E2_N: E2 (early) 24.7 1.3E+02 0.0029 26.1 4.5 26 102-139 13-38 (202)
58 PF10163 EnY2: Transcription f 24.2 46 0.001 24.5 1.4 38 88-132 41-78 (86)
59 COG4109 Predicted transcriptio 23.8 84 0.0018 30.1 3.3 18 80-97 290-307 (432)
60 PRK09913 putative fructose-lik 23.4 2.4E+02 0.0053 21.7 5.5 40 60-111 106-145 (148)
61 cd01095 Nitrilotriacetate_mono 23.1 1.8E+02 0.004 26.7 5.4 63 93-164 284-347 (358)
62 COG1438 ArgR Arginine represso 23.0 37 0.0008 28.2 0.7 20 3-23 44-63 (150)
63 PF09106 SelB-wing_2: Elongati 22.9 1E+02 0.0023 20.7 2.9 28 121-148 30-57 (59)
64 COG0599 Uncharacterized homolo 22.9 74 0.0016 24.6 2.4 27 87-113 73-99 (124)
65 PRK11183 D-lactate dehydrogena 22.5 1.6E+02 0.0034 29.5 5.0 81 54-136 271-363 (564)
66 PF03428 RP-C: Replication pro 22.4 37 0.0008 28.7 0.6 22 2-23 92-113 (177)
67 PF09330 Lact-deh-memb: D-lact 22.2 5.1E+02 0.011 23.9 7.8 119 56-197 3-133 (291)
68 PF01316 Arg_repressor: Argini 21.6 43 0.00093 24.2 0.8 20 3-23 43-62 (70)
69 PF10566 Glyco_hydro_97: Glyco 21.5 89 0.0019 28.2 2.9 25 154-178 71-97 (273)
70 cd01293 Bact_CD Bacterial cyto 21.3 3.5E+02 0.0077 23.7 6.7 46 125-172 158-205 (398)
71 PF08673 RsbU_N: Phosphoserine 21.1 77 0.0017 23.3 2.0 16 92-107 28-43 (77)
72 PRK14340 (dimethylallyl)adenos 20.7 5.8E+02 0.013 24.1 8.3 45 125-170 283-329 (445)
73 TIGR01290 nifB nitrogenase cof 20.4 7.4E+02 0.016 23.6 9.0 104 66-173 96-220 (442)
74 PF00571 CBS: CBS domain CBS d 20.2 1E+02 0.0022 19.4 2.3 18 79-96 39-56 (57)
No 1
>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=9.7e-81 Score=577.87 Aligned_cols=198 Identities=37% Similarity=0.698 Sum_probs=189.3
Q ss_pred CcccccccceeEEeecCCCCccccchhhhhhhcccCCc----cc--ccccceEEEeeCceEEEecCCHhHHHHHHHhhhh
Q 029030 1 MIKDFADLGLVKLQQVGRKESWFIPTKLATNLSMSLTD----SS--ARKEGFVVVETNFRMYAYSTSKLHCEILRLFSKI 74 (200)
Q Consensus 1 ~L~~l~~~GLvy~~~~~~~~~fy~pT~La~~l~~~~~~----~~--~~~~g~IIvETNFrvYAYT~s~l~iaiL~lF~~l 74 (200)
||+||+|+||||++ ++++++|| |||||++|++++++ ++ +.++|+|||||||||||||+||||++||++||++
T Consensus 244 ~L~dL~dlGLVy~~-~~~~~~fY-PTrLAt~Lts~~~~l~~~~~~~~~~~g~iivEtNfrvYaYt~s~l~~~il~lF~~~ 321 (448)
T TIGR00625 244 MLQDLREYGLVFQR-KRKSRRFY-PTRLAINLTSDTKTVSGAGGTVDDDLGFIIVETNYRLYAYTESPLQIALIALFSEL 321 (448)
T ss_pred HHHHHHHcCeEEEe-cCCCCccc-chHHHHHHhcCccccccccccccCCCceEEEEecceEEEecCCHHHHHHHHHHHHH
Confidence 68999999999999 88999999 99999999887553 11 2567999999999999999999999999999999
Q ss_pred hhccCceEEEEeCHHHHHHHHHcCCCHHHHHHHHhhcCCcccc-ccCCCCCccHHHHHHHHHHhcCceEecceeeeccCC
Q 029030 75 EYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVA-DRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFP 153 (200)
Q Consensus 75 ~~r~Pnlvvg~lTR~Sv~~Al~~GITA~QII~fL~~haHp~m~-~~~~~iP~tV~dQI~lWe~Er~R~~~~~g~L~~~f~ 153 (200)
.||||||+||.|||+||++|+++||||||||+||++||||+|+ ++.|+|||||+|||+|||.||||+++++|+||++|.
T Consensus 322 ~~r~pnlvvg~iTr~Sv~~A~~~GITa~qIi~fl~~~ahp~~~~~~~~~lP~tv~dQi~lWe~e~~R~~~~~~~l~~~f~ 401 (448)
T TIGR00625 322 LARFPNMVVGQITRESIRRALANGITAQQIIHYLRTHAHPQMRKEQTPVLPPTIVDQIRLWELERDRLRFTEGVLYNDFL 401 (448)
T ss_pred HhcCCceEEEEecHHHHHHHHHcCCCHHHHHHHHHhcCChhhhccCCCCCChHHHHHHHHHHHHhcceEeecceeeeecC
Confidence 9999999999999999999999999999999999999999998 478999999999999999999999999999999999
Q ss_pred CHHHHHHHHHHHHHcCeEeeecCCcceEEEeccccHHHHHHHhhccC
Q 029030 154 SRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHMREFLRGQNK 200 (200)
Q Consensus 154 s~~~f~~v~~ya~~~g~llw~~~~~r~~~V~~~~~~~v~~f~k~~~~ 200 (200)
|+++|+++++||++.|+|+|+|+.||+|||+.+||++|++|||++|+
T Consensus 402 s~~~y~~~~~ya~~~~~l~w~~~~kr~~~V~~~gh~~v~~f~k~~~~ 448 (448)
T TIGR00625 402 TQVDFELLLAYARELGVLVWENSAKRLFFITPAGHSDVKRFWKRQKH 448 (448)
T ss_pred CHHHHHHHHHHHHHcCEEEEecCCceEEEEeccchHHHHHHHHhhcC
Confidence 99999999999999999999999999999999999999999999985
No 2
>KOG3471 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB2 [Transcription; Replication, recombination and repair]
Probab=100.00 E-value=1.1e-80 Score=569.18 Aligned_cols=198 Identities=41% Similarity=0.711 Sum_probs=188.1
Q ss_pred CcccccccceeEEeecCCCCccccchhhhhhhcccCCc--------ccccccceEEEeeCceEEEecCCHhHHHHHHHhh
Q 029030 1 MIKDFADLGLVKLQQVGRKESWFIPTKLATNLSMSLTD--------SSARKEGFVVVETNFRMYAYSTSKLHCEILRLFS 72 (200)
Q Consensus 1 ~L~~l~~~GLvy~~~~~~~~~fy~pT~La~~l~~~~~~--------~~~~~~g~IIvETNFrvYAYT~s~l~iaiL~lF~ 72 (200)
||+||+|+|||||| |.+..+|| ||+||+++|++..+ ...++.||||||||||||||||||||+|+++|||
T Consensus 256 ~lq~Lre~GlvfQr-k~k~~rfy-ptrla~~~ss~~~~~~~~~~~~~~edd~G~iIVETN~riYAYT~S~lQiAvi~LF~ 333 (465)
T KOG3471|consen 256 LLQHLRELGLVFQR-KIKILRFY-PTRLAIGLSSDQLGAASLVHQNRNEDDVGFIIVETNYRIYAYTNSPLQIAVIALFT 333 (465)
T ss_pred HHHHHHHhhHHHHh-hhhhheec-chhhhhccchhhhhhhhhhhcccccccCceEEEEeccEEEEecCCHHHHHHHHHHH
Confidence 68999999999999 99999999 99999999886442 1224569999999999999999999999999999
Q ss_pred hhhhccCceEEEEeCHHHHHHHHHcCCCHHHHHHHHhhcCCccccccC--CCCCccHHHHHHHHHHhcCceEecceeeec
Q 029030 73 KIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRI--PSVPENVCDQIRLWESDLNRVEMTPAHYYE 150 (200)
Q Consensus 73 ~l~~r~Pnlvvg~lTR~Sv~~Al~~GITA~QII~fL~~haHp~m~~~~--~~iP~tV~dQI~lWe~Er~R~~~~~g~L~~ 150 (200)
++.|||||||||+|||||||+|+++||||+|||+||++||||||+... |++||||+|||+|||.||||+.++||+||+
T Consensus 334 ~l~~rf~nlvvG~iTreSVr~Al~~GITa~QII~fLet~ahpqm~~~~~~~~LPpTv~dQIrLWElernR~~~~~g~LYs 413 (465)
T KOG3471|consen 334 ELTYRFPNLVVGVITRESVRRALDNGITAEQIIHFLETHAHPQMRMLSPVPCLPPTVVDQIRLWELERNRLRMTEGYLYS 413 (465)
T ss_pred HHHhhccccceeeeeHHHHHHHHhcCCcHHHHHHHHHhccCchhhhcCCCCCCCchHHhHHHHHHHhhcceecccchhHH
Confidence 999999999999999999999999999999999999999999998865 999999999999999999999999999999
Q ss_pred cCCCHHHHHHHHHHHHHcCeEeeecCCcceEEEeccccHHHHHHHhhccC
Q 029030 151 EFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHMREFLRGQNK 200 (200)
Q Consensus 151 ~f~s~~~f~~v~~ya~~~g~llw~~~~~r~~~V~~~~~~~v~~f~k~~~~ 200 (200)
+|.|..||+.+++||++.|+|+|+|+.||+|||+.+||++|++|||+++|
T Consensus 414 ~Fls~~df~~l~eya~~~~vLvw~d~~kr~~vV~~~Ghs~Vk~f~Kr~~k 463 (465)
T KOG3471|consen 414 DFLSLSDFQLLLEYAREIGVLVWSDSDKRMFVVTKEGHSLVKRFWKRKSK 463 (465)
T ss_pred hhhhhhhHHHHHHHHHHcCeEEEecCcceEEEEecCccHHHHHHHHHhhc
Confidence 99999999999999999999999999999999999999999999999654
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=3.3e-71 Score=496.89 Aligned_cols=197 Identities=34% Similarity=0.611 Sum_probs=187.8
Q ss_pred CcccccccceeEEeecCCCCccccchhhhhhhcccCC----c--ccccccceEEEeeCceEEEecCCHhHHHHHHHhhhh
Q 029030 1 MIKDFADLGLVKLQQVGRKESWFIPTKLATNLSMSLT----D--SSARKEGFVVVETNFRMYAYSTSKLHCEILRLFSKI 74 (200)
Q Consensus 1 ~L~~l~~~GLvy~~~~~~~~~fy~pT~La~~l~~~~~----~--~~~~~~g~IIvETNFrvYAYT~s~l~iaiL~lF~~l 74 (200)
||+|+|++||||++ +-.+++|| ||+||+.||++-- . ...++.||||||||||||||||||||+|+++|||++
T Consensus 243 ml~D~R~yglv~q~-~i~~~~fY-pt~LA~glt~d~~~~~s~qnr~edd~gfiIVETN~kiYaYtnSplqiavi~LF~nl 320 (447)
T COG5144 243 MLMDRRLYGLVEQL-GILRKIFY-PTGLAIGLTFDQLFEASEQNRREDDKGFIIVETNNKIYAYTNSPLQIAVIHLFCNL 320 (447)
T ss_pred HHHHHHHhhHHHHh-ccchhhcc-ccccchhhhhHHHHHhhhhccccccCceEEEEecceEEEecCChHHHHHHHHhhhh
Confidence 68999999999999 77888999 9999999987532 1 233667999999999999999999999999999999
Q ss_pred hhccCceEEEEeCHHHHHHHHHcCCCHHHHHHHHhhcCCccccccCCCCCccHHHHHHHHHHhcCceEecceeeeccCCC
Q 029030 75 EYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPS 154 (200)
Q Consensus 75 ~~r~Pnlvvg~lTR~Sv~~Al~~GITA~QII~fL~~haHp~m~~~~~~iP~tV~dQI~lWe~Er~R~~~~~g~L~~~f~s 154 (200)
..||||||+|+|||||||+|+.+||||+|||.||++||||+|+++.+.+||||+|||+|||.|+||+...||+||+||.+
T Consensus 321 ~arf~Nlv~GiITreSirrAl~nGIta~QII~yLethahpqmr~~l~llPPtivdQI~lWele~nRi~~~pG~LysdFlt 400 (447)
T COG5144 321 TARFPNLVKGIITRESIRRALDNGITAKQIIHYLETHAHPQMRKKLELLPPTIVDQIVLWELERNRIFMVPGYLYSDFLT 400 (447)
T ss_pred hcccchhhhhhccHHHHHHHHhcCccHHHHHHHHHhccChhhhhcCCCCChhhhhheeeeeeccCcEEeecchHHhhhhc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHcCeEeeecCCcceEEEeccccHHHHHHHhhcc
Q 029030 155 RDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHMREFLRGQN 199 (200)
Q Consensus 155 ~~~f~~v~~ya~~~g~llw~~~~~r~~~V~~~~~~~v~~f~k~~~ 199 (200)
.++|+.+++||++.|+|+|++..||||||+.+||.+|++|.|++-
T Consensus 401 ~s~y~~~~eya~~~gvLvw~d~~Krmffi~~eG~s~v~~f~Kr~l 445 (447)
T COG5144 401 LSDYQKVLEYAIRGGVLVWSDVDKRMFFIKLEGHSLVKEFVKRIL 445 (447)
T ss_pred hhhHHHHHHHHHhcCeEEeecccceEEEEEccCcHHHHHHHHHHh
Confidence 999999999999999999999999999999999999999999864
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=1.8e-49 Score=361.39 Aligned_cols=112 Identities=53% Similarity=0.908 Sum_probs=106.1
Q ss_pred CcccccccceeEEeecCCCCccccchhhhhhhcccCCc-----------ccccccceEEEeeCceEEEecCCHhHHHHHH
Q 029030 1 MIKDFADLGLVKLQQVGRKESWFIPTKLATNLSMSLTD-----------SSARKEGFVVVETNFRMYAYSTSKLHCEILR 69 (200)
Q Consensus 1 ~L~~l~~~GLvy~~~~~~~~~fy~pT~La~~l~~~~~~-----------~~~~~~g~IIvETNFrvYAYT~s~l~iaiL~ 69 (200)
||+||+|+||||++ ++++++|| |||||++|+++.++ ....++|||||||||||||||+||||+|||+
T Consensus 244 ~L~~l~~~GLvy~~-~~~~~~fy-pT~La~~l~~~~~~~~~~~~~~~~~~~~~~~g~iivETNfrvYAYT~s~l~iaiL~ 321 (366)
T PF03849_consen 244 MLQDLRELGLVYQR-KRKSRRFY-PTRLATNLTSGSSALRSASSALDSSSSSNKEGFIIVETNFRVYAYTNSPLQIAILS 321 (366)
T ss_pred HHHHHHHCCeEEEe-cCCCCeEe-chHHHHHHhcCCCcccccccccccccccccCceEEEEecceEEEecCCHHHHHHHH
Confidence 68999999999999 88999999 99999999987663 2346789999999999999999999999999
Q ss_pred HhhhhhhccCceEEEEeCHHHHHHHHHcCCCHHHHHHHHhhcCCc
Q 029030 70 LFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHP 114 (200)
Q Consensus 70 lF~~l~~r~Pnlvvg~lTR~Sv~~Al~~GITA~QII~fL~~haHp 114 (200)
+||++.||||||+||+||||||++|+++||||||||+||++||||
T Consensus 322 lF~~~~~r~pnlvvg~iTr~Sv~~A~~~GIta~qIi~fL~~~aHp 366 (366)
T PF03849_consen 322 LFCELKYRFPNLVVGQITRESVRRALKNGITADQIISFLRSHAHP 366 (366)
T ss_pred HHHHHHhcCCCeEEEEEcHHHHHHHHHcCCCHHHHHHHHHhcCCC
Confidence 999999999999999999999999999999999999999999998
No 5
>PF13625 Helicase_C_3: Helicase conserved C-terminal domain
Probab=99.73 E-value=4.3e-17 Score=128.28 Aligned_cols=118 Identities=23% Similarity=0.363 Sum_probs=105.2
Q ss_pred EEEeeCceEEEecCCH--hHHHHHHHhhhhhhccCceEEEEeCHHHHHHHHHcCCCHHHHHHHHhhcCCccccccCCCCC
Q 029030 47 VVVETNFRMYAYSTSK--LHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRIPSVP 124 (200)
Q Consensus 47 IIvETNFrvYAYT~s~--l~iaiL~lF~~l~~r~Pnlvvg~lTR~Sv~~Al~~GITA~QII~fL~~haHp~m~~~~~~iP 124 (200)
+||++||.|.+.+.+| -..+.|..||++ .+..+|.+++||+.|+.+|++.|+|+++|++||+.|+. ..||
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-KSPDTMHVYRLTPASLWRAASAGLTAEEIIEFLERYSK-------NPLP 73 (129)
T ss_pred EEECCCCEEEEeCCCCCHHHHHHHHHHhcc-cccCceEEEEECHHHHHHHHHcCCCHHHHHHHHHHHcC-------CCCC
Confidence 7999999999977666 344999999999 56799999999999999999999999999999999994 5799
Q ss_pred ccHHHHHHHHHHhcCceEecceeeeccCCCHHHHHHHHHHHHHcCeEe
Q 029030 125 ENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLL 172 (200)
Q Consensus 125 ~tV~dQI~lWe~Er~R~~~~~g~L~~~f~s~~~f~~v~~ya~~~g~ll 172 (200)
+||..+|+.|+...+|+++.++.++-.+.+.+..+.+.+..+-.++.+
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 999999999999999999999777779999999999888776655443
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=97.68 E-value=0.00043 Score=69.22 Aligned_cols=106 Identities=23% Similarity=0.378 Sum_probs=85.4
Q ss_pred cceEEEeeCceEEEecCCHhH--H-HHHHHhhhhhhccCceEEEEeCHHHHHHHHHcCCCHHHHHHHHhhcCCccccccC
Q 029030 44 EGFVVVETNFRMYAYSTSKLH--C-EILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRI 120 (200)
Q Consensus 44 ~g~IIvETNFrvYAYT~s~l~--i-aiL~lF~~l~~r~Pnlvvg~lTR~Sv~~Al~~GITA~QII~fL~~haHp~m~~~~ 120 (200)
+|.|++|| .+|+- . ..|.-|+|+.+|--+|..++||-=|+-.|...|+++++||++|...+-
T Consensus 22 d~~i~lE~--------~~p~~~~a~~fl~~~aEp~~rp~~iHeY~lT~~sl~~A~s~g~~~~~ii~~L~~~sk------- 86 (732)
T TIGR00603 22 DGHIFLES--------FSPLYKQAQDFLVAIAEPVCRPEHIHEYKLTAYSLYAAVSVGLETEDIIEVLGRLSK------- 86 (732)
T ss_pred CCeEEEEe--------CCccHHHHHHHHHHhcccccChhheEEEeccHHHHHHHHHcCCCHHHHHHHHHHHhC-------
Confidence 45566665 45443 3 889999999999999999999999999999999999999999999984
Q ss_pred CCCCccHHHHHHHHHHhcCceEec--ceeeeccCCCHHHHHHHHHH
Q 029030 121 PSVPENVCDQIRLWESDLNRVEMT--PAHYYEEFPSRDVFEAACDY 164 (200)
Q Consensus 121 ~~iP~tV~dQI~lWe~Er~R~~~~--~g~L~~~f~s~~~f~~v~~y 164 (200)
..||++|.+.|+.+-.-.+++++. +.--|-+-.+.+..+.+.+-
T Consensus 87 ~~~p~~i~~~i~~~~~~ygk~klv~~~~~~~~es~~~~~l~~l~~~ 132 (732)
T TIGR00603 87 TPIPKGIIEFIRLCTQSYGKVKLVLKHNRYFVESPHPEVLQRLLKD 132 (732)
T ss_pred CCCCHHHHHHHHHHHHhcCcEEEEEcCCceEEecCCHHHHHHHHhc
Confidence 589999999999999999999883 22223344556666666543
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=94.04 E-value=0.053 Score=33.58 Aligned_cols=22 Identities=36% Similarity=0.525 Sum_probs=17.7
Q ss_pred HHHHHHHcCCCHHHHHHHHhhc
Q 029030 90 SLYNAFENGITAEQIISFLQQN 111 (200)
Q Consensus 90 Sv~~Al~~GITA~QII~fL~~h 111 (200)
=|++|...|||.+||-.||+.+
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 3689999999999999999864
No 8
>PRK06015 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional
Probab=88.00 E-value=4.4 Score=34.83 Aligned_cols=125 Identities=15% Similarity=0.249 Sum_probs=85.6
Q ss_pred cceEEEeeCceEEEecCCHhHHHHHHHhhhhhhccCceEEE---EeCHHHHHHHHHcCC-------CHHHHHHHHhhcCC
Q 029030 44 EGFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVG---AITKESLYNAFENGI-------TAEQIISFLQQNAH 113 (200)
Q Consensus 44 ~g~IIvETNFrvYAYT~s~l~iaiL~lF~~l~~r~Pnlvvg---~lTR~Sv~~Al~~GI-------TA~QII~fL~~haH 113 (200)
.|.=.+|-.++ +|--. ..+.++..++|++.|| ++|.+.+++|.+.|- .-+.++++.+.+-.
T Consensus 28 gGi~~iEit~~------tp~a~---~~I~~l~~~~~~~~vGAGTVl~~e~a~~ai~aGA~FivSP~~~~~vi~~a~~~~i 98 (201)
T PRK06015 28 GGLPAIEITLR------TPAAL---DAIRAVAAEVEEAIVGAGTILNAKQFEDAAKAGSRFIVSPGTTQELLAAANDSDV 98 (201)
T ss_pred CCCCEEEEeCC------CccHH---HHHHHHHHHCCCCEEeeEeCcCHHHHHHHHHcCCCEEECCCCCHHHHHHHHHcCC
Confidence 46667777775 44333 3444566678999999 899999999999995 45788888877765
Q ss_pred ccccccCCCCCc--cHHHHHHHHHHhcCceEecceeeeccCCCHHHHHHHHHHHHHcCeEeeecCCcceEEEeccccHHH
Q 029030 114 PRVADRIPSVPE--NVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHM 191 (200)
Q Consensus 114 p~m~~~~~~iP~--tV~dQI~lWe~Er~R~~~~~g~L~~~f~s~~~f~~v~~ya~~~g~llw~~~~~r~~~V~~~~~~~v 191 (200)
|.+|= |..+=..-|+.--+-+|+.|+-++- . .+|.+.+...+ +.-+++-+..=.-+++
T Consensus 99 -------~~iPG~~TptEi~~A~~~Ga~~vK~FPa~~~G---G-------~~yikal~~pl---p~~~l~ptGGV~~~n~ 158 (201)
T PRK06015 99 -------PLLPGAATPSEVMALREEGYTVLKFFPAEQAG---G-------AAFLKALSSPL---AGTFFCPTGGISLKNA 158 (201)
T ss_pred -------CEeCCCCCHHHHHHHHHCCCCEEEECCchhhC---C-------HHHHHHHHhhC---CCCcEEecCCCCHHHH
Confidence 45664 7788888999999999999865441 0 24555554444 3444444333344778
Q ss_pred HHHHhh
Q 029030 192 REFLRG 197 (200)
Q Consensus 192 ~~f~k~ 197 (200)
.+|++.
T Consensus 159 ~~~l~a 164 (201)
T PRK06015 159 RDYLSL 164 (201)
T ss_pred HHHHhC
Confidence 888764
No 9
>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=86.65 E-value=0.34 Score=39.36 Aligned_cols=65 Identities=18% Similarity=0.385 Sum_probs=50.3
Q ss_pred ccceEEEeeCceEEEecCCHhHHH-HHHHhhhhhhccCceEEEEeCHHHHHHHHHcCCCHHHHHHHHhhcCCccccccCC
Q 029030 43 KEGFVVVETNFRMYAYSTSKLHCE-ILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRIP 121 (200)
Q Consensus 43 ~~g~IIvETNFrvYAYT~s~l~ia-iL~lF~~l~~r~Pnlvvg~lTR~Sv~~Al~~GITA~QII~fL~~haHp~m~~~~~ 121 (200)
....+|||.||| +.+.|| ==.-+..+...+|.+.||...| -.||++.+...|--.|++++-
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 445899999999 666652 2233566777899999996554 368999999999888998888
Q ss_pred CCCc
Q 029030 122 SVPE 125 (200)
Q Consensus 122 ~iP~ 125 (200)
-+||
T Consensus 109 hlPP 112 (131)
T TIGR01615 109 PLPP 112 (131)
T ss_pred CCCC
Confidence 8888
No 10
>PRK05718 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional
Probab=84.32 E-value=12 Score=32.28 Aligned_cols=125 Identities=18% Similarity=0.270 Sum_probs=82.5
Q ss_pred cceEEEeeCceEEEecCCHhHHHHHHHhhhhhhccCceEEE---EeCHHHHHHHHHcCC-------CHHHHHHHHhhcCC
Q 029030 44 EGFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVG---AITKESLYNAFENGI-------TAEQIISFLQQNAH 113 (200)
Q Consensus 44 ~g~IIvETNFrvYAYT~s~l~iaiL~lF~~l~~r~Pnlvvg---~lTR~Sv~~Al~~GI-------TA~QII~fL~~haH 113 (200)
.|.=++|--++ +|-- +..+.++..++|++.|| ++|.+.++.|++.|- ..+.++++-..+-.
T Consensus 39 ~Gi~~iEitl~------~~~~---~~~I~~l~~~~p~~~IGAGTVl~~~~a~~a~~aGA~FivsP~~~~~vi~~a~~~~i 109 (212)
T PRK05718 39 GGLPVLEVTLR------TPAA---LEAIRLIAKEVPEALIGAGTVLNPEQLAQAIEAGAQFIVSPGLTPPLLKAAQEGPI 109 (212)
T ss_pred cCCCEEEEecC------CccH---HHHHHHHHHHCCCCEEEEeeccCHHHHHHHHHcCCCEEECCCCCHHHHHHHHHcCC
Confidence 35567776643 4433 34445555679999999 899999999999984 35588888777554
Q ss_pred ccccccCCCCCc--cHHHHHHHHHHhcCceEecceeeeccCCCHHHHHHHHHHHHHcCeEeeecCCcceEEEeccccHHH
Q 029030 114 PRVADRIPSVPE--NVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHM 191 (200)
Q Consensus 114 p~m~~~~~~iP~--tV~dQI~lWe~Er~R~~~~~g~L~~~f~s~~~f~~v~~ya~~~g~llw~~~~~r~~~V~~~~~~~v 191 (200)
+.+|- |..+=...|+.--+-+++.|+-.+- =.+|-+.+...+ +.-+.+.+..=.-+.+
T Consensus 110 -------~~iPG~~TptEi~~a~~~Ga~~vKlFPa~~~g----------g~~~lk~l~~p~---p~~~~~ptGGV~~~ni 169 (212)
T PRK05718 110 -------PLIPGVSTPSELMLGMELGLRTFKFFPAEASG----------GVKMLKALAGPF---PDVRFCPTGGISPANY 169 (212)
T ss_pred -------CEeCCCCCHHHHHHHHHCCCCEEEEccchhcc----------CHHHHHHHhccC---CCCeEEEeCCCCHHHH
Confidence 56665 4466445888888888886643220 145556655444 4455555444445789
Q ss_pred HHHHhh
Q 029030 192 REFLRG 197 (200)
Q Consensus 192 ~~f~k~ 197 (200)
++|++.
T Consensus 170 ~~~l~a 175 (212)
T PRK05718 170 RDYLAL 175 (212)
T ss_pred HHHHhC
Confidence 999874
No 11
>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=82.25 E-value=15 Score=31.65 Aligned_cols=124 Identities=15% Similarity=0.311 Sum_probs=84.4
Q ss_pred ceEEEeeCceEEEecCCHhHHHHHHHhhhhhhccCceEEE---EeCHHHHHHHHHcCC-------CHHHHHHHHhhcCCc
Q 029030 45 GFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVG---AITKESLYNAFENGI-------TAEQIISFLQQNAHP 114 (200)
Q Consensus 45 g~IIvETNFrvYAYT~s~l~iaiL~lF~~l~~r~Pnlvvg---~lTR~Sv~~Al~~GI-------TA~QII~fL~~haHp 114 (200)
|.=.+|--++ +|--...+ .++..++|++.|| ++|.+.+++|.+.|- .-..++.+.+.+--
T Consensus 33 Gi~~iEit~~------t~~a~~~i---~~l~~~~~~~~vGAGTVl~~~~a~~a~~aGA~FivsP~~~~~v~~~~~~~~i- 102 (204)
T TIGR01182 33 GLRVLEVTLR------TPVALDAI---RLLRKEVPDALIGAGTVLNPEQLRQAVDAGAQFIVSPGLTPELAKHAQDHGI- 102 (204)
T ss_pred CCCEEEEeCC------CccHHHHH---HHHHHHCCCCEEEEEeCCCHHHHHHHHHcCCCEEECCCCCHHHHHHHHHcCC-
Confidence 5456676663 55544444 4445578999999 899999999999994 34577777666543
Q ss_pred cccccCCCCCc--cHHHHHHHHHHhcCceEecceeeeccCCCHHHHHHHHHHHHHcCeEeeecCCcceEEEeccccHHHH
Q 029030 115 RVADRIPSVPE--NVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHMR 192 (200)
Q Consensus 115 ~m~~~~~~iP~--tV~dQI~lWe~Er~R~~~~~g~L~~~f~s~~~f~~v~~ya~~~g~llw~~~~~r~~~V~~~~~~~v~ 192 (200)
|.+|= |-.+=..-|+.--+-+|+.|+-.+- . .+|-+++...+ +.-+++-+..=.-+++.
T Consensus 103 ------~~iPG~~TptEi~~A~~~Ga~~vKlFPA~~~G---G-------~~yikal~~pl---p~i~~~ptGGV~~~N~~ 163 (204)
T TIGR01182 103 ------PIIPGVATPSEIMLALELGITALKLFPAEVSG---G-------VKMLKALAGPF---PQVRFCPTGGINLANVR 163 (204)
T ss_pred ------cEECCCCCHHHHHHHHHCCCCEEEECCchhcC---C-------HHHHHHHhccC---CCCcEEecCCCCHHHHH
Confidence 55663 7778888999999999999866541 0 35666666555 44555544444447899
Q ss_pred HHHhh
Q 029030 193 EFLRG 197 (200)
Q Consensus 193 ~f~k~ 197 (200)
+|++.
T Consensus 164 ~~l~a 168 (204)
T TIGR01182 164 DYLAA 168 (204)
T ss_pred HHHhC
Confidence 99874
No 12
>PRK07114 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional
Probab=81.35 E-value=27 Score=30.42 Aligned_cols=125 Identities=14% Similarity=0.188 Sum_probs=84.8
Q ss_pred cceEEEeeCceEEEecCCHhHHHHHHHhh-hhhhccCceEEE---EeCHHHHHHHHHcCC-------CHHHHHHHHhhcC
Q 029030 44 EGFVVVETNFRMYAYSTSKLHCEILRLFS-KIEYQLPNLIVG---AITKESLYNAFENGI-------TAEQIISFLQQNA 112 (200)
Q Consensus 44 ~g~IIvETNFrvYAYT~s~l~iaiL~lF~-~l~~r~Pnlvvg---~lTR~Sv~~Al~~GI-------TA~QII~fL~~ha 112 (200)
.|.=.+|-=|+ +|--...+.... +...++|++.|| ++|.+.++.|.+.|- .-..++++.+.+-
T Consensus 39 gGi~~iEiT~~------tp~a~~~i~~l~~~~~~~~p~~~vGaGTVl~~e~a~~a~~aGA~FiVsP~~~~~v~~~~~~~~ 112 (222)
T PRK07114 39 GGARVFEFTNR------GDFAHEVFAELVKYAAKELPGMILGVGSIVDAATAALYIQLGANFIVTPLFNPDIAKVCNRRK 112 (222)
T ss_pred CCCCEEEEeCC------CCcHHHHHHHHHHHHHhhCCCeEEeeEeCcCHHHHHHHHHcCCCEEECCCCCHHHHHHHHHcC
Confidence 45566776664 444444443333 444579999999 899999999999995 3568888888776
Q ss_pred CccccccCCCCCc--cHHHHHHHHHHhcCceEecceeeeccCCCHHHHHHHHHHHHHcCeEeeecCCcceEEEecccc--
Q 029030 113 HPRVADRIPSVPE--NVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIH-- 188 (200)
Q Consensus 113 Hp~m~~~~~~iP~--tV~dQI~lWe~Er~R~~~~~g~L~~~f~s~~~f~~v~~ya~~~g~llw~~~~~r~~~V~~~~~-- 188 (200)
. |.+|= |..+=...|+.--+-+|+.|+-.+ . ..|-+.+...+ +.-+++- ..|-
T Consensus 113 i-------~~iPG~~TpsEi~~A~~~Ga~~vKlFPA~~~----G-------~~~ikal~~p~---p~i~~~p--tGGV~~ 169 (222)
T PRK07114 113 V-------PYSPGCGSLSEIGYAEELGCEIVKLFPGSVY----G-------PGFVKAIKGPM---PWTKIMP--TGGVEP 169 (222)
T ss_pred C-------CEeCCCCCHHHHHHHHHCCCCEEEECccccc----C-------HHHHHHHhccC---CCCeEEe--CCCCCc
Confidence 5 45664 777888899999999999986543 1 45666655444 3333333 3333
Q ss_pred --HHHHHHHhh
Q 029030 189 --MHMREFLRG 197 (200)
Q Consensus 189 --~~v~~f~k~ 197 (200)
+++.+|++.
T Consensus 170 ~~~n~~~yl~a 180 (222)
T PRK07114 170 TEENLKKWFGA 180 (222)
T ss_pred chhcHHHHHhC
Confidence 578888863
No 13
>KOG1123 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, 3'-5' helicase subunit SSL2 [Transcription; Replication, recombination and repair]
Probab=79.78 E-value=3.8 Score=40.79 Aligned_cols=86 Identities=24% Similarity=0.356 Sum_probs=71.4
Q ss_pred ccceEEEeeCceEEEecCCHhH---HHHHHHhhhhhhccCceEEEEeCHHHHHHHHHcCCCHHHHHHHHhhcCCcccccc
Q 029030 43 KEGFVVVETNFRMYAYSTSKLH---CEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADR 119 (200)
Q Consensus 43 ~~g~IIvETNFrvYAYT~s~l~---iaiL~lF~~l~~r~Pnlvvg~lTR~Sv~~Al~~GITA~QII~fL~~haHp~m~~~ 119 (200)
.+|.|++||= ||+- ...|--.+|..+|=-.+.=+.||-=|+-.|..-|.+-+.||++|..-+.
T Consensus 81 ~dG~IfLEsF--------sp~ykqA~DFLiaIaEPvcRP~~iHEy~lTaySLYAAVSVGL~T~dIie~L~rlSK------ 146 (776)
T KOG1123|consen 81 PDGHIFLETF--------SPLYKQAQDFLIAIAEPVCRPEHIHEYKLTAYSLYAAVSVGLQTEDIIEVLDRLSK------ 146 (776)
T ss_pred CCCeEEeeec--------CHHHHhHhhhhhhhccccCChhhhhhhcchhhhhhhhhccccchHHHHHHHHHhcc------
Confidence 4688888873 4443 2566667888888888999999999999999999999999999998764
Q ss_pred CCCCCccHHHHHHHHHHhcCceEe
Q 029030 120 IPSVPENVCDQIRLWESDLNRVEM 143 (200)
Q Consensus 120 ~~~iP~tV~dQI~lWe~Er~R~~~ 143 (200)
..||+.|++=|++--..-+.+++
T Consensus 147 -t~lp~~ii~FI~~cT~sYGKVKL 169 (776)
T KOG1123|consen 147 -TPLPESIIEFIRACTVSYGKVKL 169 (776)
T ss_pred -CCCCHHHHHHHHHHhhccccEEE
Confidence 67999999999988877776654
No 14
>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=71.97 E-value=9 Score=32.78 Aligned_cols=125 Identities=18% Similarity=0.312 Sum_probs=79.6
Q ss_pred cceEEEeeCceEEEecCCHhHHHHHHHhhhhhhccCceEEE---EeCHHHHHHHHHcCC-------CHHHHHHHHhhcCC
Q 029030 44 EGFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVG---AITKESLYNAFENGI-------TAEQIISFLQQNAH 113 (200)
Q Consensus 44 ~g~IIvETNFrvYAYT~s~l~iaiL~lF~~l~~r~Pnlvvg---~lTR~Sv~~Al~~GI-------TA~QII~fL~~haH 113 (200)
.|.=++|--|| +|--. ....++..++|+|.|| ++|.|.+++|.+.|- .-++++.+-+.+-.
T Consensus 32 gGi~~iEiT~~------t~~a~---~~I~~l~~~~p~~~vGAGTV~~~e~a~~a~~aGA~FivSP~~~~~v~~~~~~~~i 102 (196)
T PF01081_consen 32 GGIRAIEITLR------TPNAL---EAIEALRKEFPDLLVGAGTVLTAEQAEAAIAAGAQFIVSPGFDPEVIEYAREYGI 102 (196)
T ss_dssp TT--EEEEETT------STTHH---HHHHHHHHHHTTSEEEEES--SHHHHHHHHHHT-SEEEESS--HHHHHHHHHHTS
T ss_pred CCCCEEEEecC------CccHH---HHHHHHHHHCCCCeeEEEeccCHHHHHHHHHcCCCEEECCCCCHHHHHHHHHcCC
Confidence 46667888777 34333 3334555678999999 899999999999994 46789999888776
Q ss_pred ccccccCCCCCc--cHHHHHHHHHHhcCceEecceeeeccCCCHHHHHHHHHHHHHcCeEeeecCCcceEEEeccccHHH
Q 029030 114 PRVADRIPSVPE--NVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHM 191 (200)
Q Consensus 114 p~m~~~~~~iP~--tV~dQI~lWe~Er~R~~~~~g~L~~~f~s~~~f~~v~~ya~~~g~llw~~~~~r~~~V~~~~~~~v 191 (200)
| .+|= |..+=...|+.-.+-+|+.|+-.+- =.+|.+++...+ +.-+++.+..=.-+++
T Consensus 103 ~-------~iPG~~TptEi~~A~~~G~~~vK~FPA~~~G----------G~~~ik~l~~p~---p~~~~~ptGGV~~~N~ 162 (196)
T PF01081_consen 103 P-------YIPGVMTPTEIMQALEAGADIVKLFPAGALG----------GPSYIKALRGPF---PDLPFMPTGGVNPDNL 162 (196)
T ss_dssp E-------EEEEESSHHHHHHHHHTT-SEEEETTTTTTT----------HHHHHHHHHTTT---TT-EEEEBSS--TTTH
T ss_pred c-------ccCCcCCHHHHHHHHHCCCCEEEEecchhcC----------cHHHHHHHhccC---CCCeEEEcCCCCHHHH
Confidence 4 5663 7777788899999999999986651 134555544333 3334444334445678
Q ss_pred HHHHhh
Q 029030 192 REFLRG 197 (200)
Q Consensus 192 ~~f~k~ 197 (200)
++|++.
T Consensus 163 ~~~l~a 168 (196)
T PF01081_consen 163 AEYLKA 168 (196)
T ss_dssp HHHHTS
T ss_pred HHHHhC
Confidence 988874
No 15
>COG1313 PflX Uncharacterized Fe-S protein PflX, homolog of pyruvate formate lyase activating proteins [General function prediction only]
Probab=71.58 E-value=5.7 Score=36.78 Aligned_cols=52 Identities=23% Similarity=0.309 Sum_probs=41.5
Q ss_pred HHHHHHHHhhcCCccccccCCCCCccHHHHH----HHHHH-hcCceEecceeeeccCCCHHHHHHHHHHHHHcCe
Q 029030 101 AEQIISFLQQNAHPRVADRIPSVPENVCDQI----RLWES-DLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSG 170 (200)
Q Consensus 101 A~QII~fL~~haHp~m~~~~~~iP~tV~dQI----~lWe~-Er~R~~~~~g~L~~~f~s~~~f~~v~~ya~~~g~ 170 (200)
..-|++||..|.- .-++.||++|- +-||. |-+ +..+.++++++.+||+..|.
T Consensus 273 TkpI~~wiae~~g-------~~~~vNiM~QY~P~ykA~eypeI~-----------R~lt~eE~e~a~~~a~~~gl 329 (335)
T COG1313 273 TKPILRWIAENLG-------NDVRVNIMFQYRPEYKAEEYPEIN-----------RRLTREEYEKALEYAEKLGL 329 (335)
T ss_pred cHHHHHHHHHhCC-------CCeeEEehhhccchhhhhhchhhc-----------ccCCHHHHHHHHHHHHHcCC
Confidence 4578899988761 26888999994 57776 444 67889999999999999985
No 16
>PRK06552 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional
Probab=66.71 E-value=70 Score=27.47 Aligned_cols=125 Identities=14% Similarity=0.253 Sum_probs=77.0
Q ss_pred ccceEEEeeCceEEEecCCHhHHHHHHHhhhhhhcc---CceEEE---EeCHHHHHHHHHcCC-------CHHHHHHHHh
Q 029030 43 KEGFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQL---PNLIVG---AITKESLYNAFENGI-------TAEQIISFLQ 109 (200)
Q Consensus 43 ~~g~IIvETNFrvYAYT~s~l~iaiL~lF~~l~~r~---Pnlvvg---~lTR~Sv~~Al~~GI-------TA~QII~fL~ 109 (200)
+.|.=++|-=|+ +|--.. .+.++..++ |++.|| ++|.+.+++|.+.|- .-+.++++-+
T Consensus 36 ~~Gi~~iEit~~------~~~a~~---~i~~l~~~~~~~p~~~vGaGTV~~~~~~~~a~~aGA~FivsP~~~~~v~~~~~ 106 (213)
T PRK06552 36 KGGIKAIEVTYT------NPFASE---VIKELVELYKDDPEVLIGAGTVLDAVTARLAILAGAQFIVSPSFNRETAKICN 106 (213)
T ss_pred HCCCCEEEEECC------CccHHH---HHHHHHHHcCCCCCeEEeeeeCCCHHHHHHHHHcCCCEEECCCCCHHHHHHHH
Confidence 346667777665 444333 344444456 679999 899999999999994 3567888877
Q ss_pred hcCCccccccCCCCCc--cHHHHHHHHHHhcCceEecceeeeccCCCHHHHHHHHHHHHHcCeEeeecCCcceEEEeccc
Q 029030 110 QNAHPRVADRIPSVPE--NVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEI 187 (200)
Q Consensus 110 ~haHp~m~~~~~~iP~--tV~dQI~lWe~Er~R~~~~~g~L~~~f~s~~~f~~v~~ya~~~g~llw~~~~~r~~~V~~~~ 187 (200)
.+-. |.+|= |..+=...|+.--+-+++.++-.+ + .+|.+.+...+ +.-+.+.+..=.
T Consensus 107 ~~~i-------~~iPG~~T~~E~~~A~~~Gad~vklFPa~~~----G-------~~~ik~l~~~~---p~ip~~atGGI~ 165 (213)
T PRK06552 107 LYQI-------PYLPGCMTVTEIVTALEAGSEIVKLFPGSTL----G-------PSFIKAIKGPL---PQVNVMVTGGVN 165 (213)
T ss_pred HcCC-------CEECCcCCHHHHHHHHHcCCCEEEECCcccC----C-------HHHHHHHhhhC---CCCEEEEECCCC
Confidence 6655 45664 566667788888888887653321 1 22222222122 223344444444
Q ss_pred cHHHHHHHhh
Q 029030 188 HMHMREFLRG 197 (200)
Q Consensus 188 ~~~v~~f~k~ 197 (200)
.+.+.+|++.
T Consensus 166 ~~N~~~~l~a 175 (213)
T PRK06552 166 LDNVKDWFAA 175 (213)
T ss_pred HHHHHHHHHC
Confidence 5778888764
No 17
>PRK14529 adenylate kinase; Provisional
Probab=66.10 E-value=38 Score=29.34 Aligned_cols=80 Identities=15% Similarity=0.225 Sum_probs=56.7
Q ss_pred hhccCceEEEEeCHHHHHHHHHcCCCHHHHHHHHhhcCCccccccCCCCCccHHHHHHHHHHhcCceEecceeeeccCCC
Q 029030 75 EYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPS 154 (200)
Q Consensus 75 ~~r~Pnlvvg~lTR~Sv~~Al~~GITA~QII~fL~~haHp~m~~~~~~iP~tV~dQI~lWe~Er~R~~~~~g~L~~~f~s 154 (200)
.+.+|.+.+|.+.|+.+.. ..-.++++=+|+.. +..+|..++-++-.+.....- ..|++++.|+-
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 3568999999999998743 12234566666654 358999999999888887653 78999999998
Q ss_pred H-HHHHHHHHHHHHcC
Q 029030 155 R-DVFEAACDYARDRS 169 (200)
Q Consensus 155 ~-~~f~~v~~ya~~~g 169 (200)
. ++.+.+-+..++.|
T Consensus 88 t~~Qa~~l~~~l~~~~ 103 (223)
T PRK14529 88 NKVQAEKLWEALQKEG 103 (223)
T ss_pred CHHHHHHHHHHHHhcC
Confidence 5 45555555544444
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=64.10 E-value=15 Score=28.56 Aligned_cols=81 Identities=17% Similarity=0.274 Sum_probs=51.9
Q ss_pred hhccCceEEEEeCHHHHHHHHHcCCCHHHHHHHHhhcCCccccccCCCCCccHHHHHHHHHHhcCceEecceeeeccCCC
Q 029030 75 EYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPS 154 (200)
Q Consensus 75 ~~r~Pnlvvg~lTR~Sv~~Al~~GITA~QII~fL~~haHp~m~~~~~~iP~tV~dQI~lWe~Er~R~~~~~g~L~~~f~s 154 (200)
.+.++.+.+|.|=|+.+.+ ..-.+++|-++|.. +..||+.++-++-.++.+.. ....|++.+.|+.
T Consensus 19 ~~~~~~is~~~llr~~~~~---~s~~g~~i~~~l~~---------g~~vp~~~v~~ll~~~l~~~--~~~~g~ildGfPr 84 (151)
T PF00406_consen 19 RYGLVHISVGDLLREEIKS---DSELGKQIQEYLDN---------GELVPDELVIELLKERLEQP--PCNRGFILDGFPR 84 (151)
T ss_dssp HHTSEEEEHHHHHHHHHHT---TSHHHHHHHHHHHT---------TSS--HHHHHHHHHHHHHSG--GTTTEEEEESB-S
T ss_pred hcCcceechHHHHHHHHhh---hhHHHHHHHHHHHh---------hccchHHHHHHHHHHHHhhh--cccceeeeeeccc
Confidence 3557777777665665532 22235777778775 35899999999998888877 6679999999998
Q ss_pred H-HHHHHHHHHHHHcC
Q 029030 155 R-DVFEAACDYARDRS 169 (200)
Q Consensus 155 ~-~~f~~v~~ya~~~g 169 (200)
. ++++...+.....+
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 44555544333333
No 19
>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=63.21 E-value=36 Score=23.51 Aligned_cols=46 Identities=13% Similarity=0.294 Sum_probs=39.0
Q ss_pred CCHHHHHHHHHHHHHcCeEeeecCC----cceEEEeccccHHHHHHHhhc
Q 029030 153 PSRDVFEAACDYARDRSGLLWEDSK----KMRLVVNAEIHMHMREFLRGQ 198 (200)
Q Consensus 153 ~s~~~f~~v~~ya~~~g~llw~~~~----~r~~~V~~~~~~~v~~f~k~~ 198 (200)
.+.++.+.+.+.....++-.|+.+. .-.+.|+++..+.+.+++++.
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 4577888899999899999998887 247899999999999999864
No 20
>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=61.63 E-value=3.8 Score=35.86 Aligned_cols=66 Identities=23% Similarity=0.384 Sum_probs=48.5
Q ss_pred cccceEEEeeCceEEEecCCHhHHH-HHHHhhhhhhccCceEEEEeCHHHHHHHHHcCCCHHHHHHHHhhcCCccccccC
Q 029030 42 RKEGFVVVETNFRMYAYSTSKLHCE-ILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRI 120 (200)
Q Consensus 42 ~~~g~IIvETNFrvYAYT~s~l~ia-iL~lF~~l~~r~Pnlvvg~lTR~Sv~~Al~~GITA~QII~fL~~haHp~m~~~~ 120 (200)
...-.+|||+||| +.+.|| -=.-+..+...+|...||...| + .||++.+-.-+.-.|++++
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 3456799999999 555442 2234566777899999994433 2 5788898888888888888
Q ss_pred CCCCc
Q 029030 121 PSVPE 125 (200)
Q Consensus 121 ~~iP~ 125 (200)
--|||
T Consensus 197 ~~lPP 201 (218)
T PF04720_consen 197 MHLPP 201 (218)
T ss_pred CCCCC
Confidence 88998
No 21
>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=57.86 E-value=14 Score=27.57 Aligned_cols=27 Identities=41% Similarity=0.694 Sum_probs=22.2
Q ss_pred eCHHHHHHHHH--------------cCCCHHHHHHHHhhcC
Q 029030 86 ITKESLYNAFE--------------NGITAEQIISFLQQNA 112 (200)
Q Consensus 86 lTR~Sv~~Al~--------------~GITA~QII~fL~~ha 112 (200)
+||+|+++|+. .|.||+++|+||...-
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 47888877774 6999999999998854
No 22
>KOG4175 consensus Tryptophan synthase alpha chain [Amino acid transport and metabolism]
Probab=53.22 E-value=62 Score=28.88 Aligned_cols=78 Identities=21% Similarity=0.234 Sum_probs=50.6
Q ss_pred HHHHHHHHHcCCCHHHHHHHHhhcCCcc--------ccccCCCCCccHHHHHHHHHHhcCceEecceeeeccCCCHHHHH
Q 029030 88 KESLYNAFENGITAEQIISFLQQNAHPR--------VADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFE 159 (200)
Q Consensus 88 R~Sv~~Al~~GITA~QII~fL~~haHp~--------m~~~~~~iP~tV~dQI~lWe~Er~R~~~~~g~L~~~f~s~~~f~ 159 (200)
..+-+.|+.+|+|-++||+-++. |.|+ |.=..|++---+..-|.-= .+ .=.+|++.-|.+ .++.+
T Consensus 66 q~~n~~aL~ng~tl~~i~emvk~-ar~~gvt~PIiLmgYYNPIl~yG~e~~iq~a-k~----aGanGfiivDlP-pEEa~ 138 (268)
T KOG4175|consen 66 QAANRRALLNGTTLNSIIEMVKE-ARPQGVTCPIILMGYYNPILRYGVENYIQVA-KN----AGANGFIIVDLP-PEEAE 138 (268)
T ss_pred hhhHHHHHHcCCcHHHHHHHHHH-hcccCcccceeeeecccHHHhhhHHHHHHHH-Hh----cCCCceEeccCC-hHHHH
Confidence 34678999999999999999887 5555 2222344433333333311 11 124677775554 68889
Q ss_pred HHHHHHHHcCeEe
Q 029030 160 AACDYARDRSGLL 172 (200)
Q Consensus 160 ~v~~ya~~~g~ll 172 (200)
.++++|++.|+-+
T Consensus 139 ~~Rne~~k~gisl 151 (268)
T KOG4175|consen 139 TLRNEARKHGISL 151 (268)
T ss_pred HHHHHHHhcCceE
Confidence 9999999998744
No 23
>TIGR00262 trpA tryptophan synthase, alpha subunit. Tryptophan synthase catalyzes the last step in the biosynthesis of tryptophan. The alpha chain is responsible for the aldol cleavage of indoleglycerol phosphate to indole and glyceraldehyde 3-phosphate. In bacteria and plants each domain is found on a separate subunit (alpha and beta chains), while in fungi the two domains are fused together on a single multifunctional protein. The signature pattern for trpA contains three conserved acidic residues. [LIVM]-E-[LIVM]-G-x(2)-[FYC]-[ST]-[DE]-[PA]-[LIVMY]-[AGLI]-[DE]-G and this is located between residues 43-58 of the model. The Sulfolobus solfataricus trpA is known to be quite divergent from other known trpA sequences.
Probab=50.77 E-value=1.7e+02 Score=25.61 Aligned_cols=26 Identities=19% Similarity=0.336 Sum_probs=22.4
Q ss_pred eCHHHHHHHHHcCCCHHHHHHHHhhc
Q 029030 86 ITKESLYNAFENGITAEQIISFLQQN 111 (200)
Q Consensus 86 lTR~Sv~~Al~~GITA~QII~fL~~h 111 (200)
+=+++-.+|+++|+|.+++++.++.-
T Consensus 56 vIq~a~~~al~~G~~~~~~~~~v~~i 81 (256)
T TIGR00262 56 TIQAADLRALRAGMTPEKCFELLKKV 81 (256)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 44667799999999999999999884
No 24
>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=49.38 E-value=22 Score=28.03 Aligned_cols=25 Identities=20% Similarity=0.250 Sum_probs=21.3
Q ss_pred HHHHHHHHHcCCCHHHHHHHHhhcC
Q 029030 88 KESLYNAFENGITAEQIISFLQQNA 112 (200)
Q Consensus 88 R~Sv~~Al~~GITA~QII~fL~~ha 112 (200)
+.-++.|+++|+|.+||..-|..-+
T Consensus 76 ~~h~~~Al~~G~T~~ei~Evl~q~~ 100 (123)
T TIGR02425 76 AMHVRATANTGVTEDDIKEVLLHVA 100 (123)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHHH
Confidence 5678999999999999999877644
No 25
>smart00195 DSPc Dual specificity phosphatase, catalytic domain.
Probab=49.07 E-value=44 Score=25.37 Aligned_cols=52 Identities=10% Similarity=0.155 Sum_probs=35.9
Q ss_pred CceEEEE--eCHHHHHHHH----HcCCCHHHHHHHHhhcCCccccccCCCCCccHHHHHHHHHH
Q 029030 79 PNLIVGA--ITKESLYNAF----ENGITAEQIISFLQQNAHPRVADRIPSVPENVCDQIRLWES 136 (200)
Q Consensus 79 Pnlvvg~--lTR~Sv~~Al----~~GITA~QII~fL~~haHp~m~~~~~~iP~tV~dQI~lWe~ 136 (200)
|-+|-+. ++|...--|. ..|.++++.++++++ ++|.+. .-+...+|+..||.
T Consensus 80 ~VlVHC~~G~~RS~~v~~~yl~~~~~~~~~~A~~~v~~-~R~~~~-----p~~~~~~qL~~~e~ 137 (138)
T smart00195 80 KVLVHCQAGVSRSATLIIAYLMKYRNLSLNDAYDFVKD-RRPIIS-----PNFGFLRQLIEYER 137 (138)
T ss_pred eEEEECCCCCchHHHHHHHHHHHHhCCCHHHHHHHHHH-HCCccC-----CCHhHHHHHHHHhh
Confidence 3344443 5787764443 579999999999986 445321 23489999999985
No 26
>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=47.68 E-value=29 Score=25.91 Aligned_cols=27 Identities=37% Similarity=0.642 Sum_probs=22.2
Q ss_pred eCHHHHHHHHH--------------cCCCHHHHHHHHhhcC
Q 029030 86 ITKESLYNAFE--------------NGITAEQIISFLQQNA 112 (200)
Q Consensus 86 lTR~Sv~~Al~--------------~GITA~QII~fL~~ha 112 (200)
+|++|+.+|+. .|.||+++|.||...-
T Consensus 20 ~t~~~L~~ai~~~FG~~arFhTCSae~m~a~eLv~FL~~rg 60 (78)
T PF10678_consen 20 YTKEELKAAIIEKFGEDARFHTCSAEGMTADELVDFLEERG 60 (78)
T ss_pred cCHHHHHHHHHHHhCCCceEEecCCCCCCHHHHHHHHHHcC
Confidence 57888877774 6999999999998854
No 27
>PF03918 CcmH: Cytochrome C biogenesis protein; InterPro: IPR005616 Members of this family include NrfF, CcmH, CycL, Ccl2.; PDB: 2KW0_A 2HL7_A.
Probab=41.05 E-value=26 Score=28.66 Aligned_cols=30 Identities=17% Similarity=0.328 Sum_probs=22.8
Q ss_pred HHHHHHHHHcCCCHHHHHHHHhhcCCcccc
Q 029030 88 KESLYNAFENGITAEQIISFLQQNAHPRVA 117 (200)
Q Consensus 88 R~Sv~~Al~~GITA~QII~fL~~haHp~m~ 117 (200)
|+-|++-++.|-|.+||++|+.+.-=+...
T Consensus 63 R~~I~~~l~~G~s~~eI~~~~v~rYG~~Vl 92 (148)
T PF03918_consen 63 RREIREMLAEGKSDEEIIDYFVERYGEFVL 92 (148)
T ss_dssp HHHHHHHHHHT--HHHHHHHHHHHHTTT-E
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHhcCccee
Confidence 778999999999999999999986554443
No 28
>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=40.96 E-value=71 Score=22.17 Aligned_cols=37 Identities=14% Similarity=0.272 Sum_probs=26.8
Q ss_pred EEEecCCHhHH-HHHHHhhhhhhccC-ceEEEEeCHHHH
Q 029030 55 MYAYSTSKLHC-EILRLFSKIEYQLP-NLIVGAITKESL 91 (200)
Q Consensus 55 vYAYT~s~l~i-aiL~lF~~l~~r~P-nlvvg~lTR~Sv 91 (200)
|+-|++.--++ ++...|.++...++ ++.++.+.-+.-
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 34566655555 77778888888888 888888876643
No 29
>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=40.00 E-value=58 Score=24.44 Aligned_cols=54 Identities=19% Similarity=0.087 Sum_probs=34.8
Q ss_pred HHHHHHhhhhhhccCceEEEEeCHHHHHHHHHcCCCHHHHHHHHhhcCCccccccCCCCCccHHHHHHHH
Q 029030 65 CEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRIPSVPENVCDQIRLW 134 (200)
Q Consensus 65 iaiL~lF~~l~~r~Pnlvvg~lTR~Sv~~Al~~GITA~QII~fL~~haHp~m~~~~~~iP~tV~dQI~lW 134 (200)
-+.+.-++++.+ -||++|++++.||+=|+.---+.-....+.....+.|||-.+
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 466666666665 799999999999999987543321111123334577777543
No 30
>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=39.93 E-value=80 Score=30.00 Aligned_cols=134 Identities=16% Similarity=0.299 Sum_probs=74.7
Q ss_pred eeCceEEEecCCHhHHHHHHHhhhhhhcc-CceEEEEeCHHHHHHHHHcC---------------------CCHHHHHHH
Q 029030 50 ETNFRMYAYSTSKLHCEILRLFSKIEYQL-PNLIVGAITKESLYNAFENG---------------------ITAEQIISF 107 (200)
Q Consensus 50 ETNFrvYAYT~s~l~iaiL~lF~~l~~r~-Pnlvvg~lTR~Sv~~Al~~G---------------------ITA~QII~f 107 (200)
|-.=||.-|=+|.--- =+.-|.+-.-.| |-+-.+...-..|.+.+..- .|-++|..|
T Consensus 164 ed~~klIGyFk~~~s~-~yk~FeeAAe~F~p~IkFfAtfd~~vAk~L~lK~nev~fyepF~~~pi~ip~~p~~e~e~~~f 242 (383)
T PF01216_consen 164 EDDIKLIGYFKSEDSE-HYKEFEEAAEHFQPYIKFFATFDKKVAKKLGLKLNEVDFYEPFMDEPITIPGKPYTEEELVEF 242 (383)
T ss_dssp -SS-EEEEE-SSTTSH-HHHHHHHHHHHCTTTSEEEEE-SHHHHHHHT-STT-EEEE-TTSSSEEEESSSS--HHHHHHH
T ss_pred ccceeEEEEeCCCCcH-HHHHHHHHHHhhcCceeEEEEecchhhhhcCccccceeeeccccCCCccCCCCCCCHHHHHHH
Confidence 3344555544331111 244555666666 66666666666666655432 356799999
Q ss_pred HhhcCCccccccCCCCCccHHHHHHHHHHhcCceEecceeeeccCCCH---HHHHHHHHHHHHcCeEeeecCCcceEEEe
Q 029030 108 LQQNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSR---DVFEAACDYARDRSGLLWEDSKKMRLVVN 184 (200)
Q Consensus 108 L~~haHp~m~~~~~~iP~tV~dQI~lWe~Er~R~~~~~g~L~~~f~s~---~~f~~v~~ya~~~g~llw~~~~~r~~~V~ 184 (200)
++.|-.|.|+|-. |. |=...||...+-+-+ +-|.+=.+. +-++.+.+.|++.. .++.-..+-|.
T Consensus 243 i~~h~rptlrkl~---~~---~m~e~Wedd~~g~hI---vaFaee~dpdG~efleilk~va~~nt----~np~LsivwID 309 (383)
T PF01216_consen 243 IEEHKRPTLRKLR---PE---DMFETWEDDIDGIHI---VAFAEEEDPDGFEFLEILKQVARDNT----DNPDLSIVWID 309 (383)
T ss_dssp HHHT-S-SEEE-----GG---GHHHHHHSSSSSEEE---EEE--TTSHHHHHHHHHHHHHHHHCT----T-TT--EEEE-
T ss_pred HHHhchhHhhhCC---hh---hhhhhhcccCCCceE---EEEecCCCCchHHHHHHHHHHHHhcC----cCCceeEEEEC
Confidence 9999999999842 33 446789976543222 234333332 55678888898877 56666677788
Q ss_pred ccccHHHHHHHhh
Q 029030 185 AEIHMHMREFLRG 197 (200)
Q Consensus 185 ~~~~~~v~~f~k~ 197 (200)
++.-.-+..||.+
T Consensus 310 PD~fPllv~yWE~ 322 (383)
T PF01216_consen 310 PDDFPLLVPYWEK 322 (383)
T ss_dssp GGG-HHHHHHHHH
T ss_pred CCCCchhHHHHHh
Confidence 8888999999876
No 31
>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=38.78 E-value=41 Score=21.55 Aligned_cols=20 Identities=35% Similarity=0.689 Sum_probs=15.7
Q ss_pred EEeCHHHHHHHHHc-C---CCHHH
Q 029030 84 GAITKESLYNAFEN-G---ITAEQ 103 (200)
Q Consensus 84 g~lTR~Sv~~Al~~-G---ITA~Q 103 (200)
|.||++.++.|+.. | +|.++
T Consensus 3 G~i~~~~~~~~l~~~g~~~~s~~e 26 (54)
T PF13833_consen 3 GKITREEFRRALSKLGIKDLSEEE 26 (54)
T ss_dssp SEEEHHHHHHHHHHTTSSSSCHHH
T ss_pred CEECHHHHHHHHHHhCCCCCCHHH
Confidence 78999999999965 5 55555
No 32
>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=38.64 E-value=47 Score=23.14 Aligned_cols=24 Identities=17% Similarity=0.225 Sum_probs=21.4
Q ss_pred HHHHHHHHcCCCHHHHHHHHhhcC
Q 029030 89 ESLYNAFENGITAEQIISFLQQNA 112 (200)
Q Consensus 89 ~Sv~~Al~~GITA~QII~fL~~ha 112 (200)
.-|.+.+....|-++++..|..||
T Consensus 3 ~lIErCl~~yMsk~E~v~~L~~~a 26 (54)
T PF09713_consen 3 NLIERCLQLYMSKEECVRALQKQA 26 (54)
T ss_pred hHHHHHHHHcCCHHHHHHHHHHHc
Confidence 347789999999999999999987
No 33
>COG1412 Uncharacterized proteins of PilT N-term./Vapc superfamily [General function prediction only]
Probab=38.56 E-value=75 Score=25.90 Aligned_cols=18 Identities=44% Similarity=0.652 Sum_probs=14.1
Q ss_pred ccceEEEeeCceEEEecC
Q 029030 43 KEGFVVVETNFRMYAYST 60 (200)
Q Consensus 43 ~~g~IIvETNFrvYAYT~ 60 (200)
..-+|+|+|||=+|.|..
T Consensus 9 ~~~~VlvDTNfl~~~~q~ 26 (136)
T COG1412 9 KPYQVLVDTNFLLYPYQF 26 (136)
T ss_pred CceEEEecchHHHHHHHc
Confidence 345699999998888765
No 34
>PRK13808 adenylate kinase; Provisional
Probab=37.80 E-value=99 Score=28.64 Aligned_cols=77 Identities=16% Similarity=0.175 Sum_probs=47.9
Q ss_pred hhccCceEEEEeCHHHHHHHHHcCCCHHH-HHHHHhhcCCccccccCCCCCccHHHHHHHHHHhcCceEecceeeeccCC
Q 029030 75 EYQLPNLIVGAITKESLYNAFENGITAEQ-IISFLQQNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFP 153 (200)
Q Consensus 75 ~~r~Pnlvvg~lTR~Sv~~Al~~GITA~Q-II~fL~~haHp~m~~~~~~iP~tV~dQI~lWe~Er~R~~~~~g~L~~~f~ 153 (200)
.|.++.+.+|.|=|+.|. .|..... +-+++.. +..+|..++.+|-.++++... ...|++++.|+
T Consensus 23 ~ygl~~is~gdlLR~~i~----~~s~~g~~~~~~~~~---------G~lVPdeiv~~li~e~l~~~~--~~~G~ILDGFP 87 (333)
T PRK13808 23 QYGIVQLSTGDMLRAAVA----AGTPVGLKAKDIMAS---------GGLVPDEVVVGIISDRIEQPD--AANGFILDGFP 87 (333)
T ss_pred HhCCceecccHHHHHHhh----cCChhhHHHHHHHHc---------CCCCCHHHHHHHHHHHHhccc--ccCCEEEeCCC
Confidence 456788888866565553 4443332 2223222 468999999999888876543 36799999999
Q ss_pred CH-HHHHHHHHHHH
Q 029030 154 SR-DVFEAACDYAR 166 (200)
Q Consensus 154 s~-~~f~~v~~ya~ 166 (200)
.. ++.+.+-....
T Consensus 88 Rt~~QA~~L~~ll~ 101 (333)
T PRK13808 88 RTVPQAEALDALLK 101 (333)
T ss_pred CCHHHHHHHHHHHH
Confidence 75 44444433333
No 35
>TIGR03147 cyt_nit_nrfF cytochrome c nitrite reductase, accessory protein NrfF.
Probab=36.03 E-value=75 Score=25.67 Aligned_cols=29 Identities=24% Similarity=0.453 Sum_probs=24.7
Q ss_pred HHHHHHHHHcCCCHHHHHHHHhhcCCccc
Q 029030 88 KESLYNAFENGITAEQIISFLQQNAHPRV 116 (200)
Q Consensus 88 R~Sv~~Al~~GITA~QII~fL~~haHp~m 116 (200)
|+-|++-++.|-|-+||++|+...-=...
T Consensus 63 R~~Vr~~i~~G~Sd~eI~~~~v~RYG~~V 91 (126)
T TIGR03147 63 RHEVYSMVNEGKSNQQIIDFMTARFGDFV 91 (126)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHhcCCeE
Confidence 78899999999999999999988654433
No 36
>PF09170 STN1_2: CST, Suppressor of cdc thirteen homolog, complex subunit STN1; InterPro: IPR015253 STN1 is a component of the CST complex, a complex that binds to single-stranded DNA and is required to protect telomeres from DNA degradation. The CST complex binds single-stranded DNA with high affinity in a sequence-independent manner, while isolated subunits bind DNA with low affinity by themselves. In addition to telomere protection, the CST complex has probably a more general role in DNA metabolism at non-telomeric sites [, ]. This entry represents a C-terminal uncharacterised domain ; PDB: 1WJ5_A.
Probab=35.40 E-value=12 Score=31.93 Aligned_cols=25 Identities=20% Similarity=0.359 Sum_probs=14.3
Q ss_pred cccccccceeEEeecCCCCccccchh
Q 029030 2 IKDFADLGLVKLQQVGRKESWFIPTK 27 (200)
Q Consensus 2 L~~l~~~GLvy~~~~~~~~~fy~pT~ 27 (200)
++-|.|-|+||++++...+-|| .|+
T Consensus 111 iq~Lqe~G~Vfqk~~~~d~lY~-VT~ 135 (174)
T PF09170_consen 111 IQLLQEKGIVFQKDKSQDELYY-VTD 135 (174)
T ss_dssp HHHHHHHTSEE-SS-SSS--BE-E-S
T ss_pred HHHHHHCCEEEeecCCCCceEE-Eec
Confidence 4568899999999544446777 553
No 37
>PLN02674 adenylate kinase
Probab=34.60 E-value=1.6e+02 Score=25.95 Aligned_cols=81 Identities=12% Similarity=0.089 Sum_probs=54.4
Q ss_pred hhccCceEEEEeCHHHHHHHHHcCCCHHHHHHHHhhcCCccccccCCCCCccHHHHHHHHHHhcCceEecceeeeccCCC
Q 029030 75 EYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPS 154 (200)
Q Consensus 75 ~~r~Pnlvvg~lTR~Sv~~Al~~GITA~QII~fL~~haHp~m~~~~~~iP~tV~dQI~lWe~Er~R~~~~~g~L~~~f~s 154 (200)
.+.++.+.+|.|=|+.|+..=..| .+|-+++.+ +..+|..++.++-.++.... ....|++++.|+-
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 566899999987777765443344 344444443 45899999999887776543 3458999999997
Q ss_pred H-HHHHHHHHHHHHcC
Q 029030 155 R-DVFEAACDYARDRS 169 (200)
Q Consensus 155 ~-~~f~~v~~ya~~~g 169 (200)
. .+.+.+.+.....|
T Consensus 120 t~~Qa~~l~~~l~~~~ 135 (244)
T PLN02674 120 TVVQAQKLDEMLAKQG 135 (244)
T ss_pred CHHHHHHHHHHHHhcC
Confidence 5 44555555555545
No 38
>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=34.21 E-value=43 Score=20.34 Aligned_cols=21 Identities=24% Similarity=0.317 Sum_probs=18.6
Q ss_pred HHHHHHHcCCCHHHHHHHHhh
Q 029030 90 SLYNAFENGITAEQIISFLQQ 110 (200)
Q Consensus 90 Sv~~Al~~GITA~QII~fL~~ 110 (200)
-++..+.++.|-++|+++|..
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 467889999999999999986
No 39
>PRK10144 formate-dependent nitrite reductase complex subunit NrfF; Provisional
Probab=33.42 E-value=88 Score=25.29 Aligned_cols=29 Identities=17% Similarity=0.376 Sum_probs=24.7
Q ss_pred HHHHHHHHHcCCCHHHHHHHHhhcCCccc
Q 029030 88 KESLYNAFENGITAEQIISFLQQNAHPRV 116 (200)
Q Consensus 88 R~Sv~~Al~~GITA~QII~fL~~haHp~m 116 (200)
|.-|++-+..|-|-+||++|+...-=...
T Consensus 63 R~~Vr~~i~~G~sd~eI~~~~v~RYG~~V 91 (126)
T PRK10144 63 RHQVYSMVAEGKSEVEIIGWMTERYGDFV 91 (126)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHhcCCeE
Confidence 77899999999999999999988654433
No 40
>COG0563 Adk Adenylate kinase and related kinases [Nucleotide transport and metabolism]
Probab=33.04 E-value=27 Score=28.99 Aligned_cols=79 Identities=15% Similarity=0.271 Sum_probs=53.9
Q ss_pred hccCceEEEEeCHHHHHHHHHcCCCHHHHHHHHhhcCCccccccCCCCCccHHHHHH-HHHHhcCceEecceeeeccCCC
Q 029030 76 YQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRIPSVPENVCDQIR-LWESDLNRVEMTPAHYYEEFPS 154 (200)
Q Consensus 76 ~r~Pnlvvg~lTR~Sv~~Al~~GITA~QII~fL~~haHp~m~~~~~~iP~tV~dQI~-lWe~Er~R~~~~~g~L~~~f~s 154 (200)
+.+|.+..|-+=|+.+.++-..|..+.+ |+... -.+|..++.++- -|=.+.+ ...|++|..|+.
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---YIDKG---------ELVPDEIVNGLVKERLDEAD---CKAGFILDGFPR 88 (178)
T ss_pred hCCcEEcHhHHhHhhhccCChHHHHHHH---HHHcC---------CccchHHHHHHHHHHHHhhc---ccCeEEEeCCCC
Confidence 6689999998888888777666655555 44442 389999986644 4443331 112899999998
Q ss_pred H-HHHHHHHHHHHHcC
Q 029030 155 R-DVFEAACDYARDRS 169 (200)
Q Consensus 155 ~-~~f~~v~~ya~~~g 169 (200)
. ..++.+.++-.+.|
T Consensus 89 ~~~qa~~l~r~l~~~g 104 (178)
T COG0563 89 TLCQARALKRLLKELG 104 (178)
T ss_pred cHHHHHHHHHHHHHcC
Confidence 5 66677777766655
No 41
>PLN02459 probable adenylate kinase
Probab=32.79 E-value=1.8e+02 Score=26.03 Aligned_cols=69 Identities=16% Similarity=0.242 Sum_probs=46.8
Q ss_pred hhccCceEEEEeCHHHHHHHHHcCCCHHHHHHHHhhcCCccccccCCCCCccHHHHHHHHHHhcCceEecceeeeccCCC
Q 029030 75 EYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPS 154 (200)
Q Consensus 75 ~~r~Pnlvvg~lTR~Sv~~Al~~GITA~QII~fL~~haHp~m~~~~~~iP~tV~dQI~lWe~Er~R~~~~~g~L~~~f~s 154 (200)
.+.++.+.+|.|=|+.|..--..| .+|-+++.+ +..||..++.++-..+.....-.-..|++++.|+-
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 457899999988888775433332 455555544 35788888888877666543223367889888887
Q ss_pred H
Q 029030 155 R 155 (200)
Q Consensus 155 ~ 155 (200)
.
T Consensus 120 t 120 (261)
T PLN02459 120 T 120 (261)
T ss_pred C
Confidence 5
No 42
>KOG2036 consensus Predicted P-loop ATPase fused to an acetyltransferase [General function prediction only]
Probab=31.91 E-value=37 Score=35.25 Aligned_cols=58 Identities=26% Similarity=0.489 Sum_probs=41.4
Q ss_pred ecCCHhHHHHHH------Hhhhh------hhccCceEE-------EEeCHHHHHHHHHcCCCHHHHHHHHhhcCCccccc
Q 029030 58 YSTSKLHCEILR------LFSKI------EYQLPNLIV-------GAITKESLYNAFENGITAEQIISFLQQNAHPRVAD 118 (200)
Q Consensus 58 YT~s~l~iaiL~------lF~~l------~~r~Pnlvv-------g~lTR~Sv~~Al~~GITA~QII~fL~~haHp~m~~ 118 (200)
|.|||-++.+|+ |||=+ .-.+|...+ |.|+|+|+...+..|=.| +
T Consensus 529 YKNSPNDLQllsDAPaH~LFvLl~PVd~~~~~iPdvlcviQv~lEG~isr~si~~sL~~G~~a-----------~----- 592 (1011)
T KOG2036|consen 529 YKNSPNDLQLLSDAPAHHLFVLLGPVDPSQNAIPDVLCVIQVCLEGRISRQSIENSLRRGKRA-----------A----- 592 (1011)
T ss_pred ccCCchhhhhhccCcccceEEEecCcCcccCCCCcceEEEEEeecceecHHHHHHHHhccccc-----------c-----
Confidence 678888888775 67644 334666332 899999999999999543 2
Q ss_pred cCCCCCccHHHHHH
Q 029030 119 RIPSVPENVCDQIR 132 (200)
Q Consensus 119 ~~~~iP~tV~dQI~ 132 (200)
+..||=+|+.|.+
T Consensus 593 -GdlIpW~vseQf~ 605 (1011)
T KOG2036|consen 593 -GDLIPWTVSEQFQ 605 (1011)
T ss_pred -CCccceehhhhhc
Confidence 3567778888764
No 43
>PF13496 DUF4120: Domain of unknown function (DUF4120)
Probab=28.98 E-value=45 Score=25.63 Aligned_cols=16 Identities=13% Similarity=0.414 Sum_probs=14.5
Q ss_pred HHHHHHHHHHHHHcCe
Q 029030 155 RDVFEAACDYARDRSG 170 (200)
Q Consensus 155 ~~~f~~v~~ya~~~g~ 170 (200)
++.|+.|++||+++|-
T Consensus 5 qEhy~kvv~yA~sI~D 20 (95)
T PF13496_consen 5 QEHYDKVVQYAESIGD 20 (95)
T ss_pred HHHHHHHHHHHHHhcc
Confidence 7899999999999883
No 44
>PRK12928 lipoyl synthase; Provisional
Probab=28.63 E-value=4.3e+02 Score=23.65 Aligned_cols=114 Identities=11% Similarity=0.027 Sum_probs=65.2
Q ss_pred HHHHHhhhhhhccCceEEEEeC-------HHHHHHHHHcCCCHHHHHHHHhhcCCcccccc-C-CCCCccHHHHHHHHHH
Q 029030 66 EILRLFSKIEYQLPNLIVGAIT-------KESLYNAFENGITAEQIISFLQQNAHPRVADR-I-PSVPENVCDQIRLWES 136 (200)
Q Consensus 66 aiL~lF~~l~~r~Pnlvvg~lT-------R~Sv~~Al~~GITA~QII~fL~~haHp~m~~~-~-~~iP~tV~dQI~lWe~ 136 (200)
.+..++-.+..+.|.+-|..+| ++.++...+.|- .|+.+.-. ..|.+.+. . ..=.+...+-++.+..
T Consensus 124 ~~~ell~~Ik~~~p~~~I~~ltp~~~~~~~e~L~~l~~Ag~---~i~~hnlE-t~~~vl~~m~r~~t~e~~le~l~~ak~ 199 (290)
T PRK12928 124 HFVATIAAIRARNPGTGIEVLTPDFWGGQRERLATVLAAKP---DVFNHNLE-TVPRLQKAVRRGADYQRSLDLLARAKE 199 (290)
T ss_pred HHHHHHHHHHhcCCCCEEEEeccccccCCHHHHHHHHHcCc---hhhcccCc-CcHHHHHHhCCCCCHHHHHHHHHHHHH
Confidence 4556666677777887777655 456666667772 12222111 11322221 1 1223445555665555
Q ss_pred hcCceEecceeeeccCCCHHHHHHHHHHHHHcCeEe-----eecCCcceEEE
Q 029030 137 DLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLL-----WEDSKKMRLVV 183 (200)
Q Consensus 137 Er~R~~~~~g~L~~~f~s~~~f~~v~~ya~~~g~ll-----w~~~~~r~~~V 183 (200)
....+.+.-++++---.+.+|+....+..+++|+-. +-.+.++.+=|
T Consensus 200 ~gp~i~~~s~iIvG~GET~ed~~etl~~Lrel~~d~v~i~~Yl~p~~~~~~v 251 (290)
T PRK12928 200 LAPDIPTKSGLMLGLGETEDEVIETLRDLRAVGCDRLTIGQYLRPSLAHLPV 251 (290)
T ss_pred hCCCceecccEEEeCCCCHHHHHHHHHHHHhcCCCEEEEEcCCCCCccCCce
Confidence 455577888888855566788899999988887622 33455555533
No 45
>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=28.58 E-value=24 Score=26.30 Aligned_cols=29 Identities=31% Similarity=0.397 Sum_probs=20.4
Q ss_pred cccccccceeEEeecCCCCccccchhhhhhh
Q 029030 2 IKDFADLGLVKLQQVGRKESWFIPTKLATNL 32 (200)
Q Consensus 2 L~~l~~~GLvy~~~~~~~~~fy~pT~La~~l 32 (200)
+++|.++|||... ...+..+- ||.-|..+
T Consensus 44 M~~Le~lGlve~~-p~~s~Gri-PT~~aYr~ 72 (78)
T PF03444_consen 44 MADLEELGLVESQ-PHPSGGRI-PTDKAYRA 72 (78)
T ss_pred HHHHHHCCCccCC-CCCCCCCC-cCHHHHHH
Confidence 5789999999854 33455555 99877654
No 46
>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=28.47 E-value=66 Score=24.10 Aligned_cols=44 Identities=20% Similarity=0.433 Sum_probs=34.6
Q ss_pred eCHHHHHHHH----HcCCCHHHHHHHHhhcCCccccccCCCCC-ccHHHHHHHHHH
Q 029030 86 ITKESLYNAF----ENGITAEQIISFLQQNAHPRVADRIPSVP-ENVCDQIRLWES 136 (200)
Q Consensus 86 lTR~Sv~~Al----~~GITA~QII~fL~~haHp~m~~~~~~iP-~tV~dQI~lWe~ 136 (200)
++|...--|. ..|+|.++-++++++.- |. +.| +...+|+..||.
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 7888775543 58999999999998865 54 344 479999999995
No 47
>PRK14526 adenylate kinase; Provisional
Probab=28.00 E-value=1.3e+02 Score=25.60 Aligned_cols=74 Identities=15% Similarity=0.267 Sum_probs=44.8
Q ss_pred ccCceEEEEeCHHHHHHHHHcCCCHHHHHHHHhhcCCccccccCCCCCccHHHHHHHHHHhcCceEecceeeeccCC-CH
Q 029030 77 QLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFP-SR 155 (200)
Q Consensus 77 r~Pnlvvg~lTR~Sv~~Al~~GITA~QII~fL~~haHp~m~~~~~~iP~tV~dQI~lWe~Er~R~~~~~g~L~~~f~-s~ 155 (200)
.++.+.+|.+-|+.+...-..| .+|-.++... ..+|..++.++-....+. .....|++++.|+ +.
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 4777888888776665433323 3455555443 467888886665554432 2236788999995 44
Q ss_pred HHHHHHHHH
Q 029030 156 DVFEAACDY 164 (200)
Q Consensus 156 ~~f~~v~~y 164 (200)
++.+.+.++
T Consensus 91 ~Qa~~l~~~ 99 (211)
T PRK14526 91 NQAKALDKF 99 (211)
T ss_pred HHHHHHHHh
Confidence 555555443
No 48
>PF14133 DUF4300: Domain of unknown function (DUF4300)
Probab=27.71 E-value=63 Score=28.90 Aligned_cols=30 Identities=23% Similarity=0.317 Sum_probs=25.6
Q ss_pred EeCHHHHHHHH-HcCCCHHHHHHHHhhcCCc
Q 029030 85 AITKESLYNAF-ENGITAEQIISFLQQNAHP 114 (200)
Q Consensus 85 ~lTR~Sv~~Al-~~GITA~QII~fL~~haHp 114 (200)
.-||+.|++|| ++||+.++|=.|+..=.+.
T Consensus 9 ~~s~~eV~~~L~~agi~~~~i~~F~~~V~~y 39 (250)
T PF14133_consen 9 KESQEEVKKALKSAGISKENIDNFFEWVNDY 39 (250)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHHHHHH
Confidence 45899999999 9999999999999875543
No 49
>TIGR01470 cysG_Nterm siroheme synthase, N-terminal domain. This model represents a subfamily of CysG N-terminal region-related sequences. All sequences in the seed alignment for this model are N-terminal regions of known or predicted siroheme synthases. The C-terminal region of each is uroporphyrin-III C-methyltransferase (EC 2.1.1.107), which catalyzes the first step committed to the biosynthesis of either siroheme or cobalamin (vitamin B12) rather than protoheme (heme). The region represented by this model completes the process of oxidation and iron insertion to yield siroheme. Siroheme is a cofactor for nitrite and sulfite reductases, so siroheme synthase is CysG of cysteine biosynthesis in some organisms.
Probab=27.03 E-value=2.6e+02 Score=23.56 Aligned_cols=78 Identities=15% Similarity=0.163 Sum_probs=46.7
Q ss_pred CCCHHH-HHHHHhhcCCccccccCCCCCccHHHHHHHHHHhcCceEecc----------ee-eeccCCCHHHHHHHHHHH
Q 029030 98 GITAEQ-IISFLQQNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTP----------AH-YYEEFPSRDVFEAACDYA 165 (200)
Q Consensus 98 GITA~Q-II~fL~~haHp~m~~~~~~iP~tV~dQI~lWe~Er~R~~~~~----------g~-L~~~f~s~~~f~~v~~ya 165 (200)
|-.|.. +-.+|+..|+.. ++-+++.+++.-|..+. +++... .. ++--=.+.+.-+.+...|
T Consensus 18 G~va~rk~~~Ll~~ga~Vt------Vvsp~~~~~l~~l~~~~-~i~~~~~~~~~~dl~~~~lVi~at~d~~ln~~i~~~a 90 (205)
T TIGR01470 18 GDVALRKARLLLKAGAQLR------VIAEELESELTLLAEQG-GITWLARCFDADILEGAFLVIAATDDEELNRRVAHAA 90 (205)
T ss_pred CHHHHHHHHHHHHCCCEEE------EEcCCCCHHHHHHHHcC-CEEEEeCCCCHHHhCCcEEEEECCCCHHHHHHHHHHH
Confidence 444444 445556666654 44456678888776543 665522 12 232323345778999999
Q ss_pred HHcCeEe--eecCCcceEE
Q 029030 166 RDRSGLL--WEDSKKMRLV 182 (200)
Q Consensus 166 ~~~g~ll--w~~~~~r~~~ 182 (200)
++.|+++ +.+++.-.|+
T Consensus 91 ~~~~ilvn~~d~~e~~~f~ 109 (205)
T TIGR01470 91 RARGVPVNVVDDPELCSFI 109 (205)
T ss_pred HHcCCEEEECCCcccCeEE
Confidence 9999999 6665543343
No 50
>PRK08508 biotin synthase; Provisional
Probab=27.02 E-value=3.5e+02 Score=23.72 Aligned_cols=99 Identities=12% Similarity=0.070 Sum_probs=62.7
Q ss_pred HHHHHhhhhhhccCceEE----EEeCHHHHHHHHHcCCCHHHHHHHHhhc--CCccccccCCCCCccHHHHHHHHHHhcC
Q 029030 66 EILRLFSKIEYQLPNLIV----GAITKESLYNAFENGITAEQIISFLQQN--AHPRVADRIPSVPENVCDQIRLWESDLN 139 (200)
Q Consensus 66 aiL~lF~~l~~r~Pnlvv----g~lTR~Sv~~Al~~GITA~QII~fL~~h--aHp~m~~~~~~iP~tV~dQI~lWe~Er~ 139 (200)
.++..+..++.++|++.+ |.+|+|.+++-.+.|+.+=.+ =|++- -.|.+.+ ..=+..+.+.|+.. .+.+
T Consensus 76 ~~~ei~~~ik~~~p~l~i~~s~G~~~~e~l~~Lk~aGld~~~~--~lEt~~~~~~~i~~--~~~~~~~l~~i~~a-~~~G 150 (279)
T PRK08508 76 YVAEAAKAVKKEVPGLHLIACNGTASVEQLKELKKAGIFSYNH--NLETSKEFFPKICT--THTWEERFQTCENA-KEAG 150 (279)
T ss_pred HHHHHHHHHHhhCCCcEEEecCCCCCHHHHHHHHHcCCCEEcc--cccchHHHhcCCCC--CCCHHHHHHHHHHH-HHcC
Confidence 567777788888898644 889999998888888832111 01110 0111110 11123455566544 4554
Q ss_pred ceEecceeeeccCCCHHHHHHHHHHHHHcCe
Q 029030 140 RVEMTPAHYYEEFPSRDVFEAACDYARDRSG 170 (200)
Q Consensus 140 R~~~~~g~L~~~f~s~~~f~~v~~ya~~~g~ 170 (200)
+..+.+.++--=.+.++-.....+.++++.
T Consensus 151 -i~v~sg~I~GlGEt~ed~~~~l~~lr~L~~ 180 (279)
T PRK08508 151 -LGLCSGGIFGLGESWEDRISFLKSLASLSP 180 (279)
T ss_pred -CeecceeEEecCCCHHHHHHHHHHHHcCCC
Confidence 888899999777777888888888888874
No 51
>cd00127 DSPc Dual specificity phosphatases (DSP); Ser/Thr and Tyr protein phosphatases. Structurally similar to tyrosine-specific phosphatases but with a shallower active site cleft and a distinctive active site signature motif, HCxxGxxR. Characterized as VHR- or Cdc25-like.
Probab=26.78 E-value=1.1e+02 Score=22.87 Aligned_cols=44 Identities=14% Similarity=0.304 Sum_probs=31.4
Q ss_pred eCHHHHHHH----HHcCCCHHHHHHHHhhcCCccccccCCCCCccHHHHHHHHH
Q 029030 86 ITKESLYNA----FENGITAEQIISFLQQNAHPRVADRIPSVPENVCDQIRLWE 135 (200)
Q Consensus 86 lTR~Sv~~A----l~~GITA~QII~fL~~haHp~m~~~~~~iP~tV~dQI~lWe 135 (200)
+.|...--| ...|.+.++.++++++. +|.+ ..-++..-|++.||
T Consensus 92 ~~Rs~~~~~~~l~~~~~~~~~~a~~~vr~~-r~~~-----~~~~~~~~~l~~~~ 139 (139)
T cd00127 92 VSRSATLVIAYLMKTLGLSLREAYEFVKSR-RPII-----SPNAGFMRQLKEYE 139 (139)
T ss_pred CchhHHHHHHHHHHHcCCCHHHHHHHHHHH-CCcc-----CCCHHHHHHHHHhC
Confidence 556663322 25699999999999985 5532 23368999999997
No 52
>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=26.63 E-value=21 Score=24.47 Aligned_cols=23 Identities=26% Similarity=0.494 Sum_probs=17.2
Q ss_pred cccccccceeEEeecCCCCccccch
Q 029030 2 IKDFADLGLVKLQQVGRKESWFIPT 26 (200)
Q Consensus 2 L~~l~~~GLvy~~~~~~~~~fy~pT 26 (200)
|+.|.+.|||.+. .++...|+ |+
T Consensus 43 L~~L~~~GlV~~~-~~~~~~Y~-a~ 65 (68)
T PF01978_consen 43 LKSLEEKGLVERE-EGRPKVYR-AV 65 (68)
T ss_dssp HHHHHHTTSEEEE-EECCEEEE-EE
T ss_pred HHHHHHCCCEEEE-cCceEEEE-Ee
Confidence 6789999999988 55555555 54
No 53
>PRK00279 adk adenylate kinase; Reviewed
Probab=26.61 E-value=3.3e+02 Score=22.42 Aligned_cols=80 Identities=14% Similarity=0.240 Sum_probs=47.6
Q ss_pred hccCceEEEEeCHHHHHHHHHcCCCHHHHHHHHhhcCCccccccCCCCCccHHHHHHHHHHhcCceEecceeeeccCCCH
Q 029030 76 YQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSR 155 (200)
Q Consensus 76 ~r~Pnlvvg~lTR~Sv~~Al~~GITA~QII~fL~~haHp~m~~~~~~iP~tV~dQI~lWe~Er~R~~~~~g~L~~~f~s~ 155 (200)
+-++.+.+|.+-|+.+...-. .+.+|-.++.. +..+|.+++.++-.-..... ....|++++.|+..
T Consensus 24 ~~~~~is~~dl~r~~~~~~~~---~~~~~~~~~~~---------g~~~p~~~~~~~i~~~l~~~--~~~~g~VlDGfPr~ 89 (215)
T PRK00279 24 YGIPHISTGDMLRAAVKAGTE---LGKEAKSYMDA---------GELVPDEIVIGLVKERLAQP--DCKNGFLLDGFPRT 89 (215)
T ss_pred hCCcEEECCccHHHHHhccch---HHHHHHHHHHc---------CCcCCHHHHHHHHHHHHhcc--CccCCEEEecCCCC
Confidence 457888888887776654222 22344455443 34788888766554443322 23458999998664
Q ss_pred -HHHHHHHHHHHHcC
Q 029030 156 -DVFEAACDYARDRS 169 (200)
Q Consensus 156 -~~f~~v~~ya~~~g 169 (200)
++.+.+.++....|
T Consensus 90 ~~qa~~l~~~l~~~~ 104 (215)
T PRK00279 90 IPQAEALDEMLKELG 104 (215)
T ss_pred HHHHHHHHHHHHHcC
Confidence 45555555555544
No 54
>PRK14089 ipid-A-disaccharide synthase; Provisional
Probab=26.29 E-value=41 Score=30.97 Aligned_cols=54 Identities=17% Similarity=0.310 Sum_probs=42.3
Q ss_pred EecCCHhHHHHHHHhhhhh-hccCceEEEEeC-HHHHHHHHHcCCCHHHHHHHHhh
Q 029030 57 AYSTSKLHCEILRLFSKIE-YQLPNLIVGAIT-KESLYNAFENGITAEQIISFLQQ 110 (200)
Q Consensus 57 AYT~s~l~iaiL~lF~~l~-~r~Pnlvvg~lT-R~Sv~~Al~~GITA~QII~fL~~ 110 (200)
+|.-|++|.++-+.+.++. .-+||++.|+|- |+=|-+-++.-.|+++|.+-+..
T Consensus 260 ~Yk~~~lty~iak~lv~~~~igL~Nii~~~~~~~~vvPEllQ~~~t~~~la~~i~~ 315 (347)
T PRK14089 260 AYKAKAIDYFIAKMFVKLKHIGLANIFFDFLGKEPLHPELLQEFVTVENLLKAYKE 315 (347)
T ss_pred EEeCCHHHHHHHHHHHcCCeeehHHHhcCCCcccccCchhhcccCCHHHHHHHHHH
Confidence 8999999999999988764 346999987554 66667777777888888877755
No 55
>PRK13761 hypothetical protein; Provisional
Probab=25.13 E-value=33 Score=30.74 Aligned_cols=19 Identities=42% Similarity=0.658 Sum_probs=17.4
Q ss_pred EeCHHHHHHHHHcCCCHHH
Q 029030 85 AITKESLYNAFENGITAEQ 103 (200)
Q Consensus 85 ~lTR~Sv~~Al~~GITA~Q 103 (200)
.++||.+-++++.||+|.|
T Consensus 12 L~~Rekiveg~~~Gi~a~q 30 (248)
T PRK13761 12 LLTREKIVEGVEKGITAKQ 30 (248)
T ss_pred HHHHHHHHHHHHcCccccc
Confidence 4789999999999999987
No 56
>PF00482 T2SF: Type II secretion system (T2SS), protein F; InterPro: IPR018076 A number of bacterial proteins, some of which are involved in a general secretion pathway (GSP) for the export of proteins (also called the type II pathway) [], have been found to be evolutionary related. These are proteins of about 400 amino acids that are highly hydrophobic and which are thought to be integral protein of the inner membrane. Proteins with this domain form a platform for the type II secretion machinery, as well as the type IV pili and the archaeal flagellae [].; PDB: 2VMA_A 3C1Q_A 2VMB_B 2WHN_B.
Probab=24.68 E-value=68 Score=22.79 Aligned_cols=29 Identities=14% Similarity=0.321 Sum_probs=22.0
Q ss_pred HHHHHHHcCCCHHHHHHHHhhcC-Cccccc
Q 029030 90 SLYNAFENGITAEQIISFLQQNA-HPRVAD 118 (200)
Q Consensus 90 Sv~~Al~~GITA~QII~fL~~ha-Hp~m~~ 118 (200)
.+...++.|++-.+++..+..++ ++.+++
T Consensus 4 ~l~~ll~sG~~l~~al~~~~~~~~~~~l~~ 33 (124)
T PF00482_consen 4 MLSSLLKSGIPLSEALEILAEESDSGPLRE 33 (124)
T ss_dssp HHHHHHHCT--HHHHHHHHCCC-SSHHHHH
T ss_pred HHHHHHHcCCCHHHHHHHHHhHcCCHHHHH
Confidence 46678999999999999999999 877654
No 57
>PF00508 PPV_E2_N: E2 (early) protein, N terminal; InterPro: IPR001866 E2 is an early regulatory protein found in the dsDNA papillomaviruses. E2 regulates viral transcription and DNA replication. It binds to the E2RE response element (5'-ACCNNNNNNGGT-3') present in multiple copies in the regulatory region. It can either activate or repress transcription, depending on E2RE's posiiton with regard to proximal promoter elements. Repression occurs by sterically hindering the assembly of the transcription initiation complex. The E1-E2 dimer complex binds to the origin of DNA replication [].; GO: 0006275 regulation of DNA replication, 0006355 regulation of transcription, DNA-dependent, 0016032 viral reproduction; PDB: 1R6K_A 1R6N_A 2JEX_A 2JEU_A 1TUE_E 1QQH_A 1DTO_A 2NNU_A.
Probab=24.65 E-value=1.3e+02 Score=26.14 Aligned_cols=26 Identities=23% Similarity=0.540 Sum_probs=20.8
Q ss_pred HHHHHHHhhcCCccccccCCCCCccHHHHHHHHHHhcC
Q 029030 102 EQIISFLQQNAHPRVADRIPSVPENVCDQIRLWESDLN 139 (200)
Q Consensus 102 ~QII~fL~~haHp~m~~~~~~iP~tV~dQI~lWe~Er~ 139 (200)
|||+..+++.++ ++.|||.-|+.-|.
T Consensus 13 e~~l~lyE~ds~------------~L~dqi~yW~lvR~ 38 (202)
T PF00508_consen 13 EQLLELYEKDST------------DLEDQIEYWKLVRK 38 (202)
T ss_dssp HHHHHHHHHT-S-------------HHHHHHHHHHHHH
T ss_pred HHHHHHHhCCCc------------cHHHHHHHHHHHHH
Confidence 788999998775 79999999998765
No 58
>PF10163 EnY2: Transcription factor e(y)2; InterPro: IPR018783 Enhancer of yellow 2 (EnY2) is a small transcription factor which is combined in a complex with the TAFII40 protein []. This protein is conserved from protozoa to humans.; PDB: 4DHX_C 3FWC_P 3M99_C 3KIK_A 3KJL_C 3FWB_C 3MHS_B 3MHH_B.
Probab=24.23 E-value=46 Score=24.54 Aligned_cols=38 Identities=18% Similarity=0.293 Sum_probs=26.2
Q ss_pred HHHHHHHHHcCCCHHHHHHHHhhcCCccccccCCCCCccHHHHHH
Q 029030 88 KESLYNAFENGITAEQIISFLQQNAHPRVADRIPSVPENVCDQIR 132 (200)
Q Consensus 88 R~Sv~~Al~~GITA~QII~fL~~haHp~m~~~~~~iP~tV~dQI~ 132 (200)
|+-+++-=...+|.++++.-+..+|. ..||+.|...+.
T Consensus 41 re~i~~~g~~~~~~~~l~~~i~P~Ar-------~~VP~~vk~ell 78 (86)
T PF10163_consen 41 REIIRERGIDNLTFEDLLEEITPKAR-------AMVPDEVKKELL 78 (86)
T ss_dssp HHHHHHH-TTTSBHHHHHHHHHHHHH-------HCS-HHHHHHHH
T ss_pred HHHHHhhCCCCCCHHHHHHHHHHHHH-------HHCCHHHHHHHH
Confidence 33343322345899999999999997 589999877653
No 59
>COG4109 Predicted transcriptional regulator containing CBS domains [Transcription]
Probab=23.81 E-value=84 Score=30.12 Aligned_cols=18 Identities=22% Similarity=0.547 Sum_probs=14.6
Q ss_pred ceEEEEeCHHHHHHHHHc
Q 029030 80 NLIVGAITKESLYNAFEN 97 (200)
Q Consensus 80 nlvvg~lTR~Sv~~Al~~ 97 (200)
|=.+|++||..|-+|++.
T Consensus 290 ~~llGiitR~dvlk~lq~ 307 (432)
T COG4109 290 NTLLGIITRQDVLKSLQM 307 (432)
T ss_pred ceEEEEEEHHHHHHHHHH
Confidence 456899999999888853
No 60
>PRK09913 putative fructose-like phosphotransferase system subunit EIIA; Provisional
Probab=23.40 E-value=2.4e+02 Score=21.71 Aligned_cols=40 Identities=13% Similarity=0.336 Sum_probs=31.3
Q ss_pred CCHhHHHHHHHhhhhhhccCceEEEEeCHHHHHHHHHcCCCHHHHHHHHhhc
Q 029030 60 TSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQN 111 (200)
Q Consensus 60 ~s~l~iaiL~lF~~l~~r~Pnlvvg~lTR~Sv~~Al~~GITA~QII~fL~~h 111 (200)
++..|+.+|+.++++.. . +...+++.+| ++++|.++|...
T Consensus 106 ~~~~~l~~l~~l~~~l~----------~-~~~~~~L~~~-~~~ei~~~l~~~ 145 (148)
T PRK09913 106 GEEDQVKIIGTLCRKII----------H-QDFIHQLKQG-DTDQVLALLNQT 145 (148)
T ss_pred CcHHHHHHHHHHHHHHc----------C-HHHHHHHHcC-CHHHHHHHHHHH
Confidence 56788888888888776 3 4467777776 899999999764
No 61
>cd01095 Nitrilotriacetate_monoxgenase nitrilotriacetate monoxygenase oxidizes nitrilotriacetate utilizing reduced flavin mononucleotide (FMNH2) and oxygen. The FMNH2 is provided by an NADH:flavin mononucleotide (FMN) oxidorductase that uses NADH to reduce FMN to FMNH2.
Probab=23.09 E-value=1.8e+02 Score=26.72 Aligned_cols=63 Identities=16% Similarity=0.100 Sum_probs=42.6
Q ss_pred HHHHcCCCHHHHHHHHhhcC-CccccccCCCCCccHHHHHHHHHHhcCceEecceeeeccCCCHHHHHHHHHH
Q 029030 93 NAFENGITAEQIISFLQQNA-HPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDY 164 (200)
Q Consensus 93 ~Al~~GITA~QII~fL~~ha-Hp~m~~~~~~iP~tV~dQI~lWe~Er~R~~~~~g~L~~~f~s~~~f~~v~~y 164 (200)
.+-..+-|..|++.++.... ++.. -+ |+.|.|||.-|-.+.. .+|+...--.....++..+++
T Consensus 284 ~~~~~~~t~~~~~~~~~~~~~~~~~----vG-p~~vAd~l~~w~~~~~----~DGF~l~~~~~p~~~~~f~~~ 347 (358)
T cd01095 284 LHRREVGTAREVADRLERAAGGGTV----VG-PEQIADELEEWFEAGA----ADGFNIMPPYLPGGLDDFVDL 347 (358)
T ss_pred hhhhcCCCHHHHHHHhhccCCCCee----EC-HHHHHHHHHHHHhcCC----CCeEEECCCCCCcCHHHHHHh
Confidence 34478899999998875432 2222 23 9999999999976654 677777655555555555443
No 62
>COG1438 ArgR Arginine repressor [Transcription]
Probab=23.03 E-value=37 Score=28.18 Aligned_cols=20 Identities=30% Similarity=0.589 Sum_probs=17.2
Q ss_pred ccccccceeEEeecCCCCccc
Q 029030 3 KDFADLGLVKLQQVGRKESWF 23 (200)
Q Consensus 3 ~~l~~~GLvy~~~~~~~~~fy 23 (200)
+||+++|+|..+ ..++.++|
T Consensus 44 RDlkelglvKv~-~~~g~~~Y 63 (150)
T COG1438 44 RDLKELGLVKVR-NEKGTYVY 63 (150)
T ss_pred HHHHHcCCEEec-CCCCcEEE
Confidence 699999999999 76777778
No 63
>PF09106 SelB-wing_2: Elongation factor SelB, winged helix ; InterPro: IPR015190 This entry represents a domain with a winged helix-type fold, which consists of a closed 3-helical bundle with a right-handed twist, and a small beta-sheet wing []. Different winged helix domains share a common structure, but can differ in sequence. This entry is designated "type 2". The winged helix motif is involved in both DNA and RNA binding. In the elongation factor SelB, the winged helix domains recognise RNA, allowing the complex to wrap around the small ribosomal subunit. In bacteria, the incorporation of the amino acid selenocysteine into proteins requires elongation factor SelB, which binds both transfer RNA (tRNA) and mRNA. SelB binds to an mRNA hairpin formed by the selenocysteine insertion sequence (SECIS) with extremely high specificity []. ; GO: 0003723 RNA binding, 0003746 translation elongation factor activity, 0005525 GTP binding, 0001514 selenocysteine incorporation, 0005737 cytoplasm; PDB: 2V9V_A 1LVA_A 2PLY_A 2UWM_A.
Probab=22.90 E-value=1e+02 Score=20.73 Aligned_cols=28 Identities=11% Similarity=0.159 Sum_probs=19.6
Q ss_pred CCCCccHHHHHHHHHHhcCceEecceee
Q 029030 121 PSVPENVCDQIRLWESDLNRVEMTPAHY 148 (200)
Q Consensus 121 ~~iP~tV~dQI~lWe~Er~R~~~~~g~L 148 (200)
|.+|+.+.+.+--+-.+.++++...+++
T Consensus 30 ~~l~~k~~~~ll~~l~~~g~l~~~g~~v 57 (59)
T PF09106_consen 30 PRLPPKLFNALLEALVAEGRLKVEGDWV 57 (59)
T ss_dssp -TS-HCCHHHHHHHHHHTTSEEEESSEE
T ss_pred ccCCHHHHHHHHHHHHHCCCeeeECCEe
Confidence 3678888888877777777777776654
No 64
>COG0599 Uncharacterized homolog of gamma-carboxymuconolactone decarboxylase subunit [Function unknown]
Probab=22.87 E-value=74 Score=24.57 Aligned_cols=27 Identities=33% Similarity=0.330 Sum_probs=22.7
Q ss_pred CHHHHHHHHHcCCCHHHHHHHHhhcCC
Q 029030 87 TKESLYNAFENGITAEQIISFLQQNAH 113 (200)
Q Consensus 87 TR~Sv~~Al~~GITA~QII~fL~~haH 113 (200)
++-.++.|+++|.|-++|..=|..-++
T Consensus 73 l~~H~~~Al~~GaT~eEI~e~i~~~a~ 99 (124)
T COG0599 73 LKVHVRAALENGATKEEIAEAIAVAAI 99 (124)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 456789999999999999998877655
No 65
>PRK11183 D-lactate dehydrogenase; Provisional
Probab=22.46 E-value=1.6e+02 Score=29.55 Aligned_cols=81 Identities=17% Similarity=0.212 Sum_probs=62.2
Q ss_pred eEEEecCCHhHHHHHHHhhhhhhccCceEEE--EeCHHHHHHHHHcCCCHHHHHHHHhhcCCcccc----------ccCC
Q 029030 54 RMYAYSTSKLHCEILRLFSKIEYQLPNLIVG--AITKESLYNAFENGITAEQIISFLQQNAHPRVA----------DRIP 121 (200)
Q Consensus 54 rvYAYT~s~l~iaiL~lF~~l~~r~Pnlvvg--~lTR~Sv~~Al~~GITA~QII~fL~~haHp~m~----------~~~~ 121 (200)
-.|+.|+++-.. ..+...+...|+++.++ .|.|+.+.-|-+.|=..=-.|.+|-+..-|.|- ++.|
T Consensus 271 vf~ig~n~~~~~--~~~rr~il~~~~~lP~a~Eym~r~~~d~~~~ygkd~~~~i~~~gt~~~p~~f~~k~~~d~~~~~~~ 348 (564)
T PRK11183 271 VFYIGTNDPAVL--TEIRRHILANFKNLPVAGEYMHRDAFDIAEKYGKDTFLMIDKLGTDKLPKLFALKGRVDAFLEKVP 348 (564)
T ss_pred EEEEeCCCHHHH--HHHHHHHHHhCCCCceeEeecCHHHHHHHHHhCCccEEehhhhCchhHHHHHhhHHHHHHHHHhcC
Confidence 358888888776 33344556668888777 899999999999987666688888888888752 2359
Q ss_pred CCCccHHHHHHHHHH
Q 029030 122 SVPENVCDQIRLWES 136 (200)
Q Consensus 122 ~iP~tV~dQI~lWe~ 136 (200)
.+|++++|.+-.|-.
T Consensus 349 ~~~~~~~d~~~q~~~ 363 (564)
T PRK11183 349 FLPPHFTDRVMQALS 363 (564)
T ss_pred CCCCCCcHHHHHHHH
Confidence 999999999988764
No 66
>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=22.40 E-value=37 Score=28.67 Aligned_cols=22 Identities=9% Similarity=0.264 Sum_probs=19.1
Q ss_pred cccccccceeEEeecCCCCccc
Q 029030 2 IKDFADLGLVKLQQVGRKESWF 23 (200)
Q Consensus 2 L~~l~~~GLvy~~~~~~~~~fy 23 (200)
|..|.|.|||-.+|.++++||-
T Consensus 92 l~~LveaGLI~rrDS~NgkRy~ 113 (177)
T PF03428_consen 92 LARLVEAGLIVRRDSPNGKRYA 113 (177)
T ss_pred HHHHHHCCCeeeccCCCCCccC
Confidence 5679999999998888888887
No 67
>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=22.17 E-value=5.1e+02 Score=23.92 Aligned_cols=119 Identities=18% Similarity=0.215 Sum_probs=40.1
Q ss_pred EEecCCHhHHHHHHHhhhhhhccCceEEE--EeCHHHHHHHHHcCCCHHHHHHHHhhcCCccccc----------cCCCC
Q 029030 56 YAYSTSKLHCEILRLFSKIEYQLPNLIVG--AITKESLYNAFENGITAEQIISFLQQNAHPRVAD----------RIPSV 123 (200)
Q Consensus 56 YAYT~s~l~iaiL~lF~~l~~r~Pnlvvg--~lTR~Sv~~Al~~GITA~QII~fL~~haHp~m~~----------~~~~i 123 (200)
|.=||.|-.+.-|+-- +...|++|-|. =|-|+...-|-+.|=--=..|..|-+..-|.|=. +.|.+
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 5567777776444432 35557776554 6999999999999999999999999999998632 24889
Q ss_pred CccHHHHHHHHHHhcCceEecceeeeccCCCHHHHHHHHHHHHHcCeEeeecCCcceEEEeccccHHHHHHHhh
Q 029030 124 PENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHMREFLRG 197 (200)
Q Consensus 124 P~tV~dQI~lWe~Er~R~~~~~g~L~~~f~s~~~f~~v~~ya~~~g~llw~~~~~r~~~V~~~~~~~v~~f~k~ 197 (200)
|++++|.+-.|-. +..-+..=..+.+|-+..--- -++-|+.+|.++.++|+++
T Consensus 81 p~~lsDr~lQ~~s--------------~l~P~hLP~Rm~~yr~ryeHH-------Lilkm~~~gi~ea~~~L~~ 133 (291)
T PF09330_consen 81 PPNLSDRVLQALS--------------NLLPNHLPKRMRDYRDRYEHH-------LILKMSGDGIEEARAYLKE 133 (291)
T ss_dssp -----------------------------------HHHHHHHHH-SEE-------EEEEE-TTHHHHHHHHHHH
T ss_pred CCCccHHHHHHHH--------------hhChhhcCHHHHHHHHhhhhh-------eeeeecCCcHHHHHHHHHH
Confidence 9999999887752 222233445555665553321 1355667777777777765
No 68
>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=21.63 E-value=43 Score=24.19 Aligned_cols=20 Identities=30% Similarity=0.584 Sum_probs=15.2
Q ss_pred ccccccceeEEeecCCCCccc
Q 029030 3 KDFADLGLVKLQQVGRKESWF 23 (200)
Q Consensus 3 ~~l~~~GLvy~~~~~~~~~fy 23 (200)
+||+++|+|-.+ ..++...|
T Consensus 43 RDLkeL~~vKv~-~~~g~~~Y 62 (70)
T PF01316_consen 43 RDLKELGAVKVP-DGNGKYRY 62 (70)
T ss_dssp HHHHHHT-EEEE-CTTSSEEE
T ss_pred HHHHHcCcEEee-CCCCCEEE
Confidence 699999999999 55666666
No 69
>PF10566 Glyco_hydro_97: Glycoside hydrolase 97 ; InterPro: IPR019563 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. This is the 97th family of glycosidases, in this case bacterial. The central part of the GH97 family protein sequences represents a typical and complete (beta/alpha)8-barrel or catalytic TIM-barrel type domain. The N- and C-terminal parts of the sequences, mainly consisting of beta-strands, most probably form two additional non-catalytic domains with as yet unknown functions. The non-catalytic domains of glycosidases from the alpha-galactosidase and alpha-glucosidase superfamilies are also predominantly composed of beta-strands, and at least some of these domains are involved in oligomerisation and carbohydrate binding. In all known glycosidases with the (beta-alpha)8-barrel fold, the amino acid residues at the active site are located on the C-termini of the beta-strands []. ; PDB: 2JKP_A 2JKE_A 2D73_B 2ZQ0_B 2JKA_A 3A24_A.
Probab=21.50 E-value=89 Score=28.18 Aligned_cols=25 Identities=24% Similarity=0.409 Sum_probs=19.0
Q ss_pred CHHHHHHHHHHHHHcC--eEeeecCCc
Q 029030 154 SRDVFEAACDYARDRS--GLLWEDSKK 178 (200)
Q Consensus 154 s~~~f~~v~~ya~~~g--~llw~~~~~ 178 (200)
...+-+.+++||+++| ++||.+...
T Consensus 71 ~~~dl~elv~Ya~~KgVgi~lw~~~~~ 97 (273)
T PF10566_consen 71 PDFDLPELVDYAKEKGVGIWLWYHSET 97 (273)
T ss_dssp TT--HHHHHHHHHHTT-EEEEEEECCH
T ss_pred CccCHHHHHHHHHHcCCCEEEEEeCCc
Confidence 3578899999999999 788876654
No 70
>cd01293 Bact_CD Bacterial cytosine deaminase and related metal-dependent hydrolases. Cytosine deaminases (CDs) catalyze the deamination of cytosine, producing uracil and ammonia. They play an important role in pyrimidine salvage. CDs are present in prokaryotes and fungi, but not mammalian cells. The bacterial enzymes, but not the fungal enzymes, are related to the adenosine deaminases (ADA). The bacterial enzymes are iron dependent and hexameric.
Probab=21.28 E-value=3.5e+02 Score=23.72 Aligned_cols=46 Identities=7% Similarity=-0.103 Sum_probs=29.1
Q ss_pred ccHHHHHHHHHHhcCceEecceeeec--cCCCHHHHHHHHHHHHHcCeEe
Q 029030 125 ENVCDQIRLWESDLNRVEMTPAHYYE--EFPSRDVFEAACDYARDRSGLL 172 (200)
Q Consensus 125 ~tV~dQI~lWe~Er~R~~~~~g~L~~--~f~s~~~f~~v~~ya~~~g~ll 172 (200)
+...+.++.|..+..++. .++-+. ...+.++++.+++.|++.|+.+
T Consensus 158 ~~~~~~v~~~~~~g~~~~--~~~~~~~~~~~s~e~l~~~~~~A~~~g~~v 205 (398)
T cd01293 158 PGGEELMREALKMGADVV--GGIPPAEIDEDGEESLDTLFELAQEHGLDI 205 (398)
T ss_pred CCHHHHHHHHHHhCCCEE--eCCCCCcCCccHHHHHHHHHHHHHHhCCCC
Confidence 345566777776544332 222222 2345799999999999988644
No 71
>PF08673 RsbU_N: Phosphoserine phosphatase RsbU, N-terminal domain; InterPro: IPR014787 The phosphoserine phosphatase RsbU acts as a positive regulator of the general stress-response factor of Gram-positive organisms, sigma-B. RsbU dephosphorylates rsbV in response to environmental stress conveyed from the rsbXST module. The phosphatase activity of RsbU is stimulated during the stress response by associating with the RsbT kinase. This association leads to the induction of sigmaB activity. The N-terminal domain forms a helix-swapped dimer that is otherwise similar to the KaiA domain dimer. Deletions in the N-terminal domain are deleterious to the activity of RsbU. The C-terminal domain of RsbU is similar to the catalytic domains of PP2C-type phosphatases [].; PDB: 2J6Y_D 2J6Z_A 2J70_A 1W53_A.
Probab=21.06 E-value=77 Score=23.27 Aligned_cols=16 Identities=25% Similarity=0.476 Sum_probs=12.3
Q ss_pred HHHHHcCCCHHHHHHH
Q 029030 92 YNAFENGITAEQIISF 107 (200)
Q Consensus 92 ~~Al~~GITA~QII~f 107 (200)
|++++++|.+++|++-
T Consensus 28 r~~i~~~I~PEeIv~i 43 (77)
T PF08673_consen 28 RELIEKDISPEEIVEI 43 (77)
T ss_dssp HHHHHTT--HHHHHHH
T ss_pred HHHHHcCCCHHHHHHH
Confidence 6789999999999975
No 72
>PRK14340 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=20.72 E-value=5.8e+02 Score=24.12 Aligned_cols=45 Identities=16% Similarity=0.139 Sum_probs=28.8
Q ss_pred ccHHHHHHHHHHhcCceEecceeeeccCCC--HHHHHHHHHHHHHcCe
Q 029030 125 ENVCDQIRLWESDLNRVEMTPAHYYEEFPS--RDVFEAACDYARDRSG 170 (200)
Q Consensus 125 ~tV~dQI~lWe~Er~R~~~~~g~L~~~f~s--~~~f~~v~~ya~~~g~ 170 (200)
+.+.+-|+......--+.+.-.+++ .|++ .++|+.+++++++.+.
T Consensus 283 ~~~~~~v~~lr~~~pgi~i~td~Iv-GfPgET~edf~~tl~~~~~~~~ 329 (445)
T PRK14340 283 EEYLEKIALIRSAIPGVTLSTDLIA-GFCGETEEDHRATLSLMEEVRF 329 (445)
T ss_pred HHHHHHHHHHHHhCCCCEEeccEEE-ECCCCCHHHHHHHHHHHHhcCC
Confidence 3444445544333334666655666 6555 6999999999999873
No 73
>TIGR01290 nifB nitrogenase cofactor biosynthesis protein NifB. This model describes NifB, a protein required for the biosynthesis of the iron-molybdenum (or iron-vanadium) cofactor used by the nitrogen-fixing enzyme nitrogenase. Archaeal homologs lack the most C-terminal region and score between the trusted and noise cutoffs of this model.
Probab=20.42 E-value=7.4e+02 Score=23.58 Aligned_cols=104 Identities=10% Similarity=0.128 Sum_probs=55.7
Q ss_pred HHHHHhhhhhhccCceEEEEeC-----HHHHHHHHHcCCCHHHHHHHHhhcCCcccccc-----------CCCCCc---c
Q 029030 66 EILRLFSKIEYQLPNLIVGAIT-----KESLYNAFENGITAEQIISFLQQNAHPRVADR-----------IPSVPE---N 126 (200)
Q Consensus 66 aiL~lF~~l~~r~Pnlvvg~lT-----R~Sv~~Al~~GITA~QII~fL~~haHp~m~~~-----------~~~iP~---t 126 (200)
.++.++..+..++|++.+++-| .+.+.+-...|+. .+.+=-.+..|...+. -.+.+. -
T Consensus 96 ~~~~~l~~~~~~~~~i~i~lsTNG~~l~e~i~~L~~~gvd---~V~islka~d~e~~~~Iy~~v~~~g~~~tG~~~~~il 172 (442)
T TIGR01290 96 KTFQTLELVARQLPDVKLCLSTNGLMLPEHVDRLVDLGVG---HVTITINAIDPAVGEKIYPWVWYEGERYTGREAADLL 172 (442)
T ss_pred ccHHHHHHHHHhcCCCeEEEECCCCCCHHHHHHHHHCCCC---eEEEeccCCCHHHHhhcchhhccccccccCcchHHHH
Confidence 5777888888888998888777 5555555555542 1111011111222110 011111 1
Q ss_pred HHHHHHH--HHHhcCceEecceeeeccCCCHHHHHHHHHHHHHcCeEee
Q 029030 127 VCDQIRL--WESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLW 173 (200)
Q Consensus 127 V~dQI~l--We~Er~R~~~~~g~L~~~f~s~~~f~~v~~ya~~~g~llw 173 (200)
+-.|+.- +-.+++....-..+|...+.+ ++.+.++++++++|+-.|
T Consensus 173 ~e~~l~~l~~l~~~G~~v~v~~vlIpGiND-~~i~~l~~~~~~lg~~~~ 220 (442)
T TIGR01290 173 IERQLEGLEKLTERGILVKVNSVLIPGIND-EHLVEVSKQVKELGAFLH 220 (442)
T ss_pred HHHHHHHHHHHHhCCCeEEEEEEeeCCcCH-HHHHHHHHHHHhCCCcEE
Confidence 2233321 123444444445677767755 899999999999987443
No 74
>PF00571 CBS: CBS domain CBS domain web page. Mutations in the CBS domain of Swiss:P35520 lead to homocystinuria.; InterPro: IPR000644 CBS (cystathionine-beta-synthase) domains are small intracellular modules, mostly found in two or four copies within a protein, that occur in a variety of proteins in bacteria, archaea, and eukaryotes [, ]. Tandem pairs of CBS domains can act as binding domains for adenosine derivatives and may regulate the activity of attached enzymatic or other domains []. In some cases, CBS domains may act as sensors of cellular energy status by being activated by AMP and inhibited by ATP []. In chloride ion channels, the CBS domains have been implicated in intracellular targeting and trafficking, as well as in protein-protein interactions, but results vary with different channels: in the CLC-5 channel, the CBS domain was shown to be required for trafficking [], while in the CLC-1 channel, the CBS domain was shown to be critical for channel function, but not necessary for trafficking []. Recent experiments revealing that CBS domains can bind adenosine-containing ligands such ATP, AMP, or S-adenosylmethionine have led to the hypothesis that CBS domains function as sensors of intracellular metabolites [, ]. Crystallographic studies of CBS domains have shown that pairs of CBS sequences form a globular domain where each CBS unit adopts a beta-alpha-beta-beta-alpha pattern []. Crystal structure of the CBS domains of the AMP-activated protein kinase in complexes with AMP and ATP shows that the phosphate groups of AMP/ATP lie in a surface pocket at the interface of two CBS domains, which is lined with basic residues, many of which are associated with disease-causing mutations []. In humans, mutations in conserved residues within CBS domains cause a variety of human hereditary diseases, including (with the gene mutated in parentheses): homocystinuria (cystathionine beta-synthase); Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase); retinitis pigmentosa (IMP dehydrogenase-1); congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members).; GO: 0005515 protein binding; PDB: 3JTF_A 3TE5_C 3TDH_C 3T4N_C 2QLV_C 3OI8_A 3LV9_A 2QH1_B 1PVM_B 3LQN_A ....
Probab=20.15 E-value=1e+02 Score=19.41 Aligned_cols=18 Identities=28% Similarity=0.462 Sum_probs=14.7
Q ss_pred CceEEEEeCHHHHHHHHH
Q 029030 79 PNLIVGAITKESLYNAFE 96 (200)
Q Consensus 79 Pnlvvg~lTR~Sv~~Al~ 96 (200)
.+=.+|.||+.++.+++.
T Consensus 39 ~~~~~G~is~~dl~~~l~ 56 (57)
T PF00571_consen 39 DGKLVGIISRSDLLKALL 56 (57)
T ss_dssp TSBEEEEEEHHHHHHHHH
T ss_pred CCEEEEEEEHHHHHhhhh
Confidence 356889999999988863
Done!