Query 028327
Match_columns 210
No_of_seqs 55 out of 57
Neff 2.1
Searched_HMMs 46136
Date Fri Mar 29 09:46:55 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028327.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028327hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF10664 NdhM: Cyanobacterial 100.0 7.6E-73 1.6E-77 442.4 10.6 107 88-197 1-107 (108)
2 PF00316 FBPase: Fructose-1-6- 90.6 0.63 1.4E-05 42.5 5.8 102 86-198 161-270 (324)
3 PLN02542 fructose-1,6-bisphosp 90.5 0.54 1.2E-05 44.5 5.4 84 92-184 258-348 (412)
4 PRK09293 fructose-1,6-bisphosp 81.8 2.8 6.1E-05 38.0 5.1 53 143-198 219-271 (327)
5 cd00354 FBPase Fructose-1,6-bi 81.7 3.6 7.7E-05 37.2 5.7 94 93-198 163-263 (315)
6 PLN02628 fructose-1,6-bisphosp 78.0 5.4 0.00012 37.2 5.7 82 91-180 190-278 (351)
7 PLN02262 fructose-1,6-bisphosp 77.8 4.4 9.6E-05 37.3 5.1 100 87-198 176-282 (340)
8 COG0158 Fbp Fructose-1,6-bisph 74.5 8.8 0.00019 36.0 6.1 102 86-198 161-270 (326)
9 PRK02079 pyrroloquinoline quin 58.9 5.1 0.00011 30.2 1.1 78 92-180 9-87 (88)
10 PLN02462 sedoheptulose-1,7-bis 48.0 37 0.0008 31.0 5.0 41 155-198 208-248 (304)
11 TIGR03859 PQQ_PqqD coenzyme PQ 44.9 20 0.00043 26.0 2.3 76 92-178 4-80 (81)
12 PF03705 CheR_N: CheR methyltr 44.7 39 0.00085 22.0 3.5 22 136-157 3-24 (57)
13 KOG1458 Fructose-1,6-bisphosph 39.1 26 0.00057 33.2 2.7 49 139-188 235-283 (343)
14 PF01764 Lipase_3: Lipase (cla 38.1 26 0.00057 25.3 2.1 61 132-197 45-107 (140)
15 PF08820 DUF1803: Domain of un 35.7 28 0.00061 27.2 2.0 39 141-180 15-59 (93)
16 cd00707 Pancreat_lipase_like P 34.9 19 0.00041 30.7 1.0 36 156-192 87-122 (275)
17 KOG4569 Predicted lipase [Lipi 34.5 30 0.00065 30.9 2.2 64 126-198 150-215 (336)
18 KOG0703 Predicted GTPase-activ 34.0 57 0.0012 30.1 3.9 73 86-176 47-121 (287)
19 PF00673 Ribosomal_L5_C: ribos 31.4 21 0.00045 27.0 0.7 37 157-195 7-51 (95)
20 PF08535 KorB: KorB domain; I 30.7 65 0.0014 23.4 3.1 43 126-179 1-43 (93)
21 PRK13656 trans-2-enoyl-CoA red 29.5 15 0.00034 34.8 -0.4 36 162-199 198-234 (398)
22 cd07477 Peptidases_S8_Subtilis 28.9 46 0.00099 26.2 2.2 12 184-195 97-108 (229)
23 PLN02324 triacylglycerol lipas 28.5 74 0.0016 30.5 3.8 64 132-198 194-267 (415)
24 cd04865 LigD_Pol_like_2 LigD_P 28.3 69 0.0015 28.4 3.4 34 112-147 97-130 (228)
25 PF13596 PAS_10: PAS domain; P 28.1 23 0.00049 24.9 0.3 59 115-177 9-67 (106)
26 PF03945 Endotoxin_N: delta en 28.0 37 0.0008 27.4 1.6 42 127-169 33-74 (226)
27 PRK00098 GTPase RsgA; Reviewed 27.8 1.6E+02 0.0034 25.7 5.4 76 90-180 204-279 (298)
28 PF14468 DUF4427: Protein of u 26.8 45 0.00098 28.0 1.9 58 130-187 2-68 (132)
29 PF12395 DUF3658: Protein of u 26.7 1E+02 0.0022 23.5 3.7 22 166-187 85-106 (111)
30 KOG4529 Uncharacterized conser 25.8 39 0.00085 32.6 1.6 19 133-151 294-312 (404)
31 PF06003 SMN: Survival motor n 25.2 39 0.00085 29.7 1.3 23 124-146 4-30 (264)
32 PHA02560 FI major tail sheath 25.1 1.4E+02 0.0031 27.5 4.9 61 118-178 273-333 (388)
33 cd04861 LigD_Pol_like LigD_Pol 25.0 87 0.0019 27.8 3.4 33 113-147 97-129 (227)
34 PF03799 FtsQ: Cell division p 24.9 41 0.00089 23.6 1.2 44 115-158 70-116 (117)
35 PLN02454 triacylglycerol lipas 24.7 90 0.002 29.9 3.7 72 122-198 198-273 (414)
36 KOG0553 TPR repeat-containing 24.6 20 0.00044 33.2 -0.5 28 116-145 173-200 (304)
37 cd08768 Cdc6_C Winged-helix do 24.1 1.1E+02 0.0024 21.1 3.2 35 132-166 23-57 (87)
38 cd04864 LigD_Pol_like_1 LigD_P 23.6 1.6E+02 0.0035 26.2 4.8 33 112-147 98-130 (228)
39 PF04984 Phage_sheath_1: Phage 23.4 56 0.0012 28.5 2.0 47 133-179 376-422 (464)
40 COG4782 Uncharacterized protei 23.4 51 0.0011 31.5 1.8 42 149-193 156-202 (377)
41 cd08051 gp6_gp15_like Head-Tai 23.1 1.8E+02 0.0039 22.0 4.4 54 119-176 7-60 (94)
42 PF13959 DUF4217: Domain of un 22.3 88 0.0019 21.9 2.4 55 137-198 2-62 (65)
43 KOG0698 Serine/threonine prote 22.2 53 0.0011 29.1 1.6 49 76-141 211-270 (330)
44 PLN02753 triacylglycerol lipas 22.1 87 0.0019 31.1 3.1 66 132-198 288-361 (531)
45 PLN02719 triacylglycerol lipas 21.5 1E+02 0.0022 30.6 3.4 66 132-198 274-347 (518)
46 cd04863 MtLigD_Pol_like MtLigD 21.2 60 0.0013 28.9 1.7 34 112-147 100-133 (231)
47 PF09457 RBD-FIP: FIP domain ; 21.2 54 0.0012 22.9 1.2 13 163-175 24-36 (48)
48 PF13426 PAS_9: PAS domain; PD 20.9 84 0.0018 20.2 2.0 58 118-178 4-61 (104)
49 KOG2861 Uncharacterized conser 20.8 79 0.0017 30.3 2.5 50 125-175 316-365 (399)
50 KOG4384 Uncharacterized SAM do 20.6 64 0.0014 30.8 1.8 17 158-176 222-238 (361)
51 PF02268 TFIIA_gamma_N: Transc 20.5 29 0.00063 24.4 -0.3 29 160-188 10-38 (49)
52 KOG1149 Glutamyl-tRNA syntheta 20.4 17 0.00037 35.9 -1.9 37 84-126 244-280 (524)
53 TIGR02778 ligD_pol DNA polymer 20.4 1.2E+02 0.0026 27.2 3.4 33 113-147 113-145 (245)
No 1
>PF10664 NdhM: Cyanobacterial and plastid NDH-1 subunit M; InterPro: IPR018922 The NADH dehydrogenase I complex shuttles electrons from an unknown electron donor, via FMN and iron-sulphur (Fe-S) centres, to quinones in the respiratory and/or the photosynthetic chain. The immediate electron acceptor for the enzyme in plants is believed to be plastoquinone. The NADH dehydrogenase I complex couples the redox reaction to proton translocation, and thus conserves the redox energy in a proton gradient. This entry represents subunit M of the NADH dehydrogenase I complex in cyanobacteria and plant chloroplasts []. ; GO: 0016655 oxidoreductase activity, acting on NADH or NADPH, quinone or similar compound as acceptor, 0055114 oxidation-reduction process
Probab=100.00 E-value=7.6e-73 Score=442.44 Aligned_cols=107 Identities=55% Similarity=0.912 Sum_probs=105.8
Q ss_pred cccccceEEEEEEEecCCCcccCcccCceeEEecCCCCccccChHHHHHHHHHHHHHHhhccCCCCChhhhhhhccchHH
Q 028327 88 LSCATRHVRIYAAYIDPETWEFDQTQMDKLTLILDPTKEFVWTDESCNKVFAYFQELVDHYEGALLTEYTLRLIGSDLEH 167 (210)
Q Consensus 88 LksTTRHVRIytA~i~~~~lv~~~tq~~~LTLdlDPDNEF~W~d~~l~kVy~~F~ELVe~y~G~~LteYnLRrIGSDLEh 167 (210)
|||||||||||||+|++++++|++ ++|||||||||||+|+|++|+|||++|+||||+|+|++|||||||||||||||
T Consensus 1 LksTTRHvrIftA~v~~~~lv~~~---~~LTLdlDPdNEF~W~~~~l~kVy~~F~eLVe~~~G~~LtdYnLRrIGSdLE~ 77 (108)
T PF10664_consen 1 LKSTTRHVRIFTAEVENNELVPSD---DKLTLDLDPDNEFNWNEEALQKVYRKFDELVESYAGEDLTDYNLRRIGSDLEH 77 (108)
T ss_pred CCcceeeEEEEEEEEecCceecCC---CeeEEecCCCcccccCHHHHHHHHHHHHHHHHhhcCCCchhhhHHHhccHHHH
Confidence 799999999999999999999997 99999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhcCccccccCCccccccCCCcccc
Q 028327 168 YIRKLLYDGEIKYNMDARVLNFSMGKPRIM 197 (210)
Q Consensus 168 fIR~LLq~GeisYNl~~RVlNySMGlPrv~ 197 (210)
|||+|||+|||||||+|||+|||||+|||+
T Consensus 78 ~iR~LLq~GeisYNl~~RVlNySMGlPr~~ 107 (108)
T PF10664_consen 78 FIRSLLQAGEISYNLDSRVLNYSMGLPRVP 107 (108)
T ss_pred HHHHHHHCCceeeCCCcceeccccCCCCCC
Confidence 999999999999999999999999999986
No 2
>PF00316 FBPase: Fructose-1-6-bisphosphatase; InterPro: IPR000146 This entry represents the fructose-1,6-bisphosphatase (FBPase) class 1 family. FBPase is a critical regulatory enzyme in gluconeogenesis that catalyses the removal of 1-phosphate from fructose 1,6-bis-phosphate to form fructose 6-phosphate [, ]. It is involved in many different metabolic pathways and found in most organisms. FBPase requires metal ions for catalysis (Mg2+ and Mn2+ being preferred) and the enzyme is potently inhibited by Li+. The fold of fructose-1,6-bisphosphatase was noted to be identical to that of inositol-1-phosphatase (IMPase) []. Inositol polyphosphate 1-phosphatase (IPPase), IMPase and FBPase share a sequence motif (Asp-Pro-Ile/Leu-Asp-Gly/Ser-Thr/Ser) which has been shown to bind metal ions and participate in catalysis. This motif is also found in the distantly-related fungal, bacterial and yeast IMPase homologues. It has been suggested that these proteins define an ancient structurally conserved family involved in diverse metabolic pathways, including inositol signalling, gluconeogenesis, sulphate assimilation and possibly quinone metabolism []. This entry also includes sedoheptulose-1,7-bisphosphatase, which is a member of the FBPase class 1 family.; GO: 0042578 phosphoric ester hydrolase activity, 0005975 carbohydrate metabolic process; PDB: 2GQ1_A 2QVR_A 2Q8M_B 2OX3_A 2OWZ_A 3KC0_C 2WBB_A 1FTA_C 2VT5_F 2Y5L_F ....
Probab=90.57 E-value=0.63 Score=42.48 Aligned_cols=102 Identities=23% Similarity=0.358 Sum_probs=66.2
Q ss_pred cccccccce-EEEEEEEecCCCcccCcccCceeEE-------ecCCCCccccChHHHHHHHHHHHHHHhhccCCCCChhh
Q 028327 86 QWLSCATRH-VRIYAAYIDPETWEFDQTQMDKLTL-------ILDPTKEFVWTDESCNKVFAYFQELVDHYEGALLTEYT 157 (210)
Q Consensus 86 ~lLksTTRH-VRIytA~i~~~~lv~~~tq~~~LTL-------dlDPDNEF~W~d~~l~kVy~~F~ELVe~y~G~~LteYn 157 (210)
+.|=-|+.+ |+.||-.-+.++++... ..+++ -++--|.-.|++. +.++.+++..-..|-. ..||
T Consensus 161 T~lV~t~g~gV~~FtLD~~~g~F~lt~---~~i~iP~~g~~ys~n~~n~~~w~~~----~~~yi~~~~~g~~~~~-~~y~ 232 (324)
T PF00316_consen 161 TMLVLTTGSGVHGFTLDPSTGEFVLTH---PNIRIPEKGKIYSINESNARHWDPP----YRAYIDYCKAGKEGPR-KKYS 232 (324)
T ss_dssp EEEEEECTTEEEEEEEETTTTEEEEEE---ESE---SSSSEEES-GGGGGGCTHH----HHHHHHHHHS-TTSST-CT-E
T ss_pred eEEEEEECCcEeEEEEeCCCCEEEEec---CceeecCCCcEeccCccccccCChH----HHHHHHHHhcCCCCCC-cccc
Confidence 344444554 89998877777777654 34444 2333355667654 3344455554445544 8999
Q ss_pred hhhhccchHHHHHHHHhcCccccccCCccccccCCCccccc
Q 028327 158 LRLIGSDLEHYIRKLLYDGEIKYNMDARVLNFSMGKPRIMF 198 (210)
Q Consensus 158 LRrIGSDLEhfIR~LLq~GeisYNl~~RVlNySMGlPrv~~ 198 (210)
||.|||=.-.|-|-|++-|--.|-.+.+ +.=|+=|.-+
T Consensus 233 ~RY~GsmVaD~HRiL~~GGif~YP~d~~---~~~GKLRlLY 270 (324)
T PF00316_consen 233 LRYIGSMVADVHRILLKGGIFLYPADKK---YPNGKLRLLY 270 (324)
T ss_dssp EEB-SSHHHHHHHHHHHTCEEEE-SBSS---BTTCSSBTTT
T ss_pred ceecCccchhHHHHHhhCcEEECCCCCC---CCCCceeEEE
Confidence 9999999999999999999999988888 7777777654
No 3
>PLN02542 fructose-1,6-bisphosphatase
Probab=90.46 E-value=0.54 Score=44.55 Aligned_cols=84 Identities=25% Similarity=0.382 Sum_probs=57.1
Q ss_pred cceEEEEEEEecCCCcccCcccCceeE-------EecCCCCccccChHHHHHHHHHHHHHHhhccCCCCChhhhhhhccc
Q 028327 92 TRHVRIYAAYIDPETWEFDQTQMDKLT-------LILDPTKEFVWTDESCNKVFAYFQELVDHYEGALLTEYTLRLIGSD 164 (210)
Q Consensus 92 TRHVRIytA~i~~~~lv~~~tq~~~LT-------LdlDPDNEF~W~d~~l~kVy~~F~ELVe~y~G~~LteYnLRrIGSD 164 (210)
-.=|++||-.-..++++... ..++ .-+++-|.-.|++ .+-++.+++.+ .|..=.+|++|.|||=
T Consensus 258 G~GV~~FtLDp~~geFvLt~---~~i~IP~~g~iySiN~~N~~~W~~----~~~~yi~~~~~--~~~~gk~ys~RYiGSm 328 (412)
T PLN02542 258 GTGVFSFTLDPMYGEFVLTQ---ENIQIPKAGKIYSFNEGNYQLWDD----KLKKYIDDLKD--PGPSGKPYSARYIGSL 328 (412)
T ss_pred CCCEEEEEEcCCCCeEEEeC---CCeeeCCCCcEeeeCcccccccCH----HHHHHHHHHhh--CCCCCCCCcceeeeec
Confidence 34678888554445666553 3333 3478899999985 44455555553 2222346999999999
Q ss_pred hHHHHHHHHhcCccccccCC
Q 028327 165 LEHYIRKLLYDGEIKYNMDA 184 (210)
Q Consensus 165 LEhfIR~LLq~GeisYNl~~ 184 (210)
.-.|-|-||+-|--.|--+.
T Consensus 329 VaDvHRiLl~GGIF~YP~d~ 348 (412)
T PLN02542 329 VGDFHRTLLYGGIYGYPRDK 348 (412)
T ss_pred hHHHHHHhhcCeEEecCCCC
Confidence 99999999997777775553
No 4
>PRK09293 fructose-1,6-bisphosphatase; Provisional
Probab=81.84 E-value=2.8 Score=38.04 Aligned_cols=53 Identities=32% Similarity=0.486 Sum_probs=37.4
Q ss_pred HHHhhccCCCCChhhhhhhccchHHHHHHHHhcCccccccCCccccccCCCccccc
Q 028327 143 ELVDHYEGALLTEYTLRLIGSDLEHYIRKLLYDGEIKYNMDARVLNFSMGKPRIMF 198 (210)
Q Consensus 143 ELVe~y~G~~LteYnLRrIGSDLEhfIR~LLq~GeisYNl~~RVlNySMGlPrv~~ 198 (210)
++...-.|.--.+||+|.|||=.-.+=|-|++-|--.|-.+ -.+.=|+=|..+
T Consensus 219 ~~~~~~~~~~~~~y~~Ry~gsmVaD~hr~L~~GGif~YP~~---~~~~~GkLRlly 271 (327)
T PRK09293 219 ELLAGKDGPRGRPYNMRYIGSMVADVHRILLKGGIFLYPAD---EPYPNGKLRLLY 271 (327)
T ss_pred HHhccccccCCCCCCceeeeeehHHHhHHhhcCeEEEcCCC---CCCCCCcEEEEe
Confidence 33333334445789999999999999999999998888666 233345555543
No 5
>cd00354 FBPase Fructose-1,6-bisphosphatase, an enzyme that catalyzes the hydrolysis of fructose-1,6-biphosphate into fructose-6-phosphate and is critical in gluconeogenesis pathway. The alignment model also includes chloroplastic FBPases and sedoheptulose-1,7-biphosphatases that play a role in pentose phosphate pathway (Calvin cycle).
Probab=81.72 E-value=3.6 Score=37.20 Aligned_cols=94 Identities=21% Similarity=0.352 Sum_probs=59.0
Q ss_pred ceEEEEEEEecCCCcccCcccCceeEE-----e--cCCCCccccChHHHHHHHHHHHHHHhhccCCCCChhhhhhhccch
Q 028327 93 RHVRIYAAYIDPETWEFDQTQMDKLTL-----I--LDPTKEFVWTDESCNKVFAYFQELVDHYEGALLTEYTLRLIGSDL 165 (210)
Q Consensus 93 RHVRIytA~i~~~~lv~~~tq~~~LTL-----d--lDPDNEF~W~d~~l~kVy~~F~ELVe~y~G~~LteYnLRrIGSDL 165 (210)
.=|+.||-.-.-++++... ..+++ . ++.-|.-.|++. +.++.+++...-+| =.+|++|.|||=.
T Consensus 163 ~gv~~ftld~~~g~f~lt~---~~~~ip~~~~~ys~n~~n~~~w~~~----~~~yi~~~~~~~~~--~~~y~~Ry~gsmV 233 (315)
T cd00354 163 QGVHGFTLDPSLGEFILTH---PNVKIPKKGKIYSINEGNYRYWDEP----VKKYIDDCKAGEDG--GKPYNLRYIGSMV 233 (315)
T ss_pred CceEEEEEcCCCCeEEEec---CCceeCCCCCEECCCCcchhcCCHH----HHHHHHHHhccccC--CCCccceeeeeee
Confidence 3466776543345666553 22333 2 233377778763 34444444443333 2469999999999
Q ss_pred HHHHHHHHhcCccccccCCccccccCCCccccc
Q 028327 166 EHYIRKLLYDGEIKYNMDARVLNFSMGKPRIMF 198 (210)
Q Consensus 166 EhfIR~LLq~GeisYNl~~RVlNySMGlPrv~~ 198 (210)
-.+-|-|++-|--.|-.+.+ +.=|+=|..+
T Consensus 234 aD~hr~L~~GGif~yP~~~~---~~~gkLRlly 263 (315)
T cd00354 234 ADVHRILVRGGIFLYPADKK---SPKGKLRLLY 263 (315)
T ss_pred hHhHHhhhcCeEEEccCCCC---CCCCcEeeee
Confidence 99999999888888877766 5556666544
No 6
>PLN02628 fructose-1,6-bisphosphatase family protein
Probab=78.00 E-value=5.4 Score=37.17 Aligned_cols=82 Identities=15% Similarity=0.255 Sum_probs=51.1
Q ss_pred ccceEEEEEEEecCCCcccCcccCceeEEe-------cCCCCccccChHHHHHHHHHHHHHHhhccCCCCChhhhhhhcc
Q 028327 91 ATRHVRIYAAYIDPETWEFDQTQMDKLTLI-------LDPTKEFVWTDESCNKVFAYFQELVDHYEGALLTEYTLRLIGS 163 (210)
Q Consensus 91 TTRHVRIytA~i~~~~lv~~~tq~~~LTLd-------lDPDNEF~W~d~~l~kVy~~F~ELVe~y~G~~LteYnLRrIGS 163 (210)
+-.-|+.||-.-..++++... ..+++- ++=-|...|.+.. .++.+++.. -.|..-..||+|.|||
T Consensus 190 ~g~gv~~Ftld~~~geF~lt~---~~i~ip~~g~iys~n~~n~~~W~~~~----~~yi~~~~~-g~~~~~k~y~~Ry~Gs 261 (351)
T PLN02628 190 FGSGTHGFTLDHSTGEFVLTH---PDIKIPERGQIYSVNDARYFDWPEGL----RKYIDTVRQ-GKGQYPKKYSARYICS 261 (351)
T ss_pred ECCCeeEEEEeCCCCEEEEeC---CceeeCCCCCEeCCCCcccccCCHHH----HHHHHHHhc-ccCCCCCCccceeeee
Confidence 334567777554455665553 333332 4445677887543 223333332 2233356799999999
Q ss_pred chHHHHHHHHhcCcccc
Q 028327 164 DLEHYIRKLLYDGEIKY 180 (210)
Q Consensus 164 DLEhfIR~LLq~GeisY 180 (210)
=.-.+-|-|++-|--.|
T Consensus 262 mVaD~Hr~L~~GGif~Y 278 (351)
T PLN02628 262 LVADLHRTILYGGIAMN 278 (351)
T ss_pred chHHHHHHhhcCeEEEC
Confidence 99999999999776666
No 7
>PLN02262 fructose-1,6-bisphosphatase
Probab=77.84 E-value=4.4 Score=37.34 Aligned_cols=100 Identities=19% Similarity=0.296 Sum_probs=59.9
Q ss_pred ccccccceEEEEEEEecCCCcccCcccCceeEE-------ecCCCCccccChHHHHHHHHHHHHHHhhccCCCCChhhhh
Q 028327 87 WLSCATRHVRIYAAYIDPETWEFDQTQMDKLTL-------ILDPTKEFVWTDESCNKVFAYFQELVDHYEGALLTEYTLR 159 (210)
Q Consensus 87 lLksTTRHVRIytA~i~~~~lv~~~tq~~~LTL-------dlDPDNEF~W~d~~l~kVy~~F~ELVe~y~G~~LteYnLR 159 (210)
|.=++-.-|+.||-.-..++++... ..+++ -++.-|.-.|++. ++ ++.+++...-.| ...||+|
T Consensus 176 lV~t~g~gv~~Ftld~~~gef~lt~---~~i~ip~~~~~ys~N~~n~~~w~~~-~~---~yi~~~~~~~~~--~~~~~~R 246 (340)
T PLN02262 176 LVLSTGGGVNGFTLDPSLGEFILTH---PDIKIPKKGKIYSVNEGNAKNWDGP-TA---KYVEKCKFPKDG--SSPKSLR 246 (340)
T ss_pred EEEEeCCCeeEEEEcCCCCEEEEeC---CCceeCCCCCEeccCccchhhcCHH-HH---HHHHHHhhcccC--CCCCCce
Confidence 3334445678888544445666553 23333 3455677778765 22 223333322233 4679999
Q ss_pred hhccchHHHHHHHHhcCccccccCCccccccCCCccccc
Q 028327 160 LIGSDLEHYIRKLLYDGEIKYNMDARVLNFSMGKPRIMF 198 (210)
Q Consensus 160 rIGSDLEhfIR~LLq~GeisYNl~~RVlNySMGlPrv~~ 198 (210)
.|||=.-.|-|-|++-|--.|-.+. .+.=|+=|..+
T Consensus 247 y~gsmVaD~hriL~~GGif~YP~d~---~~~~GkLRlly 282 (340)
T PLN02262 247 YIGSMVADVHRTLLYGGIFLYPADK---KSPNGKLRVLY 282 (340)
T ss_pred eeeechHHHHHHHhcCeEEeccCCC---CCCCCcEEEEe
Confidence 9999999999999997777775553 23335545443
No 8
>COG0158 Fbp Fructose-1,6-bisphosphatase [Carbohydrate transport and metabolism]
Probab=74.53 E-value=8.8 Score=35.98 Aligned_cols=102 Identities=21% Similarity=0.344 Sum_probs=66.9
Q ss_pred cccccccce-EEEEEEEecCCCcccCcccCceeE-------EecCCCCccccChHHHHHHHHHHHHHHhhccCCCCChhh
Q 028327 86 QWLSCATRH-VRIYAAYIDPETWEFDQTQMDKLT-------LILDPTKEFVWTDESCNKVFAYFQELVDHYEGALLTEYT 157 (210)
Q Consensus 86 ~lLksTTRH-VRIytA~i~~~~lv~~~tq~~~LT-------LdlDPDNEF~W~d~~l~kVy~~F~ELVe~y~G~~LteYn 157 (210)
+.|=-|+-| |+.||-.-..++++.+. ..+. .-+.--|---|++ .|-++-+++-+.-.|.- -.||
T Consensus 161 t~LV~t~g~gV~~ftld~~~G~F~lt~---~ni~iP~~~~iyain~gn~~~w~~----~v~~yI~~~~~~~~~~~-r~y~ 232 (326)
T COG0158 161 TMLVYTLGEGVHGFTLDPSLGEFILTH---ENIRIPEKGKIYAINEGNQRHWEE----GVKKYIKDCFAEDKGTR-RPYN 232 (326)
T ss_pred eEEEEEeCCceEEEEEcCCCCEEEEec---cccccCCCCceeeeCCcccccccH----HHHHHHHHHhccCCCcC-CCcc
Confidence 445555556 88887655555554442 2222 2333345566775 34555566666666655 9999
Q ss_pred hhhhccchHHHHHHHHhcCccccccCCccccccCCCccccc
Q 028327 158 LRLIGSDLEHYIRKLLYDGEIKYNMDARVLNFSMGKPRIMF 198 (210)
Q Consensus 158 LRrIGSDLEhfIR~LLq~GeisYNl~~RVlNySMGlPrv~~ 198 (210)
+|.|||=.-.+=|-|++-|--.|--+.|-. -|+=|..+
T Consensus 233 ~RyigSmVADvHRiL~~GGiF~YP~~~~~P---~GKLRllY 270 (326)
T COG0158 233 MRYIGSMVADVHRILLKGGIFLYPSDKRAP---NGKLRLLY 270 (326)
T ss_pred hhhHHHHHHHHHHHHHcCceEeccccCCCC---CCceeeee
Confidence 999999999999999998888897666654 35555444
No 9
>PRK02079 pyrroloquinoline quinone biosynthesis protein PqqD; Provisional
Probab=58.90 E-value=5.1 Score=30.25 Aligned_cols=78 Identities=10% Similarity=0.016 Sum_probs=48.4
Q ss_pred cceEEEEEEEecCCCcccCcccCceeEEecCCCCccccCh-HHHHHHHHHHHHHHhhccCCCCChhhhhhhccchHHHHH
Q 028327 92 TRHVRIYAAYIDPETWEFDQTQMDKLTLILDPTKEFVWTD-ESCNKVFAYFQELVDHYEGALLTEYTLRLIGSDLEHYIR 170 (210)
Q Consensus 92 TRHVRIytA~i~~~~lv~~~tq~~~LTLdlDPDNEF~W~d-~~l~kVy~~F~ELVe~y~G~~LteYnLRrIGSDLEhfIR 170 (210)
.||+|+=-=.+.+.-...-+ .. .+.||..--|+|.- +--..|..==+.|-+.|.+.+ .|..|+..||.
T Consensus 9 ~~~~rl~~d~~~~~~vlL~P---Eg-mi~Lnetg~~Iw~~~DG~~tv~eIi~~L~~~y~~~~-------~~~~DV~~fl~ 77 (88)
T PRK02079 9 RPGYRFQWEPAQNCHVLLYP---EG-MIKLNESAGEILGLIDGKRTVAAIIAELQQQFPDVP-------GLDEDVLEFLE 77 (88)
T ss_pred CCCcccccccccCceEEEcC---Ce-eeeechHHHHHHHHccCCCCHHHHHHHHHHHccchh-------hHHHHHHHHHH
Confidence 46666655455554433333 11 47788899999964 111233333445555664442 27799999999
Q ss_pred HHHhcCcccc
Q 028327 171 KLLYDGEIKY 180 (210)
Q Consensus 171 ~LLq~GeisY 180 (210)
.|..+|-|.|
T Consensus 78 ~L~~~g~i~~ 87 (88)
T PRK02079 78 VARAKHWIEL 87 (88)
T ss_pred HHHHCcCEEe
Confidence 9999998875
No 10
>PLN02462 sedoheptulose-1,7-bisphosphatase
Probab=48.04 E-value=37 Score=31.02 Aligned_cols=41 Identities=24% Similarity=0.374 Sum_probs=28.9
Q ss_pred hhhhhhhccchHHHHHHHHhcCccccccCCccccccCCCccccc
Q 028327 155 EYTLRLIGSDLEHYIRKLLYDGEIKYNMDARVLNFSMGKPRIMF 198 (210)
Q Consensus 155 eYnLRrIGSDLEhfIR~LLq~GeisYNl~~RVlNySMGlPrv~~ 198 (210)
+||+|.|||=.-.+-|-|++-|=|-.+|... .+=|+=|..+
T Consensus 208 ~y~~Ry~gsmVaD~hriL~~gGGif~yP~~~---~~~GkLRlly 248 (304)
T PLN02462 208 KYTLRYTGGMVPDVYQIIVKEKGVFTNVTSP---KSKAKLRLLF 248 (304)
T ss_pred CCCceeeccchHHHHHhhhhCCeEEECCCCC---CCCCcEeeee
Confidence 6999999999999999999955554444331 1346655443
No 11
>TIGR03859 PQQ_PqqD coenzyme PQQ biosynthesis protein PqqD. This model identifies PqqD, a protein involved in the final steps of the biosynthesis of pyrroloquinoline quinone, coenzyme PQQ.
Probab=44.87 E-value=20 Score=26.02 Aligned_cols=76 Identities=12% Similarity=0.046 Sum_probs=52.1
Q ss_pred cceEEEEEEEecCCCcccCcccCceeEEecCCCCccccCh-HHHHHHHHHHHHHHhhccCCCCChhhhhhhccchHHHHH
Q 028327 92 TRHVRIYAAYIDPETWEFDQTQMDKLTLILDPTKEFVWTD-ESCNKVFAYFQELVDHYEGALLTEYTLRLIGSDLEHYIR 170 (210)
Q Consensus 92 TRHVRIytA~i~~~~lv~~~tq~~~LTLdlDPDNEF~W~d-~~l~kVy~~F~ELVe~y~G~~LteYnLRrIGSDLEhfIR 170 (210)
-||+|+=.-.+.+.-.+.++ .. .+.||+.--|+|.- +-=..|..=-+.|.+.|...+ .+-.|+..|+.
T Consensus 4 ~~~~r~~~~~v~~~~Vl~~p---~~-~~~Ln~~g~~Iw~lldg~~tv~eI~~~L~~~Y~~~e-------~~~~dV~~fL~ 72 (81)
T TIGR03859 4 RRGYRLQWERAQDCYVLLYP---EG-MVKLNDSAGEILELCDGKRSLAEIIQELAQRFPAAE-------EIEDDVIAFLA 72 (81)
T ss_pred CCCeeeeeccccCcEEEEcC---Cc-eeeeChHHHHHHHHccCCCcHHHHHHHHHHHcCChh-------hHHHHHHHHHH
Confidence 47999988888888777776 22 57889999999963 111123333345566665421 34589999999
Q ss_pred HHHhcCcc
Q 028327 171 KLLYDGEI 178 (210)
Q Consensus 171 ~LLq~Gei 178 (210)
+|..+|-|
T Consensus 73 ~L~~~gli 80 (81)
T TIGR03859 73 VARAKHWL 80 (81)
T ss_pred HHHHCcCc
Confidence 99998865
No 12
>PF03705 CheR_N: CheR methyltransferase, all-alpha domain; InterPro: IPR022641 CheR proteins are part of the chemotaxis signaling mechanism which methylates the chemotaxis receptor at specific glutamate residues. This entry refers to the N-terminal domain of the CherR-type MCP methyltransferases, which are found in bacteria, archaea and green plants. This entry is found in association with PF01739 from PFAM. Methyl transfer from the ubiquitous S-adenosyl-L-methionine (AdoMet) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms ranging from bacteria to plants and mammals. The reaction is catalysed by methyltransferases (Mtases) and modifies DNA, RNA, proteins and small molecules, such as catechol for regulatory purposes. The various aspects of the role of DNA methylation in prokaryotic restriction-modification systems and in a number of cellular processes in eukaryotes including gene regulation and differentiation is well documented. Three classes of DNA Mtases transfer the methyl group from AdoMet to the target base to form either N-6-methyladenine, or N-4-methylcytosine, or C-5- methylcytosine. In C-5-cytosine Mtases, ten conserved motifs are arranged in the same order []. Motif I (a glycine-rich or closely related consensus sequence; FAGxGG in M.HhaI []), shared by other AdoMet-Mtases [], is part of the cofactor binding site and motif IV (PCQ) is part of the catalytic site. In contrast, sequence comparison among N-6-adenine and N-4-cytosine Mtases indicated two of the conserved segments [], although more conserved segments may be present. One of them corresponds to motif I in C-5-cytosine Mtases, and the other is named (D/N/S)PP(Y/F). Crystal structures are known for a number of Mtases [, , , ]. The cofactor binding sites are almost identical and the essential catalytic amino acids coincide. The comparable protein folding and the existence of equivalent amino acids in similar secondary and tertiary positions indicate that many (if not all) AdoMet-Mtases have a common catalytic domain structure. This permits tertiary structure prediction of other DNA, RNA, protein, and small-molecule AdoMet-Mtases from their amino acid sequences []. Flagellated bacteria swim towards favourable chemicals and away from deleterious ones. Sensing of chemoeffector gradients involves chemotaxis receptors, transmembrane (TM) proteins that detect stimuli through their periplasmic domains and transduce the signals via their cytoplasmic domains []. Signalling outputs from these receptors are influenced both by the binding of the chemoeffector ligand to their periplasmic domains and by methylation of specific glutamate residues on their cytoplasmic domains. Methylation is catalysed by CheR, an S-adenosylmethionine-dependent methyltransferase [], which reversibly methylates specific glutamate residues within a coiled coil region, to form gamma-glutamyl methyl ester residues [, ]. The structure of the Salmonella typhimurium chemotaxis receptor methyltransferase CheR, bound to S-adenosylhomocysteine, has been determined to a resolution of 2.0 A []. The structure reveals CheR to be a two-domain protein, with a smaller N-terminal helical domain linked via a single polypeptide connection to a larger C-terminal alpha/beta domain. The C-terminal domain has the characteristics of a nucleotide-binding fold, with an insertion of a small anti-parallel beta-sheet subdomain. The S-adenosylhomocysteine-binding site is formed mainly by the large domain, with contributions from residues within the N-terminal domain and the linker region [].; PDB: 1AF7_A 1BC5_A.
Probab=44.68 E-value=39 Score=21.95 Aligned_cols=22 Identities=36% Similarity=0.558 Sum_probs=15.3
Q ss_pred HHHHHHHHHHhhccCCCCChhh
Q 028327 136 KVFAYFQELVDHYEGALLTEYT 157 (210)
Q Consensus 136 kVy~~F~ELVe~y~G~~LteYn 157 (210)
.-|.+|.++|....|-+|++|.
T Consensus 3 ~~f~~~~~~i~~~~Gi~l~~~K 24 (57)
T PF03705_consen 3 AEFERFRELIYRRTGIDLSEYK 24 (57)
T ss_dssp HHHHHHHHHHHHHH-----GGG
T ss_pred HHHHHHHHHHHHHHCCCCchhh
Confidence 4588999999999999999998
No 13
>KOG1458 consensus Fructose-1,6-bisphosphatase [Carbohydrate transport and metabolism]
Probab=39.08 E-value=26 Score=33.17 Aligned_cols=49 Identities=24% Similarity=0.334 Sum_probs=38.0
Q ss_pred HHHHHHHhhccCCCCChhhhhhhccchHHHHHHHHhcCccccccCCcccc
Q 028327 139 AYFQELVDHYEGALLTEYTLRLIGSDLEHYIRKLLYDGEIKYNMDARVLN 188 (210)
Q Consensus 139 ~~F~ELVe~y~G~~LteYnLRrIGSDLEhfIR~LLq~GeisYNl~~RVlN 188 (210)
++|-+.+.-+.+..- -|.+|.|||=.-++=|-||+-|-+-|+.+..-.|
T Consensus 235 ~~Yi~~~k~p~~~~~-pysaRYvGSMVaDvHRTllyGGif~yP~~~~spn 283 (343)
T KOG1458|consen 235 TEYIDKKKYPKKGKK-PYSARYVGSMVADVHRTLLYGGIFLYPADKKSPN 283 (343)
T ss_pred HHHHHhhhccCCCCC-CcceeeeccchhhhhhhheeCcEEeccCCCCCCC
Confidence 345555655544333 8999999999999999999999999998865443
No 14
>PF01764 Lipase_3: Lipase (class 3); InterPro: IPR002921 Triglyceride lipases are lipolytic enzymes that hydrolyse ester linkages of triglycerides []. Lipases are widely distributed in animals, plants and prokaryotes. This family of lipases have been called Class 3 as they are not closely related to other lipase families.; GO: 0004806 triglyceride lipase activity, 0006629 lipid metabolic process; PDB: 1LGY_A 1DTE_A 1DT5_F 4DYH_B 1DU4_C 4EA6_B 1GT6_B 1EIN_A 1DT3_A 1TIB_A ....
Probab=38.08 E-value=26 Score=25.32 Aligned_cols=61 Identities=20% Similarity=0.401 Sum_probs=43.0
Q ss_pred HHHHHHHHHHHHHHhhccCCCCChhhhhhhccchHHHHHHHHhcCcccccc--CCccccccCCCcccc
Q 028327 132 ESCNKVFAYFQELVDHYEGALLTEYTLRLIGSDLEHYIRKLLYDGEIKYNM--DARVLNFSMGKPRIM 197 (210)
Q Consensus 132 ~~l~kVy~~F~ELVe~y~G~~LteYnLRrIGSDLEhfIR~LLq~GeisYNl--~~RVlNySMGlPrv~ 197 (210)
.....+...+.++++.|. +|+|--.|--|-+-|-.|+-.=-.+..+ ..++.-|++|-||+.
T Consensus 45 ~~~~~~~~~l~~~~~~~~-----~~~i~itGHSLGGalA~l~a~~l~~~~~~~~~~~~~~~fg~P~~~ 107 (140)
T PF01764_consen 45 SLYDQILDALKELVEKYP-----DYSIVITGHSLGGALASLAAADLASHGPSSSSNVKCYTFGAPRVG 107 (140)
T ss_dssp HHHHHHHHHHHHHHHHST-----TSEEEEEEETHHHHHHHHHHHHHHHCTTTSTTTEEEEEES-S--B
T ss_pred HHHHHHHHHHHHHHhccc-----CccchhhccchHHHHHHHHHHhhhhcccccccceeeeecCCcccc
Confidence 445677788888888887 5999999999999887776543222232 488889999999984
No 15
>PF08820 DUF1803: Domain of unknown function (DUF1803); InterPro: IPR014924 This small protein is found in one or two copies in bacteria. The function of this is unknown.
Probab=35.74 E-value=28 Score=27.20 Aligned_cols=39 Identities=31% Similarity=0.567 Sum_probs=33.7
Q ss_pred HHHHHhhccCCCCChhhhhhhccch------HHHHHHHHhcCcccc
Q 028327 141 FQELVDHYEGALLTEYTLRLIGSDL------EHYIRKLLYDGEIKY 180 (210)
Q Consensus 141 F~ELVe~y~G~~LteYnLRrIGSDL------EhfIR~LLq~GeisY 180 (210)
|.+|| .|+-.-.++.+||-|-.|. +.||..|.+.|=|.=
T Consensus 15 f~~Li-~Yl~k~~~~~lLR~iKk~f~~qk~~D~fie~li~~GYI~r 59 (93)
T PF08820_consen 15 FYDLI-NYLLKYMTDFLLRFIKKDFPKQKRLDIFIEALIKLGYIER 59 (93)
T ss_pred HHHHH-HHHHHcCCHhhHHHHHHhhccccchhHHHHHHHHcCCeEe
Confidence 88888 6777777999999998875 589999999999875
No 16
>cd00707 Pancreat_lipase_like Pancreatic lipase-like enzymes. Lipases are esterases that can hydrolyze long-chain acyl-triglycerides into di- and monoglycerides, glycerol, and free fatty acids at a water/lipid interface. A typical feature of lipases is "interfacial activation," the process of becoming active at the lipid/water interface, although several examples of lipases have been identified that do not undergo interfacial activation . The active site of a lipase contains a catalytic triad consisting of Ser - His - Asp/Glu, but unlike most serine proteases, the active site is buried inside the structure. A "lid" or "flap" covers the active site, making it inaccessible to solvent and substrates. The lid opens during the process of interfacial activation, allowing the lipid substrate access to the active site.
Probab=34.92 E-value=19 Score=30.72 Aligned_cols=36 Identities=17% Similarity=0.493 Sum_probs=24.6
Q ss_pred hhhhhhccchHHHHHHHHhcCccccccCCccccccCC
Q 028327 156 YTLRLIGSDLEHYIRKLLYDGEIKYNMDARVLNFSMG 192 (210)
Q Consensus 156 YnLRrIGSDLEhfIR~LLq~GeisYNl~~RVlNySMG 192 (210)
++++.+|.++..+|+.|.....+..+ +.-++-+|||
T Consensus 87 ~~~~~v~~~la~~l~~L~~~~g~~~~-~i~lIGhSlG 122 (275)
T cd00707 87 NNTRVVGAELAKFLDFLVDNTGLSLE-NVHLIGHSLG 122 (275)
T ss_pred HhHHHHHHHHHHHHHHHHHhcCCChH-HEEEEEecHH
Confidence 46788888888888888776422221 4566777777
No 17
>KOG4569 consensus Predicted lipase [Lipid transport and metabolism]
Probab=34.49 E-value=30 Score=30.93 Aligned_cols=64 Identities=20% Similarity=0.389 Sum_probs=47.9
Q ss_pred ccccChHHHHHHHHHHHHHHhhccCCCCChhhhhhhccchHHHHHHHHhcCccccc--cCCccccccCCCccccc
Q 028327 126 EFVWTDESCNKVFAYFQELVDHYEGALLTEYTLRLIGSDLEHYIRKLLYDGEIKYN--MDARVLNFSMGKPRIMF 198 (210)
Q Consensus 126 EF~W~d~~l~kVy~~F~ELVe~y~G~~LteYnLRrIGSDLEhfIR~LLq~GeisYN--l~~RVlNySMGlPrv~~ 198 (210)
...|+ ..+++.++.|++.|. +|.+=.-|-.|-+=+-.|.-..-+.=. ...+|--|+||.|||..
T Consensus 150 ~~~~~----~~~~~~~~~L~~~~~-----~~~i~vTGHSLGgAlA~laa~~i~~~~~~~~~~v~v~tFG~PRvGn 215 (336)
T KOG4569|consen 150 TSLWN----SGLDAELRRLIELYP-----NYSIWVTGHSLGGALASLAALDLVKNGLKTSSPVKVYTFGQPRVGN 215 (336)
T ss_pred ccccH----HHHHHHHHHHHHhcC-----CcEEEEecCChHHHHHHHHHHHHHHcCCCCCCceEEEEecCCCccc
Confidence 44566 678888999999998 777777888888877776544332222 46899999999999863
No 18
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=34.00 E-value=57 Score=30.09 Aligned_cols=73 Identities=26% Similarity=0.390 Sum_probs=46.3
Q ss_pred cccccccceEEEEEEEecCCCcccCcccCceeEEecCCCCccccChHHHHHHHHHHHHHHhhccCCCCChhhhhhhc-cc
Q 028327 86 QWLSCATRHVRIYAAYIDPETWEFDQTQMDKLTLILDPTKEFVWTDESCNKVFAYFQELVDHYEGALLTEYTLRLIG-SD 164 (210)
Q Consensus 86 ~lLksTTRHVRIytA~i~~~~lv~~~tq~~~LTLdlDPDNEF~W~d~~l~kVy~~F~ELVe~y~G~~LteYnLRrIG-SD 164 (210)
..|+|..-|--+.+ ..+ .++.++|| -|++|-++....-=..-+.+|--+.|-+ +.++-| +|
T Consensus 47 iC~~C~giHR~lg~--------hiS----kVkSv~LD-----~W~~eqv~~m~~~GN~~an~~~ea~~p~-~~~~p~~d~ 108 (287)
T KOG0703|consen 47 ICLRCAGIHRSLGV--------HIS----KVKSVTLD-----EWTDEQVDFMISMGNAKANSYYEAKLPD-PFRRPGPDD 108 (287)
T ss_pred EEeecccccccccc--------hhh----eeeeeecc-----ccCHHHHHHHHHHcchhhhhhccccCCc-cccCCChHH
Confidence 35789998887776 334 56777777 5999999887654444444444444443 233333 33
Q ss_pred -hHHHHHHHHhcC
Q 028327 165 -LEHYIRKLLYDG 176 (210)
Q Consensus 165 -LEhfIR~LLq~G 176 (210)
+|+|||.=...+
T Consensus 109 ~~e~FIR~KYE~k 121 (287)
T KOG0703|consen 109 LVEQFIRDKYERK 121 (287)
T ss_pred HHHHHHHHHHhhh
Confidence 899999754433
No 19
>PF00673 Ribosomal_L5_C: ribosomal L5P family C-terminus; InterPro: IPR002132 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L5, ~180 amino acids in length, is one of the proteins from the large ribosomal subunit. In Escherichia coli, L5 is known to be involved in binding 5S RNA to the large ribosomal subunit. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, , , ], groups: Eubacterial L5. Algal chloroplast L5. Cyanelle L5. Archaebacterial L5. Mammalian L11. Tetrahymena thermophila L21. Dictyostelium discoideum (Slime mold) L5 Saccharomyces cerevisiae (Baker's yeast) L16 (39A). Plant mitochondrial L5. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1IQ4_B 2ZJR_D 2ZJP_D 3PIO_D 3CF5_D 2ZJQ_D 3DLL_D 3PIP_D 2WDL_G 3UZN_G ....
Probab=31.44 E-value=21 Score=26.95 Aligned_cols=37 Identities=30% Similarity=0.373 Sum_probs=26.3
Q ss_pred hhhhhccchHHHHHHHHhc---C-----ccccccCCccccccCCCcc
Q 028327 157 TLRLIGSDLEHYIRKLLYD---G-----EIKYNMDARVLNFSMGKPR 195 (210)
Q Consensus 157 nLRrIGSDLEhfIR~LLq~---G-----eisYNl~~RVlNySMGlPr 195 (210)
||| |+....|+.+|+.. - .++.+.-..-=|||+|+.-
T Consensus 7 TLR--g~~m~~FL~kli~~vlPrik~f~g~~~~~fd~~Gn~sfGi~e 51 (95)
T PF00673_consen 7 TLR--GKKMYEFLDKLITIVLPRIKDFKGLKASSFDNSGNFSFGIKE 51 (95)
T ss_dssp EEE--HHHHHHHHHHHHHTTTTTSSSTSSBSSTTBSSSSEEEEEESS
T ss_pred EEc--cHHHHHHHHHHHHHhhhhcccccccCccccCCCceEEEEeee
Confidence 577 89999999999977 2 3444433344589999843
No 20
>PF08535 KorB: KorB domain; InterPro: IPR013741 This entry contains several KorB transcriptional repressor proteins. The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon []. This domain includes the DNA-binding HTH motif []. ; PDB: 1R71_C.
Probab=30.73 E-value=65 Score=23.41 Aligned_cols=43 Identities=35% Similarity=0.540 Sum_probs=21.9
Q ss_pred ccccChHHHHHHHHHHHHHHhhccCCCCChhhhhhhccchHHHHHHHHhcCccc
Q 028327 126 EFVWTDESCNKVFAYFQELVDHYEGALLTEYTLRLIGSDLEHYIRKLLYDGEIK 179 (210)
Q Consensus 126 EF~W~d~~l~kVy~~F~ELVe~y~G~~LteYnLRrIGSDLEhfIR~LLq~Geis 179 (210)
||.|+.+.|.+---+=.-.|..+ ||.+ ||-..|+.|+.+|.|+
T Consensus 1 ~~G~tq~eIA~~lGks~s~Vs~~---------l~Ll--~lP~~i~~~v~~g~~~ 43 (93)
T PF08535_consen 1 EFGWTQEEIAKRLGKSRSWVSNH---------LALL--DLPEEIKELVRSGRIS 43 (93)
T ss_dssp HTT--HHHHHHHTT--HHHHHHH---------HGGG--S--HHHHHHHHTTS--
T ss_pred CCCCCHHHHHHHHCCCHHHHHHH---------HHHH--cCCHHHHHHHHcCCCc
Confidence 57777777776655555555443 3333 5777777777777665
No 21
>PRK13656 trans-2-enoyl-CoA reductase; Provisional
Probab=29.48 E-value=15 Score=34.78 Aligned_cols=36 Identities=25% Similarity=0.286 Sum_probs=29.9
Q ss_pred ccchHHHHHHHHhcCccccccCCccccccC-CCcccccC
Q 028327 162 GSDLEHYIRKLLYDGEIKYNMDARVLNFSM-GKPRIMFN 199 (210)
Q Consensus 162 GSDLEhfIR~LLq~GeisYNl~~RVlNySM-GlPrv~~~ 199 (210)
|.|++-+|..|..+|-+ +.+|+++.||. |-.++-.+
T Consensus 198 gedw~~Wi~al~~a~ll--a~g~~~va~TY~G~~~t~p~ 234 (398)
T PRK13656 198 GEDWELWIDALDEAGVL--AEGAKTVAYSYIGPELTHPI 234 (398)
T ss_pred cchHHHHHHHHHhcccc--cCCcEEEEEecCCcceeecc
Confidence 67999999999999987 57899999998 66665443
No 22
>cd07477 Peptidases_S8_Subtilisin_subset Peptidase S8 family domain in Subtilisin proteins. This group is composed of many different subtilisins: Pro-TK-subtilisin, subtilisin Carlsberg, serine protease Pb92 subtilisin, and BPN subtilisins just to name a few. Pro-TK-subtilisin is a serine protease from the hyperthermophilic archaeon Thermococcus kodakaraensis and consists of a signal peptide, a propeptide, and a mature domain. TK-subtilisin is matured from pro-TK-subtilisin upon autoprocessing and degradation of the propeptide. Unlike other subtilisins though, the folding of the unprocessed form of pro-TK-subtilisin is induced by Ca2+ binding which is almost completed prior to autoprocessing. Ca2+ is required for activity unlike the bacterial subtilisins. The propeptide is not required for folding of the mature domain unlike the bacterial subtilases because of the stability produced from Ca2+ binding. Subtilisin Carlsberg is extremely similar in structure to subtilisin BPN'/Novo thoug
Probab=28.93 E-value=46 Score=26.24 Aligned_cols=12 Identities=33% Similarity=0.783 Sum_probs=10.2
Q ss_pred CccccccCCCcc
Q 028327 184 ARVLNFSMGKPR 195 (210)
Q Consensus 184 ~RVlNySMGlPr 195 (210)
+||+|+|+|.+.
T Consensus 97 ~~Vin~S~g~~~ 108 (229)
T cd07477 97 MDIINMSLGGPS 108 (229)
T ss_pred CCEEEECCccCC
Confidence 899999999764
No 23
>PLN02324 triacylglycerol lipase
Probab=28.55 E-value=74 Score=30.53 Aligned_cols=64 Identities=20% Similarity=0.348 Sum_probs=42.4
Q ss_pred HHHHHHHHHHHHHHhhccCCCCChhhhhhhccchHHHHHHHH-----hcCccc-----cccCCccccccCCCccccc
Q 028327 132 ESCNKVFAYFQELVDHYEGALLTEYTLRLIGSDLEHYIRKLL-----YDGEIK-----YNMDARVLNFSMGKPRIMF 198 (210)
Q Consensus 132 ~~l~kVy~~F~ELVe~y~G~~LteYnLRrIGSDLEhfIR~LL-----q~Geis-----YNl~~RVlNySMGlPrv~~ 198 (210)
.+-++|...+.+|++.|.++++ .+=-.|--|-+=|-.|. ..|.-+ .+..+.|.-|++|-|||..
T Consensus 194 SareqVl~eV~~L~~~Yp~e~~---sItvTGHSLGGALAtLaA~dl~~~~~n~~~~~~~~~~~~V~v~TFGsPRVGN 267 (415)
T PLN02324 194 SAQEQVQGELKRLLELYKNEEI---SITFTGHSLGAVMSVLSAADLVYGKKNKINISLQKKQVPITVFAFGSPRIGD 267 (415)
T ss_pred HHHHHHHHHHHHHHHHCCCCCc---eEEEecCcHHHHHHHHHHHHHHHhcccccccccccCCCceEEEEecCCCcCC
Confidence 5667899999999999987653 33355777766554432 122211 1235568889999999965
No 24
>cd04865 LigD_Pol_like_2 LigD_Pol_like_2: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD, subgroup 2. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The Pol domains of PaeLigD and Mycobacterium tuberculosis (Mt)LigD are stimulated by manganese, are error-prone, and prefer adding rNTPs to dNTPs in vitro; however PaeLigD and MtLigD belong to other subgroups, proteins in this subgroup await functional characterization.
Probab=28.33 E-value=69 Score=28.40 Aligned_cols=34 Identities=26% Similarity=0.397 Sum_probs=22.7
Q ss_pred ccCceeEEecCCCCccccChHHHHHHHHHHHHHHhh
Q 028327 112 TQMDKLTLILDPTKEFVWTDESCNKVFAYFQELVDH 147 (210)
Q Consensus 112 tq~~~LTLdlDPDNEF~W~d~~l~kVy~~F~ELVe~ 147 (210)
...|.|.+||||+.+.-|.+ |-.+=..-+|+.++
T Consensus 97 e~PD~lvfDLDP~~~~~f~~--v~~~A~~vr~~L~~ 130 (228)
T cd04865 97 DHPDELVIDLDPQPGTSFED--VVEVALLVREVLDE 130 (228)
T ss_pred CCCCEEEEECCCCCCCCHHH--HHHHHHHHHHHHHH
Confidence 34688999999998887754 34444444555543
No 25
>PF13596 PAS_10: PAS domain; PDB: 3CAX_A 2QKP_D.
Probab=28.07 E-value=23 Score=24.92 Aligned_cols=59 Identities=15% Similarity=0.161 Sum_probs=43.2
Q ss_pred ceeEEecCCCCccccChHHHHHHHHHHHHHHhhccCCCCChhhhhhhccchHHHHHHHHhcCc
Q 028327 115 DKLTLILDPTKEFVWTDESCNKVFAYFQELVDHYEGALLTEYTLRLIGSDLEHYIRKLLYDGE 177 (210)
Q Consensus 115 ~~LTLdlDPDNEF~W~d~~l~kVy~~F~ELVe~y~G~~LteYnLRrIGSDLEhfIR~LLq~Ge 177 (210)
+.=++-+|.|..+.|=..+..+++. +.+..-|.+|.+..-+..=.+++..|++++..++
T Consensus 9 ~~~i~~vD~~~~I~~~n~~a~~~f~----~~~~~iGr~l~~~~~~~~~~~l~~~i~~~~~~~~ 67 (106)
T PF13596_consen 9 PIGIIFVDRNLRIRYFNPAAARLFN----LSPSDIGRPLFDIHPPLSYPNLKKIIEQVRSGKE 67 (106)
T ss_dssp SSEEEEEETTSBEEEE-SCGC-SS-------GGGTTSBCCCSS-HHHHHHHHHHHHHHHTTSB
T ss_pred CCCEEEEcCCCeEEEeChhHhhhcC----CChHHCCCCHHHcCCccchHHHHHHHHHHHcCCC
Confidence 4456789999999987777776665 6788899999999888777888899988886553
No 26
>PF03945 Endotoxin_N: delta endotoxin, N-terminal domain; InterPro: IPR005639 This family contains insecticidal toxins produced by Bacillus species of bacteria. During spore formation the bacteria produce crystals of this protein. When an insect ingests these proteins, they are activated by proteolytic cleavage. The N terminus is cleaved in all of the proteins and a C-terminal extension is cleaved in some members. Once activated, the endotoxin binds to the gut epithelium and causes cell lysis by the formation of cation-selective channels, which leads to death. The activated region of the delta toxin is composed of three distinct structural domains: an N-terminal helical bundle domain involved in membrane insertion and pore formation; a beta-sheet central domain (IPR001178 from INTERPRO) involved in receptor binding; and a C-terminal beta-sandwich domain (IPR005638 from INTERPRO) that interacts with the N-terminal domain to form a channel [, ]. This entry represents the conserved N-terminal domain.; GO: 0009405 pathogenesis; PDB: 3EB7_A 1I5P_A 2C9K_A 1CIY_A 1JI6_A 1DLC_A 1W99_A.
Probab=28.03 E-value=37 Score=27.42 Aligned_cols=42 Identities=17% Similarity=0.441 Sum_probs=35.1
Q ss_pred cccChHHHHHHHHHHHHHHhhccCCCCChhhhhhhccchHHHH
Q 028327 127 FVWTDESCNKVFAYFQELVDHYEGALLTEYTLRLIGSDLEHYI 169 (210)
Q Consensus 127 F~W~d~~l~kVy~~F~ELVe~y~G~~LteYnLRrIGSDLEhfI 169 (210)
++|++..=. +++.|.+.|+..-.+.+++|....+.+.+++.-
T Consensus 33 ~lwp~~~~~-~~~~~~~~ve~lI~~~I~~~~~~~~~~~l~gl~ 74 (226)
T PF03945_consen 33 ILWPSSSPD-IWEEIIKQVENLIDQKITEYDINILNAELNGLQ 74 (226)
T ss_dssp HCSSTGSHH-HHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHH
T ss_pred HHCCCCCch-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 578776555 888999999999999999999999998888843
No 27
>PRK00098 GTPase RsgA; Reviewed
Probab=27.81 E-value=1.6e+02 Score=25.69 Aligned_cols=76 Identities=17% Similarity=0.172 Sum_probs=42.0
Q ss_pred cccceEEEEEEEecCCCcccCcccCceeEEecCCCCccccChHHHHHHHHHHHHHHhhccCCCCChhhhhhhccchHHHH
Q 028327 90 CATRHVRIYAAYIDPETWEFDQTQMDKLTLILDPTKEFVWTDESCNKVFAYFQELVDHYEGALLTEYTLRLIGSDLEHYI 169 (210)
Q Consensus 90 sTTRHVRIytA~i~~~~lv~~~tq~~~LTLdlDPDNEF~W~d~~l~kVy~~F~ELVe~y~G~~LteYnLRrIGSDLEhfI 169 (210)
-||||.++|.- .++-.+.|. +....+++ .-++.+.+.+.|..|.++.+.- -.. +.+.+| +---.|
T Consensus 204 htT~~~~~~~~--~~~~~~~Dt--pG~~~~~~-----~~~~~~~~~~~f~~~~~~~~~c---~f~--~c~h~~-ep~c~v 268 (298)
T PRK00098 204 HTTTHVELYDL--PGGGLLIDT--PGFSSFGL-----HDLEAEELEHYFPEFRPLSGDC---KFR--NCTHLH-EPGCAV 268 (298)
T ss_pred cccccEEEEEc--CCCcEEEEC--CCcCccCC-----CCCCHHHHHHHHHHHHHHhCCC---CCC--CCcCCC-CCCChH
Confidence 48899888743 334455554 12222221 1245566777777777776532 222 222333 233568
Q ss_pred HHHHhcCcccc
Q 028327 170 RKLLYDGEIKY 180 (210)
Q Consensus 170 R~LLq~GeisY 180 (210)
+..+.+|+|+.
T Consensus 269 ~~a~~~g~i~~ 279 (298)
T PRK00098 269 KAAVEEGEIAP 279 (298)
T ss_pred HHHHHcCCCCH
Confidence 88999999863
No 28
>PF14468 DUF4427: Protein of unknown function (DUF4427)
Probab=26.78 E-value=45 Score=28.01 Aligned_cols=58 Identities=22% Similarity=0.315 Sum_probs=39.6
Q ss_pred ChHHHHHHHHHHHHHHhhccC-CC-CChhhhhhhcc-------chHHHHHHHHhcCccccccCCccc
Q 028327 130 TDESCNKVFAYFQELVDHYEG-AL-LTEYTLRLIGS-------DLEHYIRKLLYDGEIKYNMDARVL 187 (210)
Q Consensus 130 ~d~~l~kVy~~F~ELVe~y~G-~~-LteYnLRrIGS-------DLEhfIR~LLq~GeisYNl~~RVl 187 (210)
+++++.++-++|.+.|+.-.- .+ +++=..|--|- .--.++|.|||+|.++-|-++|-|
T Consensus 2 s~~~v~~~~~~i~~~i~~l~S~~d~~~~~~~~e~G~~wvWi~DN~~~~vRALl~~grV~v~~eGRYL 68 (132)
T PF14468_consen 2 SEERVKEYADRINEYISELYSKKDFLNDDYDREFGNAWVWIHDNQSEVVRALLQAGRVKVNKEGRYL 68 (132)
T ss_pred cHHHHHHHHHHHHHHHHHHhccchhhcccchhhcCceEEEEecCcCHHHHHHHHcCceeeccCceee
Confidence 467788888889888876433 22 23323333331 234689999999999999999965
No 29
>PF12395 DUF3658: Protein of unknown function ; InterPro: IPR022123 This domain family is found in bacteria, and is approximately 110 amino acids in length. The family is found in association with PF08874 from PFAM. There are two completely conserved residues (D and R) that may be functionally important.
Probab=26.73 E-value=1e+02 Score=23.53 Aligned_cols=22 Identities=27% Similarity=0.428 Sum_probs=16.4
Q ss_pred HHHHHHHHhcCccccccCCccc
Q 028327 166 EHYIRKLLYDGEIKYNMDARVL 187 (210)
Q Consensus 166 EhfIR~LLq~GeisYNl~~RVl 187 (210)
+.=||.|..+|.+.+-=+..-+
T Consensus 85 ~~Ri~~Li~~G~le~~g~~~~m 106 (111)
T PF12395_consen 85 EYRIRELISQGVLEIKGDPKDM 106 (111)
T ss_pred HHHHHHHHHCCCEEEecCCCcc
Confidence 3448999999999887665533
No 30
>KOG4529 consensus Uncharacterized conserved protein [Function unknown]
Probab=25.80 E-value=39 Score=32.59 Aligned_cols=19 Identities=37% Similarity=0.716 Sum_probs=17.0
Q ss_pred HHHHHHHHHHHHHhhccCC
Q 028327 133 SCNKVFAYFQELVDHYEGA 151 (210)
Q Consensus 133 ~l~kVy~~F~ELVe~y~G~ 151 (210)
+|+-+|++|+|+|+.+.|.
T Consensus 294 ~Celay~~fqeIvd~vgGp 312 (404)
T KOG4529|consen 294 VCELAYSEFQEIVDMVGGP 312 (404)
T ss_pred EeHHHHHHHHHHHHhcCCC
Confidence 4788999999999999984
No 31
>PF06003 SMN: Survival motor neuron protein (SMN); InterPro: IPR010304 This family consists of several eukaryotic survival motor neuron (SMN) proteins. The Survival of Motor Neurons (SMN) protein, the product of the spinal muscular atrophy-determining gene, is part of a large macromolecular complex (SMN complex) that functions in the assembly of spliceosomal small nuclear ribonucleoproteins (snRNPs). The SMN complex functions as a specificity factor essential for the efficient assembly of Sm proteins on U snRNAs and likely protects cells from illicit, and potentially deleterious, non-specific binding of Sm proteins to RNAs.; GO: 0003723 RNA binding, 0006397 mRNA processing, 0005634 nucleus, 0005737 cytoplasm; PDB: 1MHN_A 4A4G_A 3S6N_M 4A4E_A 1G5V_A 4A4H_A 4A4F_A 2D9T_A.
Probab=25.19 E-value=39 Score=29.73 Aligned_cols=23 Identities=22% Similarity=0.495 Sum_probs=7.7
Q ss_pred CCccccChHHHHHHHHH----HHHHHh
Q 028327 124 TKEFVWTDESCNKVFAY----FQELVD 146 (210)
Q Consensus 124 DNEF~W~d~~l~kVy~~----F~ELVe 146 (210)
||+=+|+|.+|-|+|++ |++.+.
T Consensus 4 ~~~diWDDtaLIkaYdkav~~~k~a~~ 30 (264)
T PF06003_consen 4 DDSDIWDDTALIKAYDKAVNSFKEALK 30 (264)
T ss_dssp ---------HHHHHHHHHHTT------
T ss_pred ccccccccHHHHHHHHHHHHHHHHHHh
Confidence 68889999999999998 666443
No 32
>PHA02560 FI major tail sheath protein; Provisional
Probab=25.13 E-value=1.4e+02 Score=27.52 Aligned_cols=61 Identities=21% Similarity=0.097 Sum_probs=45.3
Q ss_pred EEecCCCCccccChHHHHHHHHHHHHHHhhccCCCCChhhhhhhccchHHHHHHHHhcCcc
Q 028327 118 TLILDPTKEFVWTDESCNKVFAYFQELVDHYEGALLTEYTLRLIGSDLEHYIRKLLYDGEI 178 (210)
Q Consensus 118 TLdlDPDNEF~W~d~~l~kVy~~F~ELVe~y~G~~LteYnLRrIGSDLEhfIR~LLq~Gei 178 (210)
|+.-||...|+=---...-+-+.|.+-...+-+++++.=..+.|-..++.|+|.|-.+|-|
T Consensus 273 T~s~d~~w~fi~vrR~~~~I~~si~~~~~~~Vdep~~~~l~~~v~~si~~~L~~L~~~Gal 333 (388)
T PHA02560 273 TCSDDPLFAFENYVRTAQVIADTIAEAHMWAVDKPLTPSLVRDIVEGINAKFRDLVANGYI 333 (388)
T ss_pred cCCCCCCeeEEeeHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHhCCce
Confidence 3455676555544444455555566666667789999888889999999999999999987
No 33
>cd04861 LigD_Pol_like LigD_Pol_like: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. PaeLigD is monomeric, containing an N-terminal phosphoesterase module, a central polymerase (Pol) domain, and a C-terminal ATP-dependent ligase domain. Mycobacterium tuberculosis (Mt)LigD, also found in this group, is monomeric and contains the same modules but these are arranged differently: an N-terminal Pol domain, a central phosphoesterase module, and a C-terminal ligase domain. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase do
Probab=25.01 E-value=87 Score=27.79 Aligned_cols=33 Identities=27% Similarity=0.431 Sum_probs=21.9
Q ss_pred cCceeEEecCCCCccccChHHHHHHHHHHHHHHhh
Q 028327 113 QMDKLTLILDPTKEFVWTDESCNKVFAYFQELVDH 147 (210)
Q Consensus 113 q~~~LTLdlDPDNEF~W~d~~l~kVy~~F~ELVe~ 147 (210)
..|.|.+||||+...-|.+ |-.+=..-+|+.++
T Consensus 97 ~PD~lvfDLDP~~~~~f~~--v~~~A~~vr~~L~~ 129 (227)
T cd04861 97 RPDRLVFDLDPGPGVPFED--VVEAALLLRELLDE 129 (227)
T ss_pred CCCEEEEECCCCCCCCHHH--HHHHHHHHHHHHHH
Confidence 4689999999998887754 33344444444443
No 34
>PF03799 FtsQ: Cell division protein FtsQ; InterPro: IPR005548 FtsQ is one of several cell division proteins. FtsQ interacts with other Fts proteins, reviewed in []. The precise function of FtsQ is unknown.; PDB: 2VH1_B 2VH2_B 2ALJ_A 1YR1_A.
Probab=24.92 E-value=41 Score=23.64 Aligned_cols=44 Identities=18% Similarity=0.209 Sum_probs=32.2
Q ss_pred ceeEEecCCCCccccChHHHHHHHHHHHHHHhhcc---CCCCChhhh
Q 028327 115 DKLTLILDPTKEFVWTDESCNKVFAYFQELVDHYE---GALLTEYTL 158 (210)
Q Consensus 115 ~~LTLdlDPDNEF~W~d~~l~kVy~~F~ELVe~y~---G~~LteYnL 158 (210)
..++|.++-.++..|..+.+.+=.++|..+..... +.++.-..|
T Consensus 70 ~~~~l~l~dg~~V~lg~~~~~~kl~~~~~i~~~~~~~~~~~i~~IDL 116 (117)
T PF03799_consen 70 GSWTLYLDDGVEVKLGRSDLAEKLQRLVKILPQLEKSKGKKIAYIDL 116 (117)
T ss_dssp SCEEEE-SSS-EEEEESSTHHHHHHHHHHHHHCCC-HHCCCEEEEEE
T ss_pred CeEEEEECCCcEEEEcCcCHHHHHHHHHHHHHHHHHhhcCCCeEEeC
Confidence 44888888899999999999999999999988765 444433333
No 35
>PLN02454 triacylglycerol lipase
Probab=24.65 E-value=90 Score=29.91 Aligned_cols=72 Identities=24% Similarity=0.373 Sum_probs=48.2
Q ss_pred CCCCccccChHHHHHHHHHHHHHHhhccCCCCChhhhhhhccchHHHHHHHHhcCccc---cc-cCCccccccCCCcccc
Q 028327 122 DPTKEFVWTDESCNKVFAYFQELVDHYEGALLTEYTLRLIGSDLEHYIRKLLYDGEIK---YN-MDARVLNFSMGKPRIM 197 (210)
Q Consensus 122 DPDNEF~W~d~~l~kVy~~F~ELVe~y~G~~LteYnLRrIGSDLEhfIR~LLq~Geis---YN-l~~RVlNySMGlPrv~ 197 (210)
||...|. ...+.+.|....++|++.|.+..+ .+=..|--|-+-|-.|.- =+|. || .+..|-.|++|-|||.
T Consensus 198 ~~~~~f~-~~S~r~qvl~~V~~l~~~Yp~~~~---sI~vTGHSLGGALAtLaA-~di~~~g~~~~~~~V~~~TFGsPRVG 272 (414)
T PLN02454 198 DPRSPFT-KLSARSQLLAKIKELLERYKDEKL---SIVLTGHSLGASLATLAA-FDIVENGVSGADIPVTAIVFGSPQVG 272 (414)
T ss_pred Cccccch-hHHHHHHHHHHHHHHHHhCCCCCc---eEEEEecCHHHHHHHHHH-HHHHHhcccccCCceEEEEeCCCccc
Confidence 3444442 347888999999999999976553 233678888887766542 2222 22 3556777999999985
Q ss_pred c
Q 028327 198 F 198 (210)
Q Consensus 198 ~ 198 (210)
.
T Consensus 273 N 273 (414)
T PLN02454 273 N 273 (414)
T ss_pred C
Confidence 4
No 36
>KOG0553 consensus TPR repeat-containing protein [General function prediction only]
Probab=24.57 E-value=20 Score=33.22 Aligned_cols=28 Identities=25% Similarity=0.162 Sum_probs=21.1
Q ss_pred eeEEecCCCCccccChHHHHHHHHHHHHHH
Q 028327 116 KLTLILDPTKEFVWTDESCNKVFAYFQELV 145 (210)
Q Consensus 116 ~LTLdlDPDNEF~W~d~~l~kVy~~F~ELV 145 (210)
+--|+||||||-.|+. |...-.++.|.-
T Consensus 173 kKaLeldP~Ne~~K~n--L~~Ae~~l~e~~ 200 (304)
T KOG0553|consen 173 KKALELDPDNESYKSN--LKIAEQKLNEPK 200 (304)
T ss_pred HhhhccCCCcHHHHHH--HHHHHHHhcCCC
Confidence 4569999999977754 666777777665
No 37
>cd08768 Cdc6_C Winged-helix domain of essential DNA replication protein Cell division control protein (Cdc6), which mediates DNA binding. This model characterizes the winged-helix, C-terminal domain of the Cell division control protein (Cdc6_C). Cdc6 (also known as Cell division cycle 6 or Cdc18) functions as a regulator at the early stages of DNA replication, by helping to recruit and load the Minichromosome Maintenance Complex (MCM) onto DNA and may have additional roles in the control of mitotic entry. Precise duplication of chromosomal DNA is required for genomic stability during replication. Cdc6 has an essential role in DNA replication and irregular expression of Cdc6 may lead to genomic instability. Cdc6 over-expression is observed in many cancerous lesions. DNA replication begins when an origin recognition complex (ORC) binds to a replication origin site on the chromatin. Studies indicate that Cdc6 interacts with ORC through the Orc1 subunit, and that this association increases
Probab=24.13 E-value=1.1e+02 Score=21.08 Aligned_cols=35 Identities=23% Similarity=0.342 Sum_probs=25.6
Q ss_pred HHHHHHHHHHHHHHhhccCCCCChhhhhhhccchH
Q 028327 132 ESCNKVFAYFQELVDHYEGALLTEYTLRLIGSDLE 166 (210)
Q Consensus 132 ~~l~kVy~~F~ELVe~y~G~~LteYnLRrIGSDLE 166 (210)
-....||+.+.++.+...-.+|+.=..+.|-++||
T Consensus 23 ~~~~~vy~~Y~~~c~~~~~~~l~~~~~~~~l~~L~ 57 (87)
T cd08768 23 ATTGEVYEVYEELCEEIGVDPLTQRRISDLLSELE 57 (87)
T ss_pred ccHHHHHHHHHHHHHHcCCCCCcHHHHHHHHHHHH
Confidence 36789999999999988556777655555555554
No 38
>cd04864 LigD_Pol_like_1 LigD_Pol_like_1: Polymerase (Pol) domain of mostly bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD, subgroup 1. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The Pol domains of PaeLigD and Mycobacterium tuberculosis (Mt)LigD are stimulated by manganese, are error-prone, and prefer adding rNTPs to dNTPs in vitro; however PaeLigD and MtLigD belong to other subgroups, proteins in this subgroup await functional characterization.
Probab=23.62 E-value=1.6e+02 Score=26.17 Aligned_cols=33 Identities=24% Similarity=0.269 Sum_probs=22.8
Q ss_pred ccCceeEEecCCCCccccChHHHHHHHHHHHHHHhh
Q 028327 112 TQMDKLTLILDPTKEFVWTDESCNKVFAYFQELVDH 147 (210)
Q Consensus 112 tq~~~LTLdlDPDNEF~W~d~~l~kVy~~F~ELVe~ 147 (210)
...|.+.+||||+ +--| +.|-.+=...+|+.++
T Consensus 98 e~PD~~vfDLDP~-~~~f--~~v~~~A~~~r~~L~~ 130 (228)
T cd04864 98 EHPDLMVFDLDPS-ADDI--EAVRTAALAVRELLDE 130 (228)
T ss_pred CCCCEEEEecCCC-CCCH--HHHHHHHHHHHHHHHH
Confidence 3468999999999 4445 4455666666777665
No 39
>PF04984 Phage_sheath_1: Phage tail sheath protein; InterPro: IPR007067 This entry represents tail sheath proteins from various bacteriophage [, ], including GpL from Bacteriophage Mu [] and Gp18 from Bacteriophage T4 [, ]. ; PDB: 3FOI_B 3FOH_D 3FOA_D 3FO8_D 3LML_A 3HXL_A.
Probab=23.43 E-value=56 Score=28.53 Aligned_cols=47 Identities=13% Similarity=0.213 Sum_probs=37.5
Q ss_pred HHHHHHHHHHHHHhhccCCCCChhhhhhhccchHHHHHHHHhcCccc
Q 028327 133 SCNKVFAYFQELVDHYEGALLTEYTLRLIGSDLEHYIRKLLYDGEIK 179 (210)
Q Consensus 133 ~l~kVy~~F~ELVe~y~G~~LteYnLRrIGSDLEhfIR~LLq~Geis 179 (210)
.+..|-+.++.....+-+++.++-+...|-+.+++|++.|-.+|-|.
T Consensus 376 ~~d~i~~~i~~~~~~~~~~~n~~~~~~~i~~~i~~~l~~l~~~g~l~ 422 (464)
T PF04984_consen 376 TFDYIERSIRATLRQYVFEPNDDATREAIKSSINAFLNELVAQGALE 422 (464)
T ss_dssp HHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHTTSB-
T ss_pred HHHHHHHHHHHHHHHhcCccCChhHHHHHHHHHHHHHHHHHhCCcEE
Confidence 33445555666666678888899999999999999999999999885
No 40
>COG4782 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.39 E-value=51 Score=31.52 Aligned_cols=42 Identities=26% Similarity=0.300 Sum_probs=32.0
Q ss_pred cCCCCChhhhhh-----hccchHHHHHHHHhcCccccccCCccccccCCC
Q 028327 149 EGALLTEYTLRL-----IGSDLEHYIRKLLYDGEIKYNMDARVLNFSMGK 193 (210)
Q Consensus 149 ~G~~LteYnLRr-----IGSDLEhfIR~LLq~GeisYNl~~RVlNySMGl 193 (210)
++..|.+||.=| =+-+||++||.|..++.+ .+--||.-|||-
T Consensus 156 S~g~l~~Yn~DreS~~~Sr~aLe~~lr~La~~~~~---~~I~ilAHSMGt 202 (377)
T COG4782 156 SRGSLLGYNYDRESTNYSRPALERLLRYLATDKPV---KRIYLLAHSMGT 202 (377)
T ss_pred CCCeeeecccchhhhhhhHHHHHHHHHHHHhCCCC---ceEEEEEecchH
Confidence 456689998754 567899999999999863 244578889983
No 41
>cd08051 gp6_gp15_like Head-Tail Connector Proteins gp6 and gp15, and similar proteins. Members of this family include the proteins gp6 and gp15 from bacteriophage HK97 and SPP1, respectively. They are critical in the assembly of the connector, a specialized structure that serves as an interface for head and tail attachment, as well as a point at which DNA exits the head during infection by the bacteriophage. They form dodecameric ring structures that comprise the middle ring of the connector, located between the portal protein (attached to the head) and the gp7/gp16 ring (attached to the tail). They are components of the mature phage and the absence or mutation of HK97 gp6 or SPP1 gp15, respectively, result in defective head-tail joining and the absence of mature phage particles. The genome maps of HK97 and SPP1 show that genes encoding gp6 and gp15 are in the same relative position on the genome, located adjacent to the major capsid protein (MCP) gene and in between head and tail gene
Probab=23.08 E-value=1.8e+02 Score=21.97 Aligned_cols=54 Identities=7% Similarity=-0.039 Sum_probs=42.0
Q ss_pred EecCCCCccccChHHHHHHHHHHHHHHhhccCCCCChhhhhhhccchHHHHHHHHhcC
Q 028327 119 LILDPTKEFVWTDESCNKVFAYFQELVDHYEGALLTEYTLRLIGSDLEHYIRKLLYDG 176 (210)
Q Consensus 119 LdlDPDNEF~W~d~~l~kVy~~F~ELVe~y~G~~LteYnLRrIGSDLEhfIR~LLq~G 176 (210)
+.+|+|. +|+-|+..-....+-++.|-|.++.+---=-|-.|++.++-.|.+-.
T Consensus 7 ~~id~d~----dD~lL~~~i~aA~~~~e~~~~~~~~~~~~~~lp~~vk~A~l~li~~~ 60 (94)
T cd08051 7 IEFEEDD----RDELLTLYAQAAFDYCXRWCDEPFWDAVAADIPAAVKGAVLKVFQFY 60 (94)
T ss_pred cCCCCCC----CHHHHHHHHHHHHHHHHHHhccccccccccCCCHHHHHHHHHHHHHH
Confidence 6677773 89999999999999999999988776322246678888888887654
No 42
>PF13959 DUF4217: Domain of unknown function (DUF4217)
Probab=22.29 E-value=88 Score=21.94 Aligned_cols=55 Identities=18% Similarity=0.239 Sum_probs=29.6
Q ss_pred HHHHHHHHHhhccCCCCChhhhhhhccc-hHHHHHHHHhcCccccccCCc-----cccccCCCccccc
Q 028327 137 VFAYFQELVDHYEGALLTEYTLRLIGSD-LEHYIRKLLYDGEIKYNMDAR-----VLNFSMGKPRIMF 198 (210)
Q Consensus 137 Vy~~F~ELVe~y~G~~LteYnLRrIGSD-LEhfIR~LLq~GeisYNl~~R-----VlNySMGlPrv~~ 198 (210)
|+.+++.+|. ++++|...|.+ .-.|||+.---++.++--+-+ -+..||||+++|.
T Consensus 2 iq~~l~~~~~-------~d~~l~~lA~~Af~SyvraY~~~~~~k~iF~~~~L~l~~~A~sfGL~~~P~ 62 (65)
T PF13959_consen 2 IQQKLEKLVA-------KDRELKELAQKAFVSYVRAYASHKELKDIFNVKKLDLGHLAKSFGLLEAPK 62 (65)
T ss_pred HHHHHHHHHH-------hCHHHHHHHHHHHHHHHHHHHHHhhhhhhCCcccCCHHHHHHHcCCCCCCC
Confidence 3445555554 35556555554 355666665224455433333 3346899987763
No 43
>KOG0698 consensus Serine/threonine protein phosphatase [Signal transduction mechanisms]
Probab=22.24 E-value=53 Score=29.09 Aligned_cols=49 Identities=18% Similarity=0.324 Sum_probs=35.6
Q ss_pred ccccchhhcCcccccccceEEEEEEEecCCCcccCcccCceeEEecCCCCccc-------c----ChHHHHHHHHHH
Q 028327 76 SKNMSREYGGQWLSCATRHVRIYAAYIDPETWEFDQTQMDKLTLILDPTKEFV-------W----TDESCNKVFAYF 141 (210)
Q Consensus 76 sKnm~r~~~~~lLksTTRHVRIytA~i~~~~lv~~~tq~~~LTLdlDPDNEF~-------W----~d~~l~kVy~~F 141 (210)
.=+|+|.+||..||. .-++..+ +.-...+++++||+ | |++++.-|...+
T Consensus 211 ~LavsRa~GD~~~k~--------------~~v~a~P---ei~~~~~~~~deFLiLasDGiwDv~s~qeav~~V~~~~ 270 (330)
T KOG0698|consen 211 VLAVSRAFGDVELKS--------------QGVIAEP---EIQQVKINSDDEFLILASDGIWDVVSNQEAVDLVRDEL 270 (330)
T ss_pred eEEEeeecCCHHhcC--------------CcEecCC---ceEEEEcCCCCcEEEEeCCchhcccChHHHHHHHHHHh
Confidence 568999999999998 2233333 44478889999994 7 477777776655
No 44
>PLN02753 triacylglycerol lipase
Probab=22.14 E-value=87 Score=31.13 Aligned_cols=66 Identities=17% Similarity=0.206 Sum_probs=48.4
Q ss_pred HHHHHHHHHHHHHHhhccCCCCChhhhhhhccchHHHHHHHHhcCccc---cc-----cCCccccccCCCccccc
Q 028327 132 ESCNKVFAYFQELVDHYEGALLTEYTLRLIGSDLEHYIRKLLYDGEIK---YN-----MDARVLNFSMGKPRIMF 198 (210)
Q Consensus 132 ~~l~kVy~~F~ELVe~y~G~~LteYnLRrIGSDLEhfIR~LLq~Geis---YN-----l~~RVlNySMGlPrv~~ 198 (210)
.+-+.|....++|++.|.+++-.+|.+=-.|--|-+=|-.|.-. .|. || ....|--|++|-|||..
T Consensus 288 S~reQVl~eVkrLl~~Y~~e~~~~~sItVTGHSLGGALAtLaA~-Dla~~g~n~~~~~~~~pV~vyTFGsPRVGN 361 (531)
T PLN02753 288 SAREQILTEVKRLVEEHGDDDDSDLSITVTGHSLGGALAILSAY-DIAEMGLNRSKKGKVIPVTVLTYGGPRVGN 361 (531)
T ss_pred hHHHHHHHHHHHHHHHcccccCCCceEEEEccCHHHHHHHHHHH-HHHHhcccccccCccCceEEEEeCCCCccC
Confidence 35677888889999999887777888888888888877666421 121 22 23457789999999964
No 45
>PLN02719 triacylglycerol lipase
Probab=21.52 E-value=1e+02 Score=30.64 Aligned_cols=66 Identities=21% Similarity=0.297 Sum_probs=45.4
Q ss_pred HHHHHHHHHHHHHHhhccCCCCChhhhhhhccchHHHHHHHHhcCccc---cc-----cCCccccccCCCccccc
Q 028327 132 ESCNKVFAYFQELVDHYEGALLTEYTLRLIGSDLEHYIRKLLYDGEIK---YN-----MDARVLNFSMGKPRIMF 198 (210)
Q Consensus 132 ~~l~kVy~~F~ELVe~y~G~~LteYnLRrIGSDLEhfIR~LLq~Geis---YN-----l~~RVlNySMGlPrv~~ 198 (210)
.+-++|...+++|++.|...+=.+|.+=-.|--|-+=|-.| -+-+|. || ..+.|--|++|-|||..
T Consensus 274 SaReQVl~eV~rL~~~Ypd~~ge~~sItVTGHSLGGALAtL-aA~Dl~~~gln~~~~~~~~pVtvyTFGsPRVGN 347 (518)
T PLN02719 274 SAREQVLTEVKRLVERYGDEEGEELSITVTGHSLGGALAVL-SAYDVAEMGLNRTRKGKVIPVTAFTYGGPRVGN 347 (518)
T ss_pred hHHHHHHHHHHHHHHHCCcccCCcceEEEecCcHHHHHHHH-HHHHHHHhcccccccccccceEEEEecCCCccC
Confidence 34577899999999998643334666778888888877655 233333 22 23457789999999964
No 46
>cd04863 MtLigD_Pol_like MtLigD_Pol_like: Polymerase (Pol) domain of bacterial LigD proteins similar to Mycobacterium tuberculosis (Mt)LigD. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. MtLigD is monomeric and contains an N-terminal Pol domain, a central phosphoesterase module, and a C-terminal ligase domain. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The MtLigD Pol domain is stimulated by manganese, is error-prone, and prefers adding rNTPs to dNTPs in vitro. The MtLigD Pol domain has been shown to prefer DNA gapped substrates
Probab=21.25 E-value=60 Score=28.86 Aligned_cols=34 Identities=21% Similarity=0.401 Sum_probs=22.9
Q ss_pred ccCceeEEecCCCCccccChHHHHHHHHHHHHHHhh
Q 028327 112 TQMDKLTLILDPTKEFVWTDESCNKVFAYFQELVDH 147 (210)
Q Consensus 112 tq~~~LTLdlDPDNEF~W~d~~l~kVy~~F~ELVe~ 147 (210)
...|.+.+||||+...-|.+ |-.+=.--+|+.++
T Consensus 100 e~PD~~vfDLDP~~~~~f~~--v~~~A~~~r~~L~~ 133 (231)
T cd04863 100 GPPDRLVFDLDPGEPAGLVE--CARVALWLRDRLAA 133 (231)
T ss_pred CCCCEEEEECCCCCCCCHHH--HHHHHHHHHHHHHH
Confidence 34689999999998877754 44444445555554
No 47
>PF09457 RBD-FIP: FIP domain ; InterPro: IPR019018 The Rab11 GTPase regulates recycling of internalized plasma membrane receptors and is essential for completion of cytokinesis. A family of Rab11 interacting proteins (FIPs) that conserve a C-terminal Rab-binding domain (RBD) selectively recognise the active form of Rab11. FIPs are diverse in sequence length and composition toward their N-termini, presumably a feature that underpins their specific roles in Rab11-mediated vesicle trafficking. They have been divided into three subfamilies (classe I, II, and III)on the basis of domain architecture. Class I FIPs comprises a subfamily of three proteins (Rip11/pp75/FIP5, Rab-coupling protein (RCP), and FIP2) that possess an N- terminal C2 domain, localize to recycling endosomes, and regulate plasma membrane recycling. The class II subfamily consists of two proteins (FIP3/eferin/arfophilin and FIP4) with tandem EF hands and a proline-rich region. Class II FIPs localize to recycling endosomes, the trans-Golgi network, and have been implicated in the regulation of membrane trafficking during cytokinesis. The class III subfamily consists of a single protein, FIP1, which does not contain obvious homology domains or motifs other than the FIP-RBD [, , , ]. The FIP-RBD domain is also found in Rab6-interacting protein Erc1/Elks. Erc1 is the regulatory subunit of the IKK complex and probably recruits IkappaBalpha/NFKBIA to the complex []. It may be involved in the organisation of the cytomatrix at the nerve terminals active zone (CAZ) which regulates neurotransmitter release. It may also be involved in vesicle trafficking at the CAZ, as well as in Rab-6 regulated endosomes to Golgi transport []. The FIB-RBD domain consists of an N-terminal long alpha-helix, followed by a 90 degrees bend at a conserved proline residue, a 3(10) helix and a C-terminal short beta-strand, adopting an "L" shape. The long alpha-helix forms a parallel coiled-coil homodimer that symmetrically interacts with two Rab11 molecules on both sides, forming a quaternary Rab11-(FIP)2-Rab11 complex. The Rab11-interacting region of FIP-RBD is confined to the C-terminal 24 amino acids, which cover the C-terminal half of the long alpha-helix and the short beta-strand [, , , ]. This entry represents the FIP-RBD domain.; PDB: 2HV8_E 2D7C_D 2K6S_B 2GZD_D 2GZH_B.
Probab=21.18 E-value=54 Score=22.87 Aligned_cols=13 Identities=46% Similarity=0.754 Sum_probs=10.7
Q ss_pred cchHHHHHHHHhc
Q 028327 163 SDLEHYIRKLLYD 175 (210)
Q Consensus 163 SDLEhfIR~LLq~ 175 (210)
.|||+||-.||..
T Consensus 24 ~eLe~YiD~LL~r 36 (48)
T PF09457_consen 24 RELEDYIDNLLVR 36 (48)
T ss_dssp HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHH
Confidence 4799999999863
No 48
>PF13426 PAS_9: PAS domain; PDB: 3ULF_B 3UE6_E 2Z6D_B 2Z6C_B 3P7N_B 1LL8_A 3MJQ_A 3BWL_A 4EET_B 4EEP_A ....
Probab=20.91 E-value=84 Score=20.24 Aligned_cols=58 Identities=19% Similarity=0.435 Sum_probs=35.7
Q ss_pred EEecCCCCccccChHHHHHHHHHHHHHHhhccCCCCChhhhhhhccchHHHHHHHHhcCcc
Q 028327 118 TLILDPTKEFVWTDESCNKVFAYFQELVDHYEGALLTEYTLRLIGSDLEHYIRKLLYDGEI 178 (210)
Q Consensus 118 TLdlDPDNEF~W~d~~l~kVy~~F~ELVe~y~G~~LteYnLRrIGSDLEhfIR~LLq~Gei 178 (210)
.+.+|||..++|-.++..+++.+=. +..-|..+.++--..--..+...|.+.+..|..
T Consensus 4 i~i~d~~g~i~~~N~~~~~~~g~~~---~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 61 (104)
T PF13426_consen 4 IFILDPDGRILYVNPAFERLFGYSR---EELIGKSISDFFPEEDRPEFEEQIERALEEGGS 61 (104)
T ss_dssp EEEEETTSBEEEE-HHHHHHHTS-H---HHHTTSBGGGGCSTTSCHHHHHHHHHHHHHTSS
T ss_pred EEEECCcCcEEehhHHHHHHHCcCH---HHHcCCCcccccCcccchhhHHHHHHHHhcCCc
Confidence 4678899999998888888876422 445677776654322233455566666664443
No 49
>KOG2861 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.77 E-value=79 Score=30.31 Aligned_cols=50 Identities=16% Similarity=0.398 Sum_probs=36.3
Q ss_pred CccccChHHHHHHHHHHHHHHhhccCCCCChhhhhhhccchHHHHHHHHhc
Q 028327 125 KEFVWTDESCNKVFAYFQELVDHYEGALLTEYTLRLIGSDLEHYIRKLLYD 175 (210)
Q Consensus 125 NEF~W~d~~l~kVy~~F~ELVe~y~G~~LteYnLRrIGSDLEhfIR~LLq~ 175 (210)
-||.|+++.+..+|..+++-.|=---..+=+|.|--|. |+=+++...|+.
T Consensus 316 Pdf~W~ep~Le~iY~~~r~yleI~qRv~vLN~kl~~i~-~~~~~l~e~ln~ 365 (399)
T KOG2861|consen 316 PDFYWDEPQLEPIYEATRRYLEIGQRVNVLNYKLKVIE-DLLDILQENLNE 365 (399)
T ss_pred cccccCchhHHHHHHHHHHHcccchHHHHHHHHHHHHH-HHHHHHHHHhhh
Confidence 47999999999999999988776555556667776664 444555555543
No 50
>KOG4384 consensus Uncharacterized SAM domain protein [General function prediction only]
Probab=20.61 E-value=64 Score=30.83 Aligned_cols=17 Identities=65% Similarity=1.009 Sum_probs=15.8
Q ss_pred hhhhccchHHHHHHHHhcC
Q 028327 158 LRLIGSDLEHYIRKLLYDG 176 (210)
Q Consensus 158 LRrIGSDLEhfIR~LLq~G 176 (210)
||+|| ||+||-.||.+|
T Consensus 222 L~~i~--le~y~~~~L~nG 238 (361)
T KOG4384|consen 222 LRRIG--LEEYIETLLENG 238 (361)
T ss_pred HHHhh--HHHHHHHHHHcc
Confidence 88998 999999999988
No 51
>PF02268 TFIIA_gamma_N: Transcription initiation factor IIA, gamma subunit, helical domain; InterPro: IPR015872 Transcription factor IIA (TFIIA) is one of several factors that form part of a transcription pre-initiation complex along with RNA polymerase II, the TATA-box-binding protein (TBP) and TBP-associated factors, on the TATA-box sequence upstream of the initiation start site. After initiation, some components of the pre-initiation complex (including TFIIA) remain attached and re-initiate a subsequent round of transcription. TFIIA binds to TBP to stabilise TBP binding to the TATA element. TFIIA also inhibits the cytokine HMGB1 (high mobility group 1 protein) binding to TBP [], and can dissociate HMGB1 already bound to TBP/TATA-box. Human and Drosophila TFIIA have three subunits: two large subunits, LN/alpha and LC/beta, derived from the same gene, and a small subunit, S/gamma. Yeast TFIIA has two subunits: a large TOA1 subunit that shows sequence similarity to the N-terminal of LN/alpha and the C-terminal of LC/beta, and a small subunit, TOA2 that is highly homologous with S/gamma. The conserved regions of the large and small subunits of TFIIA combine to form two domains: a four-helix bundle (helical domain) composed of two helices from each of the N-terminal regions of TOA1 and TOA2 in yeast; and a beta-barrel (beta-barrel domain) composed of beta-sheets from the C-terminal regions of TOA1 and TOA2 []. This entry represents the alpha-helical domain found at the N-terminal of the gamma subunit of transcription factor TFIIA.; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005672 transcription factor TFIIA complex; PDB: 1NVP_D 1RM1_B 1YTF_D 1NH2_D.
Probab=20.53 E-value=29 Score=24.39 Aligned_cols=29 Identities=24% Similarity=0.486 Sum_probs=24.9
Q ss_pred hhccchHHHHHHHHhcCccccccCCcccc
Q 028327 160 LIGSDLEHYIRKLLYDGEIKYNMDARVLN 188 (210)
Q Consensus 160 rIGSDLEhfIR~LLq~GeisYNl~~RVlN 188 (210)
-||.-|.+-+-.|+++|.|+=.+..+||+
T Consensus 10 tlG~aL~dtLDeli~~~~I~p~La~kVL~ 38 (49)
T PF02268_consen 10 TLGIALTDTLDELIQEGKITPQLAMKVLE 38 (49)
T ss_dssp HHHHHHHHHHHHHHHTTSS-HHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHcCCCCHHHHHHHHH
Confidence 48999999999999999999888887764
No 52
>KOG1149 consensus Glutamyl-tRNA synthetase (mitochondrial) [Translation, ribosomal structure and biogenesis]
Probab=20.37 E-value=17 Score=35.94 Aligned_cols=37 Identities=30% Similarity=0.820 Sum_probs=28.1
Q ss_pred cCcccccccceEEEEEEEecCCCcccCcccCceeEEecCCCCc
Q 028327 84 GGQWLSCATRHVRIYAAYIDPETWEFDQTQMDKLTLILDPTKE 126 (210)
Q Consensus 84 ~~~lLksTTRHVRIytA~i~~~~lv~~~tq~~~LTLdlDPDNE 126 (210)
|.-||.||++|+-||-|- .+.| -+--+|-|.+.||.-
T Consensus 244 GeEWlpST~KH~lLYkAf----gW~p--PkFaHlpLl~n~d~s 280 (524)
T KOG1149|consen 244 GEEWLPSTLKHILLYKAF----GWQP--PKFAHLPLLLNPDGS 280 (524)
T ss_pred cchhccccHHHHHHHHHh----CCCC--CceeeeeeeecCCcc
Confidence 678999999999999874 2222 235788899999853
No 53
>TIGR02778 ligD_pol DNA polymerase LigD, polymerase domain. DNA repair of double-stranded breaks by non-homologous end joining (NHEJ) is accomplished by a two-protein system that is present in a minority of prokaryotes. One component is the Ku protein (see TIGR02772), which binds DNA ends. The other is a DNA ligase, a protein that is a multidomain polypeptide in most of those bacteria that have NHEJ, a permuted polypeptide in Mycobacterium tuberculosis and a few other species, and the product of tandem genes in some other bacteria. This model represents the polymerase domain.
Probab=20.37 E-value=1.2e+02 Score=27.22 Aligned_cols=33 Identities=24% Similarity=0.460 Sum_probs=22.7
Q ss_pred cCceeEEecCCCCccccChHHHHHHHHHHHHHHhh
Q 028327 113 QMDKLTLILDPTKEFVWTDESCNKVFAYFQELVDH 147 (210)
Q Consensus 113 q~~~LTLdlDPDNEF~W~d~~l~kVy~~F~ELVe~ 147 (210)
..|.|.+||||+...-|.+ |..+=...+|+.++
T Consensus 113 ~PD~lvfDLDP~~~~~f~~--v~~~A~~~r~~L~~ 145 (245)
T TIGR02778 113 KPDRIVFDLDPGPGVAWKL--VVEAAQLIRELLDE 145 (245)
T ss_pred CCCEEEEECCCCCCCCHHH--HHHHHHHHHHHHHH
Confidence 3588999999998877754 44444555555554
Done!