Query 048140
Match_columns 334
No_of_seqs 44 out of 46
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 06:39:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/048140.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/048140hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05667 DUF812: Protein of un 70.5 1.2E+02 0.0026 32.8 14.2 152 42-246 408-568 (594)
2 PF02520 DUF148: Domain of unk 62.5 87 0.0019 25.8 11.2 47 165-211 59-107 (113)
3 PF04858 TH1: TH1 protein; In 62.4 2.3E+02 0.0051 30.7 16.0 66 179-278 277-342 (584)
4 TIGR02284 conserved hypothetic 62.1 1E+02 0.0022 26.7 9.8 28 56-86 16-43 (139)
5 PF08637 NCA2: ATP synthase re 54.6 39 0.00085 33.0 6.7 127 184-331 145-283 (290)
6 PF03194 LUC7: LUC7 N_terminus 54.3 1.3E+02 0.0028 29.0 9.9 123 119-265 79-209 (254)
7 PF03705 CheR_N: CheR methyltr 53.0 42 0.00092 23.9 5.1 56 48-108 2-57 (57)
8 KOG3251 Golgi SNAP receptor co 52.3 88 0.0019 30.0 8.3 130 80-213 37-187 (213)
9 PRK14964 DNA polymerase III su 51.3 1.5E+02 0.0033 31.2 10.7 126 192-319 200-346 (491)
10 PF07200 Mod_r: Modifier of ru 47.9 1.2E+02 0.0026 25.9 8.0 96 99-199 9-108 (150)
11 PF05276 SH3BP5: SH3 domain-bi 46.3 2.8E+02 0.0061 26.8 10.9 48 200-247 114-164 (239)
12 PF02520 DUF148: Domain of unk 45.6 1.7E+02 0.0037 24.0 10.0 83 171-256 2-106 (113)
13 PF06552 TOM20_plant: Plant sp 43.3 82 0.0018 29.6 6.6 65 123-188 5-71 (186)
14 KOG0994 Extracellular matrix g 43.2 6.8E+02 0.015 30.3 16.2 224 69-319 1488-1733(1758)
15 PF10508 Proteasom_PSMB: Prote 43.0 4.1E+02 0.0088 27.6 12.3 60 137-197 303-363 (503)
16 TIGR00984 3a0801s03tim44 mitoc 41.9 77 0.0017 32.6 6.7 96 46-156 171-278 (378)
17 COG0143 MetG Methionyl-tRNA sy 39.8 1.5E+02 0.0031 32.0 8.6 188 85-297 348-553 (558)
18 smart00502 BBC B-Box C-termina 39.0 1.9E+02 0.0042 22.7 10.9 98 82-185 6-107 (127)
19 COG4660 RnfE Predicted NADH:ub 38.8 8.4 0.00018 36.5 -0.6 42 234-275 52-93 (212)
20 PRK14963 DNA polymerase III su 38.7 4.9E+02 0.011 27.4 12.8 135 191-333 199-372 (504)
21 PF10540 Membr_traf_MHD: Munc1 38.1 98 0.0021 26.8 5.9 81 219-310 20-104 (137)
22 KOG4559 Uncharacterized conser 37.8 74 0.0016 27.8 5.0 22 156-177 95-116 (120)
23 PF01213 CAP_N: Adenylate cycl 36.9 1.1E+02 0.0024 30.5 6.8 56 75-135 85-140 (312)
24 PF09537 DUF2383: Domain of un 36.9 47 0.001 26.8 3.6 78 143-223 4-85 (111)
25 TIGR02284 conserved hypothetic 36.9 2.3E+02 0.0049 24.6 8.0 106 144-250 4-118 (139)
26 KOG0796 Spliceosome subunit [R 36.6 3E+02 0.0064 28.0 9.7 123 120-265 80-205 (319)
27 PF08376 NIT: Nitrate and nitr 36.2 3E+02 0.0066 24.2 16.7 203 80-307 29-235 (247)
28 PF04048 Sec8_exocyst: Sec8 ex 35.9 77 0.0017 27.5 5.0 80 95-182 42-125 (142)
29 PF11570 E2R135: Coiled-coil r 34.2 85 0.0018 28.2 5.0 43 141-203 20-62 (136)
30 TIGR02531 yecD_yerC TrpR-relat 32.8 36 0.00078 27.9 2.3 29 248-276 5-33 (88)
31 PRK15084 formate hydrogenlyase 32.0 46 0.001 29.8 2.9 53 169-221 49-103 (133)
32 PF00196 GerE: Bacterial regul 31.8 1.1E+02 0.0024 22.0 4.6 56 241-314 1-56 (58)
33 cd07908 Mn_catalase_like Manga 31.7 1.6E+02 0.0034 25.2 6.1 46 47-102 25-70 (154)
34 KOG3030 Lipid phosphate phosph 31.2 11 0.00024 37.5 -1.1 17 52-68 134-150 (317)
35 PF08900 DUF1845: Domain of un 30.7 4.6E+02 0.0099 24.6 9.5 108 56-186 40-150 (217)
36 cd03313 enolase Enolase: Enola 30.1 1.7E+02 0.0036 29.7 6.9 83 224-306 171-279 (408)
37 TIGR03042 PS_II_psbQ_bact phot 28.6 2.7E+02 0.0058 25.1 7.2 92 71-179 31-130 (142)
38 COG3937 Uncharacterized conser 27.2 3.3E+02 0.0071 23.8 7.2 47 186-252 24-73 (108)
39 PF12041 DELLA: Transcriptiona 26.6 42 0.0009 27.4 1.6 47 261-307 19-67 (73)
40 PF07450 HycH: Formate hydroge 25.5 94 0.002 27.8 3.7 53 169-221 47-101 (131)
41 PF11269 DUF3069: Protein of u 25.3 4.9E+02 0.011 23.2 10.4 91 107-230 28-120 (121)
42 KOG0240 Kinesin (SMY1 subfamil 25.1 6.2E+02 0.013 27.9 10.2 126 74-203 419-549 (607)
43 PRK10512 selenocysteinyl-tRNA- 25.0 3.8E+02 0.0083 28.9 8.8 74 244-321 504-577 (614)
44 cd07316 terB_like_DjlA N-termi 24.9 3.4E+02 0.0073 21.2 8.0 45 65-109 11-55 (106)
45 PF12348 CLASP_N: CLASP N term 24.1 5E+02 0.011 22.9 13.4 148 117-267 40-197 (228)
46 PF09537 DUF2383: Domain of un 24.0 1.2E+02 0.0026 24.4 3.9 36 57-95 18-53 (111)
47 PF11588 DUF3243: Protein of u 24.0 1.8E+02 0.0038 24.1 4.8 55 208-266 13-70 (81)
48 PF06810 Phage_GP20: Phage min 23.7 5.3E+02 0.011 23.0 8.7 43 155-199 25-67 (155)
49 PF12397 U3snoRNP10: U3 small 23.3 4.2E+02 0.0091 21.7 8.1 84 185-272 23-107 (121)
50 PF09371 Tex_N: Tex-like prote 23.1 1.5E+02 0.0032 27.6 4.7 51 111-165 26-77 (193)
51 cd05509 Bromo_gcn5_like Bromod 23.0 1.6E+02 0.0035 23.6 4.4 47 285-331 54-101 (101)
52 PF06160 EzrA: Septation ring 22.5 7.7E+02 0.017 26.2 10.4 63 47-109 65-127 (560)
53 PF01503 PRA-PH: Phosphoribosy 22.0 1.7E+02 0.0037 22.9 4.3 27 213-239 39-67 (83)
54 PF13949 ALIX_LYPXL_bnd: ALIX 21.7 6.6E+02 0.014 23.4 9.4 59 72-130 137-201 (296)
55 PRK04778 septation ring format 21.6 5.1E+02 0.011 27.4 8.9 209 47-255 69-322 (569)
56 PF13514 AAA_27: AAA domain 21.4 1.3E+03 0.027 26.6 14.2 132 70-201 723-859 (1111)
57 cd07177 terB_like tellurium re 21.2 3.7E+02 0.008 20.3 7.7 85 66-150 12-102 (104)
58 PF11363 DUF3164: Protein of u 21.0 1.3E+02 0.0028 28.0 3.9 28 246-274 138-167 (195)
59 PF01347 Vitellogenin_N: Lipop 21.0 5.6E+02 0.012 26.5 8.9 54 209-268 542-597 (618)
60 COG2206 c-di-GMP phosphodieste 20.6 2E+02 0.0043 28.3 5.4 60 148-219 258-317 (344)
61 PF03869 Arc: Arc-like DNA bin 20.6 1.1E+02 0.0024 22.5 2.8 33 286-330 8-40 (50)
62 PF09675 Chlamy_scaf: Chlamydi 20.5 75 0.0016 27.8 2.1 48 94-149 32-82 (114)
63 PRK13441 F0F1 ATP synthase sub 20.4 2.9E+02 0.0063 24.5 5.9 43 164-206 29-75 (180)
64 PF05478 Prominin: Prominin; 20.1 9.7E+02 0.021 26.6 10.9 83 37-120 192-283 (806)
No 1
>PF05667 DUF812: Protein of unknown function (DUF812); InterPro: IPR008530 This family consists of several eukaryotic proteins of unknown function.
Probab=70.46 E-value=1.2e+02 Score=32.78 Aligned_cols=152 Identities=24% Similarity=0.424 Sum_probs=93.0
Q ss_pred hhhhcchhhhhhhhhhhH---HHhHHhhhh-ccCH-HHHHHHHHHHHHhhhhcHHHHHHHHHHHH----HHcCCchhhHH
Q 048140 42 RRLLVFSKEWNNLRSNFF---KRCQDRADA-EVDP-EMKHKLLRLGRKLKEIDEDVQSHNELLEV----IEAAPSEVSQI 112 (334)
Q Consensus 42 r~llafs~eW~~~R~~ff---~Rc~~rA~~-e~Dp-~~k~kl~~L~Rklk~ide~~~~hneLLe~----i~~~p~eie~i 112 (334)
.++.....+|..+|.-.- ++.+..... +.+. .+.+.+-.+.++++++-++++...++... +...|.+++
T Consensus 408 ~rl~~L~~qWe~~R~pL~~e~r~lk~~~~~~~~e~~~~~~~ik~~r~~~k~~~~e~~~Kee~~~qL~~e~e~~~k~~~-- 485 (594)
T PF05667_consen 408 QRLVELAQQWEKHRAPLIEEYRRLKEKASNRESESKQKLQEIKELREEIKEIEEEIRQKEELYKQLVKELEKLPKDVN-- 485 (594)
T ss_pred HHHHHHHHHHHHHHhHHHHHHHHHHHHHhhcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCC--
Confidence 356678899999998774 455544442 2222 34466777888888888888765555444 444454432
Q ss_pred HhhhccCCChHHHHHHHHHHHHhcCChhhHHHHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHhhhhhCCcchHHHHHHH
Q 048140 113 VSRRCKDFTQEFFEHLHTVAESYYNDPAKQDDIAKLGKLCVAAVQAYDTTTESIEALNAAELKFQDIINSPSVDAACRKI 192 (334)
Q Consensus 113 VArrRkdFT~eFF~hL~~~~ea~~d~~dr~~~La~L~~~claaveAyD~a~~d~~~L~~A~~kf~dILnS~Sldaa~~KI 192 (334)
|.-|| + ++++.|-...+--+++..+-.=...+|+=||+-
T Consensus 486 ----Rs~Yt-------~---------------------RIlEIv~NI~KQk~eI~KIl~DTr~lQkeiN~l--------- 524 (594)
T PF05667_consen 486 ----RSAYT-------R---------------------RILEIVKNIRKQKEEIEKILSDTRELQKEINSL--------- 524 (594)
T ss_pred ----HHHHH-------H---------------------HHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHH---------
Confidence 22222 2 334444444444444443333333344433332
Q ss_pred HHHHHhccCCHHHHHHHHHHHHHhhhchhhhHHHHHHHHHHHHHHHhhhhhcCc
Q 048140 193 DSLAEKNQLDSALVLMITKAWSAAKESNMMKEEVKDILYHLYMTARGNLQRLMP 246 (334)
Q Consensus 193 d~LAe~~eLDsaLvLli~kA~aAAKeS~~~k~EvKDIm~hLY~~ak~~l~r~~P 246 (334)
.|+|+.++-.+-..=+..|| |||+.-=+|.+..++.+++..++-
T Consensus 525 -----~gkL~RtF~v~dElifrdAK-----kDe~~rkaYK~La~lh~~c~~Li~ 568 (594)
T PF05667_consen 525 -----TGKLDRTFTVTDELIFRDAK-----KDEAARKAYKLLASLHENCSQLIE 568 (594)
T ss_pred -----HHHHHhHHHHHHHHHHHHhh-----cCHHHHHHHHHHHHHHHHHHHHHH
Confidence 35678888888888888888 788888888888888888887653
No 2
>PF02520 DUF148: Domain of unknown function DUF148; InterPro: IPR003677 This entry represents the domain DUF148, which has no known function.
Probab=62.46 E-value=87 Score=25.77 Aligned_cols=47 Identities=23% Similarity=0.306 Sum_probs=35.1
Q ss_pred hHHHHHHHHHHhhhhhCCcc--hHHHHHHHHHHHHhccCCHHHHHHHHH
Q 048140 165 SIEALNAAELKFQDIINSPS--VDAACRKIDSLAEKNQLDSALVLMITK 211 (334)
Q Consensus 165 d~~~L~~A~~kf~dILnS~S--ldaa~~KId~LAe~~eLDsaLvLli~k 211 (334)
-+..|-.|-.+|..|++.+| ..+.+++|++|.+.--.....+.-|.+
T Consensus 59 vi~~L~~a~~~l~~I~~n~~lT~~q~~~~I~~l~~~~~~e~~~l~~i~~ 107 (113)
T PF02520_consen 59 VISNLSSAFAKLSAILDNKSLTRQQQQEAIDALRKQYPEEVDTLFFIRK 107 (113)
T ss_pred HHHHHHHHHHHHHHHHcCcccCHHHHHHHHHHHHHHCCHHHHHHHHHHH
Confidence 34457789999999999877 788899999999877665444444433
No 3
>PF04858 TH1: TH1 protein; InterPro: IPR006942 TH1 is a highly conserved but uncharacterised metazoan protein. No homologue has been identified in Caenorhabditis elegans []. TH1 binds specifically to A-Raf kinase [].; GO: 0045892 negative regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=62.37 E-value=2.3e+02 Score=30.68 Aligned_cols=66 Identities=30% Similarity=0.494 Sum_probs=44.0
Q ss_pred hhCCcchHHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhchhhhHHHHHHHHHHHHHHHhhhhhcCchhHHHHHHHhcc
Q 048140 179 IINSPSVDAACRKIDSLAEKNQLDSALVLMITKAWSAAKESNMMKEEVKDILYHLYMTARGNLQRLMPKEVRILKYLLTI 258 (334)
Q Consensus 179 ILnS~Sldaa~~KId~LAe~~eLDsaLvLli~kA~aAAKeS~~~k~EvKDIm~hLY~~ak~~l~r~~PkEvrilkyLL~I 258 (334)
+-.|++.-.||.-|.+|-.+|.|+|+=|..+ |+.|.... ||=|-+|+|
T Consensus 277 L~~s~~~p~a~~ai~smLs~~~l~paDI~~L---------------------y~~Y~~~~-------pPPV~lLR~---- 324 (584)
T PF04858_consen 277 LNGSSSYPEACQAIASMLSSNALNPADITKL---------------------YRMYSSPD-------PPPVELLRH---- 324 (584)
T ss_pred HhcCccCchHHHHHHHHHhcCCCCHHHHHHH---------------------HHHhccCC-------CCCchhhcC----
Confidence 3444555677888888888888877755444 44443221 777877764
Q ss_pred CChHHHHhhhhhhcCCCccc
Q 048140 259 EDPEERLCGLKDAFTPGEEI 278 (334)
Q Consensus 259 eDP~er~~aL~~AFtPG~e~ 278 (334)
|.==-..|...|.||..+
T Consensus 325 --P~~l~lLld~LF~pg~~i 342 (584)
T PF04858_consen 325 --PQFLDLLLDALFKPGSKI 342 (584)
T ss_pred --HHHHHHHHHHHcCCCccC
Confidence 655567788999999865
No 4
>TIGR02284 conserved hypothetical protein. Members of this protein family are found mostly in the Proteobacteria, although one member is found in the the marine planctomycete Pirellula sp. strain 1. The function is unknown.
Probab=62.10 E-value=1e+02 Score=26.73 Aligned_cols=28 Identities=18% Similarity=0.347 Sum_probs=17.9
Q ss_pred hhhHHHhHHhhhhccCHHHHHHHHHHHHHhh
Q 048140 56 SNFFKRCQDRADAEVDPEMKHKLLRLGRKLK 86 (334)
Q Consensus 56 ~~ff~Rc~~rA~~e~Dp~~k~kl~~L~Rklk 86 (334)
-.+|.+|-+++ .||..|.-+.+.+..=.
T Consensus 16 ~~gY~~aae~v---~~~~lk~~f~~~~~~~~ 43 (139)
T TIGR02284 16 KDGFEESAEEV---KDPELATLFRRIAGEKS 43 (139)
T ss_pred HHHHHHHHHHC---CCHHHHHHHHHHHHHHH
Confidence 35677777776 67877777665554433
No 5
>PF08637 NCA2: ATP synthase regulation protein NCA2; InterPro: IPR013946 NCA2 (Nuclear Control of ATPase), is one of the two nuclear genes involved in the control of mitochondrial expression of subunits 6 and 8 of the Fo-F1 ATP synthase in Saccharomyces cerevisiae (Baker's yeast). Mutations in either NCA2 or NCA3 (IPR005556 from INTERPRO) dramatically lower the level of the co-transcript encoding subunits 6 and 8 [, ].
Probab=54.58 E-value=39 Score=33.04 Aligned_cols=127 Identities=25% Similarity=0.280 Sum_probs=86.4
Q ss_pred chHHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhchhhhHHHHHHHHHHHHHHHhhhh-------hcCc--hhHHHHHH
Q 048140 184 SVDAACRKIDSLAEKNQLDSALVLMITKAWSAAKESNMMKEEVKDILYHLYMTARGNLQ-------RLMP--KEVRILKY 254 (334)
Q Consensus 184 Sldaa~~KId~LAe~~eLDsaLvLli~kA~aAAKeS~~~k~EvKDIm~hLY~~ak~~l~-------r~~P--kEvrilky 254 (334)
+++-|---||.|-+.|||+=++|.++ ++-=|+|-+|...+..+. +..+ +.+|+.+.
T Consensus 145 D~~~Am~gID~LLkSneL~F~iva~~---------------Pa~li~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~ 209 (290)
T PF08637_consen 145 DVEVAMSGIDKLLKSNELNFGIVAAS---------------PAFLISYGLYRWLRRLFKSRKGARRRRRQRRKQRRMRRS 209 (290)
T ss_pred HHHHHHHHHHHHHHhchHHHHHHHHh---------------HHHHHHHHHHHHHHHHHccCccccccchhhHHHHHHHHH
Confidence 36778889999999999999998876 556677888877765542 1122 45688889
Q ss_pred HhccCChHHHHhhhhh-hcCCCccccccCcccccCChHHHHHHHHHHHHHhhhccccchHHHHHhhcCHH--HHHHHHHH
Q 048140 255 LLTIEDPEERLCGLKD-AFTPGEEIEGKDVDTLYTTPEMLHALMKTLVDAYNFSREGSLLKEAKDMMNPN--MIEKIEEL 331 (334)
Q Consensus 255 LL~IeDP~er~~aL~~-AFtPG~e~e~~d~d~LyttP~~L~~~i~~ilday~~~~~~tl~~eA~~l~~P~--vi~rl~~l 331 (334)
|-+|| --++.... ..+++.+..-.+...|.++-..|+.+...++ +....+....+-.+|.+|. +-+||.++
T Consensus 210 L~~ie---RlL~~~~~~~~~~~~~~~~~~~GlLl~~~~~L~~~~~~~~---p~~~~~e~~eDl~dL~~~~~~~~~kl~vv 283 (290)
T PF08637_consen 210 LRNIE---RLLNSSNNETPTQDGELSYKDHGLLLLELHRLRRSAERLL---PASERREWLEDLNDLADPRLGVSQKLRVV 283 (290)
T ss_pred HHHHH---HHHhccccccccccccchHHhHhHHHHHHHHHHHHHHHhC---CHhHHHHHHHHHHHHhcccCCHHHHHHHH
Confidence 99887 12222222 2556666667788889998888888888766 2222355677788888884 34444433
No 6
>PF03194 LUC7: LUC7 N_terminus; InterPro: IPR004882 This family consists of several LUC7 protein homologues that are restricted to eukaryotes. LUC7 has been shown to be a U1 snRNA associated protein [] with a role in splice site recognition []. The entry contains human and mouse LUC7 like (LUC7L) proteins [] and human cisplatin resistance-associated overexpressed protein (CROP) [].
Probab=54.28 E-value=1.3e+02 Score=28.98 Aligned_cols=123 Identities=20% Similarity=0.303 Sum_probs=63.1
Q ss_pred CCChHHHHHHHHHHHHhcCChhhHHHHHH--HHHHHHHHHHHhhhhhhhHHHHHHHHHHhhhhhCCcchHHHHHHHHHHH
Q 048140 119 DFTQEFFEHLHTVAESYYNDPAKQDDIAK--LGKLCVAAVQAYDTTTESIEALNAAELKFQDIINSPSVDAACRKIDSLA 196 (334)
Q Consensus 119 dFT~eFF~hL~~~~ea~~d~~dr~~~La~--L~~~claaveAyD~a~~d~~~L~~A~~kf~dILnS~Sldaa~~KId~LA 196 (334)
.|-.+||++|..++..+ |++.+-++ |...--.....-+ ....+.|..-..+ +...-.++..|.
T Consensus 79 ~YE~e~~~~L~~~i~d~----drrI~~~k~RL~~~~~~~~~~~~--~~~~~~i~~l~~~---------I~~ll~~aE~LG 143 (254)
T PF03194_consen 79 GYEREFLRYLQRLIRDC----DRRIERAKERLEQTQEEQAKEAD--EEKAEKIDELDEK---------IGELLKEAEELG 143 (254)
T ss_pred hhHHHHHHHHHHHHHHH----HHHHHHHHHHHHhCccccccchh--hhHHHHHHHHHHH---------HHHHHHHHHHHH
Confidence 58899999999999988 67664433 2211111100000 0001112211111 566667889999
Q ss_pred HhccCCHHHHHHHHHHHHHhhhchhhhHHHHHHHH---HHHHHHHhhhhhcCchhHH---HHHHHhccCChHHHH
Q 048140 197 EKNQLDSALVLMITKAWSAAKESNMMKEEVKDILY---HLYMTARGNLQRLMPKEVR---ILKYLLTIEDPEERL 265 (334)
Q Consensus 197 e~~eLDsaLvLli~kA~aAAKeS~~~k~EvKDIm~---hLY~~ak~~l~r~~PkEvr---ilkyLL~IeDP~er~ 265 (334)
+.|++|-|.-+ ..+....+.|-+.+-. .... ...+....+-+..+ |==-+|++-|-..|+
T Consensus 144 eeG~VdeA~~~--------~~~~e~Lk~ek~~le~~~~~~~~-~~~~~~~~~~qkl~VCeVCGA~Ls~~D~d~Rl 209 (254)
T PF03194_consen 144 EEGDVDEAQKL--------MEEVEKLKEEKEELEKELEEYRN-SIENSAQSQQQKLEVCEVCGAFLSVGDNDRRL 209 (254)
T ss_pred HCCCHHHHHHH--------HHHHHHHHHHHHHHHhhhhhhhh-hhhhhhcccccCccchhhhhhHHhccchHHHH
Confidence 99998876533 3333444444444333 2222 22222111222233 334788999988886
No 7
>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=52.98 E-value=42 Score=23.95 Aligned_cols=56 Identities=21% Similarity=0.340 Sum_probs=36.7
Q ss_pred hhhhhhhhhhhHHHhHHhhhhccCHHHHHHHHHHHHHhhhhcHHHHHHHHHHHHHHcCCch
Q 048140 48 SKEWNNLRSNFFKRCQDRADAEVDPEMKHKLLRLGRKLKEIDEDVQSHNELLEVIEAAPSE 108 (334)
Q Consensus 48 s~eW~~~R~~ff~Rc~~rA~~e~Dp~~k~kl~~L~Rklk~ide~~~~hneLLe~i~~~p~e 108 (334)
..+|..++..++.+|--.-..--....+.+|.++.+... +..+.+.+..++.+|.|
T Consensus 2 d~~f~~~~~~i~~~~Gi~l~~~K~~~l~rRl~~rm~~~~-----~~~~~~y~~~L~~d~~E 57 (57)
T PF03705_consen 2 DAEFERFRELIYRRTGIDLSEYKRSLLERRLARRMRALG-----LPSFAEYYELLRSDPDE 57 (57)
T ss_dssp HHHHHHHHHHHHHHH-----GGGHHHHHHHHHHHHHHHT--------HHHHHHHHHH-T--
T ss_pred HHHHHHHHHHHHHHHCCCCchhhHHHHHHHHHHHHHHcC-----CCCHHHHHHHHHhCCCC
Confidence 357888899999999888888888888888887777665 67788888888877754
No 8
>KOG3251 consensus Golgi SNAP receptor complex member [Intracellular trafficking, secretion, and vesicular transport]
Probab=52.28 E-value=88 Score=29.99 Aligned_cols=130 Identities=16% Similarity=0.198 Sum_probs=97.9
Q ss_pred HHHHHhhhhcHHHHHHHHHHHHHHcCCchhhHHHhhhccCCChHHHHHHHHHHHHhcCChhhHHHHHHHHHHHHH-----
Q 048140 80 RLGRKLKEIDEDVQSHNELLEVIEAAPSEVSQIVSRRCKDFTQEFFEHLHTVAESYYNDPAKQDDIAKLGKLCVA----- 154 (334)
Q Consensus 80 ~L~Rklk~ide~~~~hneLLe~i~~~p~eie~iVArrRkdFT~eFF~hL~~~~ea~~d~~dr~~~La~L~~~cla----- 154 (334)
.+-+.+..+...++++..++...--++ -.-+++|-+=..+=|.||+.=+..+++--++|..+++=..-++.
T Consensus 37 ~i~~sI~~~~s~~~rl~~~~~~epp~~----rq~~rlr~dQl~~d~~~l~~~l~~~~~R~~~r~~~~~er~~lL~~~~~~ 112 (213)
T KOG3251|consen 37 SIQRSIDQYASRCQRLDVLVSKEPPKS----RQAARLRVDQLLEDVEHLQTSLRTSMNRNNRREQQARERVELLDRRFTN 112 (213)
T ss_pred HHHHhHHHHHHHHHHHHhHhhcCCCCc----HHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhcCCCCC
Confidence 466677777777777776665443322 23456665556667889999888888777888888877766663
Q ss_pred ---HHHH-hhhhhhhHHHHHHHHHHhhhhhCCcc------------hHHHHHHHHHHHHhccCCHHHHHHHHHHH
Q 048140 155 ---AVQA-YDTTTESIEALNAAELKFQDIINSPS------------VDAACRKIDSLAEKNQLDSALVLMITKAW 213 (334)
Q Consensus 155 ---aveA-yD~a~~d~~~L~~A~~kf~dILnS~S------------ldaa~~KId~LAe~~eLDsaLvLli~kA~ 213 (334)
+++- ||.-+.....+..+...++|+|.+++ +..+-+||.+.+..=-|.-+++-+|.+=.
T Consensus 113 ~~~~~~~~~D~el~~~d~l~~s~~~lDd~l~~G~~ile~l~~Q~~~L~~~~~ki~~~~ntLGlSn~ti~lIeRR~ 187 (213)
T KOG3251|consen 113 GATGTSIPFDEELQENDSLKRSHNMLDDLLESGSAILENLVEQRLTLKGTQKKILDILNTLGLSNQTIRLIERRV 187 (213)
T ss_pred CCccCCCcchHHHHhhhHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHH
Confidence 3444 88888888889999999999999887 77888899999888889999998888754
No 9
>PRK14964 DNA polymerase III subunits gamma and tau; Provisional
Probab=51.25 E-value=1.5e+02 Score=31.23 Aligned_cols=126 Identities=15% Similarity=0.212 Sum_probs=66.7
Q ss_pred HHHHHHhccCCH-HHHHHHHHHHHHhhhchhhhHHHHHHH----HHHHHHH-HhhhhhcCchhHHHHHHHhccCChHHHH
Q 048140 192 IDSLAEKNQLDS-ALVLMITKAWSAAKESNMMKEEVKDIL----YHLYMTA-RGNLQRLMPKEVRILKYLLTIEDPEERL 265 (334)
Q Consensus 192 Id~LAe~~eLDs-aLvLli~kA~aAAKeS~~~k~EvKDIm----~hLY~~a-k~~l~r~~PkEvrilkyLL~IeDP~er~ 265 (334)
+..+++...=|. ..+-++.+++..+++ ..+.+.|++++ ....+.. ..=+.+..++=.+++..|+.-.||..-+
T Consensus 200 L~lIa~~s~GslR~alslLdqli~y~~~-~It~e~V~~llg~~~~~~If~L~~aI~~~d~~~Al~~l~~Ll~~g~~~~i~ 278 (491)
T PRK14964 200 LKLIAENSSGSMRNALFLLEQAAIYSNN-KISEKSVRDLLGCVDKHILEDLVEAILLGDAQSALNVFRELCNTSNPVIIL 278 (491)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHHHhcCC-CCCHHHHHHHHccCCHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCHHHHH
Confidence 334444433332 233445566555543 55666666643 1222222 2334444555667777777777777655
Q ss_pred hhhhh--------hcCCCccccc-c------CcccccCChHHHHHHHHHHHHHhhhccccchHHHHHhh
Q 048140 266 CGLKD--------AFTPGEEIEG-K------DVDTLYTTPEMLHALMKTLVDAYNFSREGSLLKEAKDM 319 (334)
Q Consensus 266 ~aL~~--------AFtPG~e~e~-~------d~d~LyttP~~L~~~i~~ilday~~~~~~tl~~eA~~l 319 (334)
..|.. ..+|+..... . ..-+- .+|..|+.+++.++++...-+..+.-+-|-.|
T Consensus 279 ~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~l~~~~~~l~~~~~~~~~~~~~~~~~e~ 346 (491)
T PRK14964 279 EGMLQIIYEICYFSITKEIDFLLGEDLITRIKSLKI-GSTIFLSRLWQMLLKGIQEVKSSTCVKQAAEM 346 (491)
T ss_pred HHHHHHHHHHHHHhcCccccccCCHHHHHHHHHHhC-CCHHHHHHHHHHHHHHHHHhccCCCchHHHHH
Confidence 54433 2344322210 0 00112 67889999999999998877665554444444
No 10
>PF07200 Mod_r: Modifier of rudimentary (Mod(r)) protein; InterPro: IPR009851 This entry represents a conserved region approximately 150 residues long within a number of eukaryotic proteins that show homology with Drosophila melanogaster Modifier of rudimentary (Mod(r)) proteins. The N-terminal half of Mod(r) proteins is acidic, whereas the C-terminal half is basic [], and both of these regions are represented in this family.; PDB: 2CAZ_F 2P22_C 2F66_F.
Probab=47.95 E-value=1.2e+02 Score=25.93 Aligned_cols=96 Identities=10% Similarity=0.105 Sum_probs=54.2
Q ss_pred HHHHHcCCchhhHHHhhhccCCChHHHHHHHHHHHHhc----CChhhHHHHHHHHHHHHHHHHHhhhhhhhHHHHHHHHH
Q 048140 99 LEVIEAAPSEVSQIVSRRCKDFTQEFFEHLHTVAESYY----NDPAKQDDIAKLGKLCVAAVQAYDTTTESIEALNAAEL 174 (334)
Q Consensus 99 Le~i~~~p~eie~iVArrRkdFT~eFF~hL~~~~ea~~----d~~dr~~~La~L~~~claaveAyD~a~~d~~~L~~A~~ 174 (334)
|..+..+|+.++++|...- ..+++......+..+.. .+...+..|..+.+.|....+.+-..-.. ...-..
T Consensus 9 L~~Ll~d~~~l~~~v~~l~--~~~~~~~~~~~l~~~n~~lAe~nL~~~~~l~~~r~~l~~~~~~~~~L~~~---~~~k~~ 83 (150)
T PF07200_consen 9 LQELLSDEEKLDAFVKSLP--QVQELQQEREELLAENEELAEQNLSLEPELEELRSQLQELYEELKELESE---YQEKEQ 83 (150)
T ss_dssp HHHHHHH-HHHHHHGGGGS----HHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHH---HHHHHH
T ss_pred HHHHHcCHHHHHHHHHcCH--HHHHHHHHHHHHHHHHHHHHHHhcccchHHHHHHHHHHHHHHHHHHHHHH---HHHHHH
Confidence 4456667777777777532 24444444444444442 44555677777777776555544444444 555556
Q ss_pred HhhhhhCCcchHHHHHHHHHHHHhc
Q 048140 175 KFQDIINSPSVDAACRKIDSLAEKN 199 (334)
Q Consensus 175 kf~dILnS~Sldaa~~KId~LAe~~ 199 (334)
.++.+...-|+++...++...+...
T Consensus 84 ~~~~l~~~~s~~~l~~~L~~~~~e~ 108 (150)
T PF07200_consen 84 QQDELSSNYSPDALLARLQAAASEA 108 (150)
T ss_dssp HHHHHHHCHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHccCCHHHHHHHHHHHHHHH
Confidence 7788877888887666666554443
No 11
>PF05276 SH3BP5: SH3 domain-binding protein 5 (SH3BP5); InterPro: IPR007940 The SH3 domain-binding protein inhibits the auto and transphophorylation of BTK and acts as a negative regulator of BTK-related signalling in B cells.
Probab=46.26 E-value=2.8e+02 Score=26.76 Aligned_cols=48 Identities=23% Similarity=0.243 Sum_probs=37.9
Q ss_pred cCCHHHHHHHHHHHHHhhhchhhhHHHHHHHH---HHHHHHHhhhhhcCch
Q 048140 200 QLDSALVLMITKAWSAAKESNMMKEEVKDILY---HLYMTARGNLQRLMPK 247 (334)
Q Consensus 200 eLDsaLvLli~kA~aAAKeS~~~k~EvKDIm~---hLY~~ak~~l~r~~Pk 247 (334)
++||+..=||+.|..-+-++...+.++.-+=. ++|..+-..++.+.=+
T Consensus 114 ~~D~~wqEmLn~A~~kVneAE~ek~~ae~eH~~~~~~~~~ae~~v~~Lek~ 164 (239)
T PF05276_consen 114 TFDPAWQEMLNHATQKVNEAEQEKTRAEREHQRRARIYNEAEQRVQQLEKK 164 (239)
T ss_pred cccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 79999999999999999999999988776543 5577766666555433
No 12
>PF02520 DUF148: Domain of unknown function DUF148; InterPro: IPR003677 This entry represents the domain DUF148, which has no known function.
Probab=45.62 E-value=1.7e+02 Score=24.04 Aligned_cols=83 Identities=22% Similarity=0.292 Sum_probs=50.4
Q ss_pred HHHHHhhhhhCCcc--hHHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhchhhhHHHHHHHHHHHH-------------
Q 048140 171 AAELKFQDIINSPS--VDAACRKIDSLAEKNQLDSALVLMITKAWSAAKESNMMKEEVKDILYHLYM------------- 235 (334)
Q Consensus 171 ~A~~kf~dILnS~S--ldaa~~KId~LAe~~eLDsaLvLli~kA~aAAKeS~~~k~EvKDIm~hLY~------------- 235 (334)
.|+..|.+|++.|+ ..+...+|.+.|++.-+- +.+--....+.+.+ ..++..|..|+..|=.
T Consensus 2 ea~~ef~~I~~n~~lt~~e~~~~l~~Wa~~~~v~-~~~~~f~~~~~~~~--~~~~~~~~~vi~~L~~a~~~l~~I~~n~~ 78 (113)
T PF02520_consen 2 EARKEFFQIFQNPNLTKAEIEEQLDEWAEKYGVQ-DQYNEFKAQVQAQK--EEVRKNVTAVISNLSSAFAKLSAILDNKS 78 (113)
T ss_pred hHHHHHHHHHcCCCCCHHHHHHHHHHHHHHCCcH-HHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHcCcc
Confidence 57888999999887 566778999999987733 33333333333322 2334455555555431
Q ss_pred -------HHHhhhhhcCchhHHHHHHHh
Q 048140 236 -------TARGNLQRLMPKEVRILKYLL 256 (334)
Q Consensus 236 -------~ak~~l~r~~PkEvrilkyLL 256 (334)
++-.+|..+.|+|++.|.|+.
T Consensus 79 lT~~q~~~~I~~l~~~~~~e~~~l~~i~ 106 (113)
T PF02520_consen 79 LTRQQQQEAIDALRKQYPEEVDTLFFIR 106 (113)
T ss_pred cCHHHHHHHHHHHHHHCCHHHHHHHHHH
Confidence 233455666777777666654
No 13
>PF06552 TOM20_plant: Plant specific mitochondrial import receptor subunit TOM20; InterPro: IPR010547 This family consists of several plant specific mitochondrial import receptor subunit TOM20 (translocase of outer membrane 20 kDa subunit) proteins. Most mitochondrial proteins are encoded by the nuclear genome, and are synthesised in the cytosol. TOM20 is a general import receptor that binds to mitochondrial pre-sequences in the early step of protein import into the mitochondria [].; GO: 0045040 protein import into mitochondrial outer membrane, 0005742 mitochondrial outer membrane translocase complex; PDB: 1ZU2_A.
Probab=43.27 E-value=82 Score=29.59 Aligned_cols=65 Identities=28% Similarity=0.450 Sum_probs=47.2
Q ss_pred HHHHHHHHHHHH-hcCChhhHHHHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHhhhhhC-CcchHHH
Q 048140 123 EFFEHLHTVAES-YYNDPAKQDDIAKLGKLCVAAVQAYDTTTESIEALNAAELKFQDIIN-SPSVDAA 188 (334)
Q Consensus 123 eFF~hL~~~~ea-~~d~~dr~~~La~L~~~claaveAyD~a~~d~~~L~~A~~kf~dILn-S~Sldaa 188 (334)
=||+|-+...++ |..+|.+-+.|.+=|-.++..-+. -...+...-++.|..||+..|. .|+.-+|
T Consensus 5 ~~FE~ark~aea~y~~nP~DadnL~~WG~ALLELAqf-k~g~es~~miedAisK~eeAL~I~P~~hdA 71 (186)
T PF06552_consen 5 LFFEHARKKAEAAYAKNPLDADNLTNWGGALLELAQF-KQGPESKKMIEDAISKFEEALKINPNKHDA 71 (186)
T ss_dssp HHHHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHHHHH-S-HHHHHHHHHHHHHHHHHHHHH-TT-HHH
T ss_pred HHHHHHHHHHHHHHHhCcHhHHHHHHHHHHHHHHHhc-cCcchHHHHHHHHHHHHHHHHhcCCchHHH
Confidence 389999999998 679999999999999999988664 2333555668899999988775 4555443
No 14
>KOG0994 consensus Extracellular matrix glycoprotein Laminin subunit beta [Extracellular structures]
Probab=43.16 E-value=6.8e+02 Score=30.32 Aligned_cols=224 Identities=19% Similarity=0.191 Sum_probs=107.9
Q ss_pred ccCHHHHHHH--HHHHHHhhhhcHHHHHHHHHHHHHHcCCchhhHHHhhhccCCChHHHHHHHHHHHHhc-CChhhHHHH
Q 048140 69 EVDPEMKHKL--LRLGRKLKEIDEDVQSHNELLEVIEAAPSEVSQIVSRRCKDFTQEFFEHLHTVAESYY-NDPAKQDDI 145 (334)
Q Consensus 69 e~Dp~~k~kl--~~L~Rklk~ide~~~~hneLLe~i~~~p~eie~iVArrRkdFT~eFF~hL~~~~ea~~-d~~dr~~~L 145 (334)
.+||+.-..| -.|+--|.-.-++|+.-..=+.+..++=..+++|+.+-+.|...- +.|+..++..+ ..++-+...
T Consensus 1488 ~adp~si~~vA~~vL~l~lp~tpeqi~~L~~~I~e~v~sL~nVd~IL~~T~~di~ra--~~L~s~A~~a~~~A~~v~~~a 1565 (1758)
T KOG0994|consen 1488 DADPDSIEEVAEEVLALELPLTPEQIQQLTGEIQERVASLPNVDAILSRTKGDIARA--ENLQSEAERARSRAEDVKGQA 1565 (1758)
T ss_pred CCCHHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHhcccHHHHHHhhhhhHHHH--HHHHHHHHHHHhHHHHHHHHH
Confidence 3455543332 123334444556666655555555566678899999998887654 56666665553 223334444
Q ss_pred HHHHHHHHHHHHHhhhhhhhHH----HHHHHHHHhhhhhCCcc-----hHHHHHHHHHHHHhccCCHHHHHHHHHHHHHh
Q 048140 146 AKLGKLCVAAVQAYDTTTESIE----ALNAAELKFQDIINSPS-----VDAACRKIDSLAEKNQLDSALVLMITKAWSAA 216 (334)
Q Consensus 146 a~L~~~claaveAyD~a~~d~~----~L~~A~~kf~dILnS~S-----ldaa~~KId~LAe~~eLDsaLvLli~kA~aAA 216 (334)
+.....+-+|-+||-+++.-++ .+..|+..+.+|=++-- +-.|...|.+|...= ..|-.-+.++=++|
T Consensus 1566 e~V~eaL~~Ad~Aq~~a~~ai~~a~~~~~~a~~~l~kv~~~t~~aE~~~~~a~q~~~eL~~~~---e~lk~~~~qns~~A 1642 (1758)
T KOG0994|consen 1566 EDVVEALEEADVAQGEAQDAIQGADRDIRLAQQLLAKVQEETAAAEKLATSATQQLGELETRM---EELKHKAAQNSAEA 1642 (1758)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHhccHHH
Confidence 4444555555555555544332 34455666666544321 222333333333221 12222222333333
Q ss_pred hhchhhhHHHH----------HHHHHHHHHHHhhhhhcCchhHHHHHHHhccCChHHHHhhhhhhcCCCccccccCcccc
Q 048140 217 KESNMMKEEVK----------DILYHLYMTARGNLQRLMPKEVRILKYLLTIEDPEERLCGLKDAFTPGEEIEGKDVDTL 286 (334)
Q Consensus 217 KeS~~~k~EvK----------DIm~hLY~~ak~~l~r~~PkEvrilkyLL~IeDP~er~~aL~~AFtPG~e~e~~d~d~L 286 (334)
|....+-.-|| +++-.-|.++..-+. |-.....+|++|-..|.+- -.+.|
T Consensus 1643 ~~a~~~a~sa~~~A~~a~q~~~~lq~~~~~~~~l~~----------~r~~g~~~ar~rAe~L~~e----------A~~Ll 1702 (1758)
T KOG0994|consen 1643 KQAEKTAGSAKEQALSAEQGLEILQKYYELVDRLLE----------KRMEGSQAARERAEQLRTE----------AEKLL 1702 (1758)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----------HHhhcchhHHHHHHHHHHH----------HHHHH
Confidence 33333322222 244444444443333 2334567888888877642 11233
Q ss_pred cCChHHHHHHHHHHHHHhhhccccchHHHHHhh
Q 048140 287 YTTPEMLHALMKTLVDAYNFSREGSLLKEAKDM 319 (334)
Q Consensus 287 yttP~~L~~~i~~ilday~~~~~~tl~~eA~~l 319 (334)
+-|-.+ +.-|+.+=.-|..+ +-.|..-|++|
T Consensus 1703 ~~a~~k-l~~l~dLe~~y~~~-~~~L~~~~aeL 1733 (1758)
T KOG0994|consen 1703 GQANEK-LDRLKDLELEYLRN-EQALEDKAAEL 1733 (1758)
T ss_pred HHHHHH-HHHHHHHHHHHhhh-hHHHHHHHHHh
Confidence 333333 34455554445544 55555555555
No 15
>PF10508 Proteasom_PSMB: Proteasome non-ATPase 26S subunit; InterPro: IPR019538 The 26S proteasome is an enzymatic complex that degrades ubiquitinated proteins in eukaryotic cells. 26S proteasome non-ATPase regulatory subunit 5 is one of a number of chaperones that are involved in the assembly of the proteasome. The chaperones dissociate before 26S proteasome formation is complete [].; GO: 0044183 protein binding involved in protein folding
Probab=42.97 E-value=4.1e+02 Score=27.62 Aligned_cols=60 Identities=18% Similarity=0.235 Sum_probs=44.8
Q ss_pred CChhhHHHHHHHHHHHHHHHHHhhhh-hhhHHHHHHHHHHhhhhhCCcchHHHHHHHHHHHH
Q 048140 137 NDPAKQDDIAKLGKLCVAAVQAYDTT-TESIEALNAAELKFQDIINSPSVDAACRKIDSLAE 197 (334)
Q Consensus 137 d~~dr~~~La~L~~~claaveAyD~a-~~d~~~L~~A~~kf~dILnS~Sldaa~~KId~LAe 197 (334)
|...+-.++..+|.-| +.+|...-. .....++..+=..+-+...+++.+--++.+..|+.
T Consensus 303 d~~~~~~A~dtlg~ig-st~~G~~~L~~~~~~~~~~~l~~~~~~~~~~~~~lk~r~l~al~~ 363 (503)
T PF10508_consen 303 DPTIREVAFDTLGQIG-STVEGKQLLLQKQGPAMKHVLKAIGDAIKSGSTELKLRALHALAS 363 (503)
T ss_pred ChhHHHHHHHHHHHHh-CCHHHHHHHHhhcchHHHHHHHHHHHHhcCCchHHHHHHHHHHHH
Confidence 4445577788999877 777888877 66667788888888888888887776666666654
No 16
>TIGR00984 3a0801s03tim44 mitochondrial import inner membrane, translocase subunit. translocase (Tom) import receptor, five proteins of the Tom channel complex, five proteins of the inner membrane translocase (Tim) and three "motor" proteins. This family is specific for the Tim proteins.
Probab=41.93 E-value=77 Score=32.59 Aligned_cols=96 Identities=17% Similarity=0.344 Sum_probs=52.7
Q ss_pred cchhhhhhhhhh--hHHHhH---HhhhhccCHHHHHHHHHHHHHhhhhcHHHHHHHHHHHHHHcCC-chhhHHHhhhccC
Q 048140 46 VFSKEWNNLRSN--FFKRCQ---DRADAEVDPEMKHKLLRLGRKLKEIDEDVQSHNELLEVIEAAP-SEVSQIVSRRCKD 119 (334)
Q Consensus 46 afs~eW~~~R~~--ff~Rc~---~rA~~e~Dp~~k~kl~~L~Rklk~ide~~~~hneLLe~i~~~p-~eie~iVArrRkd 119 (334)
+|.+.|.+++.. +|.|.+ .+-+..++|... .++.|-|.|.+-.. ..|.++| ...=..+..+-|.
T Consensus 171 ~~~~~w~~fk~~~~~~~~~~~lk~~~~eSeNp~i~--------~~r~itdkv~~~~~--~lF~ete~a~~l~eIk~~DPs 240 (378)
T TIGR00984 171 SWYSKVEDFKESNVVYRKIQELKKKYDESENPLVR--------MMRGVTDKIGGVFS--GMFSETEVSEVLTEFKKIDPT 240 (378)
T ss_pred HHHHHHHHHHhhCHHHHHHHHHHHHhhcccChhhh--------HhHHhhhhhhhhhh--cccCCCHHHHHHHHHHHhCCC
Confidence 478899999865 566654 566777777552 33344444333110 0144565 3334446677799
Q ss_pred CChHHHH-HH-----HHHHHHhcCChhhHHHHHHHHHHHHHHH
Q 048140 120 FTQEFFE-HL-----HTVAESYYNDPAKQDDIAKLGKLCVAAV 156 (334)
Q Consensus 120 FT~eFF~-hL-----~~~~ea~~d~~dr~~~La~L~~~claav 156 (334)
|+.+-|- ++ -.+++|| -+-.+..|-..|-.++
T Consensus 241 Fd~~~Fl~gar~aI~p~ILeAf-----~kGD~e~LK~~lse~v 278 (378)
T TIGR00984 241 FDKEHFLRFLREYIVPEILEAY-----VKGDLEVLKSWCSEAP 278 (378)
T ss_pred CCHHHHHHHHHHHHHHHHHHHH-----HcCCHHHHHHhhCHHH
Confidence 9987653 23 3346666 2223444555555443
No 17
>COG0143 MetG Methionyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=39.77 E-value=1.5e+02 Score=32.00 Aligned_cols=188 Identities=17% Similarity=0.164 Sum_probs=107.3
Q ss_pred hhhhcHHHHHHHHHHHHHHcCCc--hhhHHHhhhccCCChHHHHHHHHHHHHh---cCCh--hhH----HHHHHHHHHHH
Q 048140 85 LKEIDEDVQSHNELLEVIEAAPS--EVSQIVSRRCKDFTQEFFEHLHTVAESY---YNDP--AKQ----DDIAKLGKLCV 153 (334)
Q Consensus 85 lk~ide~~~~hneLLe~i~~~p~--eie~iVArrRkdFT~eFF~hL~~~~ea~---~d~~--dr~----~~La~L~~~cl 153 (334)
+....-|+=||-=+.+.=...+. .++++|+|...|+-..+=.+++..+.-. .++. ... +.-..+=+.+.
T Consensus 348 ~~~~~~D~lRYyL~~~~p~~~D~dFs~~~f~~rvN~dL~n~lgNl~~R~~~fi~k~~~g~vp~~~~~~~~~d~~~~~~~~ 427 (558)
T COG0143 348 LEQYGVDALRYYLARELPEGSDGDFSWEDFVERVNADLANKLGNLANRTLGFINKYFDGVVPAAGAPDLEEDEELLALAR 427 (558)
T ss_pred HHHcCchHhHHHHHHhCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCcCCccccccchhhHHHHHHHH
Confidence 33466667777644443333333 5699999999999999888888877722 2210 000 11112222222
Q ss_pred HHHHHhhhhhhhHHHHHHHHHHhhhhhCCcchHHHHHHHHHHHHhccCCHHHHHHHH--HHHHHhhhchhhhHHHHHHHH
Q 048140 154 AAVQAYDTTTESIEALNAAELKFQDIINSPSVDAACRKIDSLAEKNQLDSALVLMIT--KAWSAAKESNMMKEEVKDILY 231 (334)
Q Consensus 154 aaveAyD~a~~d~~~L~~A~~kf~dILnS~Sldaa~~KId~LAe~~eLDsaLvLli~--kA~aAAKeS~~~k~EvKDIm~ 231 (334)
++. ..+.+-+..-.+..|.+.|-+|+..+- -.++ +=|..||+ -..+++..||+
T Consensus 428 ~~~-----------------~~~~~~~e~~~~~~Al~~i~~l~~~~N------~Yi~~~~PW~l~k~--~~~~~~~~vl~ 482 (558)
T COG0143 428 EAL-----------------EAVAEAMEKYEFRKALEEIMALASRAN------KYIDEQAPWKLAKE--DKRERLATVLY 482 (558)
T ss_pred HHH-----------------HHHHHHHHhhhHHHHHHHHHHHHHHHH------HHhhcCCCchhhcc--CcHHHHHHHHH
Confidence 233 333333333447777777777775432 2233 34999999 44678999999
Q ss_pred HHHHHHHhhhh---hcCchhHHHHHHHhccCChHHHHhhhhhhcCCCccccccCcccccC--ChHHHHHHH
Q 048140 232 HLYMTARGNLQ---RLMPKEVRILKYLLTIEDPEERLCGLKDAFTPGEEIEGKDVDTLYT--TPEMLHALM 297 (334)
Q Consensus 232 hLY~~ak~~l~---r~~PkEvrilkyLL~IeDP~er~~aL~~AFtPG~e~e~~d~d~Lyt--tP~~L~~~i 297 (334)
+++...+.-.- =.+|.=-.=+-..|+++....-+.-......+++.+.......||+ +++++-.++
T Consensus 483 ~~~~~~r~la~ll~P~mP~~a~ki~~~L~~~~~~~~~~~~~~~~~l~~~~~~~~~~~lF~ri~~~~~~~~~ 553 (558)
T COG0143 483 LALELVRVLAILLYPFMPETAEKIWDQLGLEEDARNFTWLGARQPLLPGHKLGPPEPLFPRIEEEAIEELI 553 (558)
T ss_pred HHHHHHHHHHHHhcCcCcchHHHHHHHhCCccccccchhhhhccccCCCcccCCcccCccccCHHHHHHHH
Confidence 99988776544 4455443334455666644333444444445666677777777776 344444444
No 18
>smart00502 BBC B-Box C-terminal domain. Coiled coil region C-terminal to (some) B-Box domains
Probab=39.00 E-value=1.9e+02 Score=22.74 Aligned_cols=98 Identities=15% Similarity=0.145 Sum_probs=51.8
Q ss_pred HHHhhhhcHHHHHHHHHHHHHHcCCchhhHHHhhhccCCChHHHHHHHHHHHHhcCChhhHHHHHHHHHHH----HHHHH
Q 048140 82 GRKLKEIDEDVQSHNELLEVIEAAPSEVSQIVSRRCKDFTQEFFEHLHTVAESYYNDPAKQDDIAKLGKLC----VAAVQ 157 (334)
Q Consensus 82 ~Rklk~ide~~~~hneLLe~i~~~p~eie~iVArrRkdFT~eFF~hL~~~~ea~~d~~dr~~~La~L~~~c----laave 157 (334)
...+..+....+.+..-+..+.+.-..|+.=+..-|.+-+.+| ..|+..++.- +..-|..|...+ ...-+
T Consensus 6 ~~~l~~l~~~~~~~~~~~~~l~~~~~~l~~~~~~~~~~I~~~f-~~l~~~L~~~-----e~~ll~~l~~~~~~~~~~l~~ 79 (127)
T smart00502 6 EELLTKLRKKAAELEDALKQLISIIQEVEENAADVEAQIKAAF-DELRNALNKR-----KKQLLEDLEEQKENKLKVLEQ 79 (127)
T ss_pred HHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHH
Confidence 3334444444445555555555555555555555666655554 6666666553 333344444433 22333
Q ss_pred HhhhhhhhHHHHHHHHHHhhhhhCCcch
Q 048140 158 AYDTTTESIEALNAAELKFQDIINSPSV 185 (334)
Q Consensus 158 AyD~a~~d~~~L~~A~~kf~dILnS~Sl 185 (334)
..+........+..+....+..|+.+|.
T Consensus 80 q~~~l~~~l~~l~~~~~~~e~~l~~~~~ 107 (127)
T smart00502 80 QLESLTQKQEKLSHAINFTEEALNSGDP 107 (127)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHcCCC
Confidence 3445555555666677777777766553
No 19
>COG4660 RnfE Predicted NADH:ubiquinone oxidoreductase, subunit RnfE [Energy production and conversion]
Probab=38.79 E-value=8.4 Score=36.47 Aligned_cols=42 Identities=26% Similarity=0.346 Sum_probs=36.2
Q ss_pred HHHHHhhhhhcCchhHHHHHHHhccCChHHHHhhhhhhcCCC
Q 048140 234 YMTARGNLQRLMPKEVRILKYLLTIEDPEERLCGLKDAFTPG 275 (334)
Q Consensus 234 Y~~ak~~l~r~~PkEvrilkyLL~IeDP~er~~aL~~AFtPG 275 (334)
-+++.+.+++.+|+|+||=-|..=|..----...|-+||||+
T Consensus 52 sN~~iSl~Rk~iP~eiRiPi~vmIIAs~VT~V~mlm~Ayt~~ 93 (212)
T COG4660 52 SNTTISLFRKWIPKEIRIPIYVMIIASVVTAVQMLMNAYTYD 93 (212)
T ss_pred hhHHHHHHHHhCcccceeeeEeehHHHHHHHHHHHHHHhhhH
Confidence 466889999999999999888877777777788999999996
No 20
>PRK14963 DNA polymerase III subunits gamma and tau; Provisional
Probab=38.65 E-value=4.9e+02 Score=27.37 Aligned_cols=135 Identities=17% Similarity=0.140 Sum_probs=81.6
Q ss_pred HHHHHHHhccCCHH-HHHHHHHHHHHhhhchhhhHHHHHHH-----HHHHHHHHhhhhhcCchhHHHHHHHhcc-CChHH
Q 048140 191 KIDSLAEKNQLDSA-LVLMITKAWSAAKESNMMKEEVKDIL-----YHLYMTARGNLQRLMPKEVRILKYLLTI-EDPEE 263 (334)
Q Consensus 191 KId~LAe~~eLDsa-LvLli~kA~aAAKeS~~~k~EvKDIm-----~hLY~~ak~~l~r~~PkEvrilkyLL~I-eDP~e 263 (334)
-+..+++...=|.- ++.++.+..+. ....+.+.|..++ ..+|.-+..-+.+...+=++++..|+.- ++|..
T Consensus 199 Al~~ia~~s~GdlR~aln~Lekl~~~--~~~It~~~V~~~l~~~~~~~if~Li~al~~~d~~~Al~~l~~Ll~~G~~~~~ 276 (504)
T PRK14963 199 ALQLVARLADGAMRDAESLLERLLAL--GTPVTRKQVEEALGLPPQERLRGIAAALAQGDAAEALSGAAQLYRDGFAART 276 (504)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHHHhc--CCCCCHHHHHHHHCCCcHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCHHH
Confidence 34555555554543 23344454433 3356666666652 1233333333567777788888888754 58999
Q ss_pred HHhhhhhhcC--------CCccccccCcccccCChHHHHHHHHHHHHHhhhccccc--------hHHHHHhh--------
Q 048140 264 RLCGLKDAFT--------PGEEIEGKDVDTLYTTPEMLHALMKTLVDAYNFSREGS--------LLKEAKDM-------- 319 (334)
Q Consensus 264 r~~aL~~AFt--------PG~e~e~~d~d~LyttP~~L~~~i~~ilday~~~~~~t--------l~~eA~~l-------- 319 (334)
-+..|...|. .|.+ +.+--.|+.+...++.+-+..+.-..++ +++-++.+
T Consensus 277 Il~~L~~~~r~ll~~k~~~~~~------~~~~~~~~~~~~~l~~l~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~ 350 (504)
T PRK14963 277 LVEGLLEAFRAALYAELGLGGG------PRLEGAEPRLLAAMTALDEQMERFARRSDALSLELALLHALLALGGAPSEGV 350 (504)
T ss_pred HHHHHHHHHHHHHHHHhccCcc------cccccCcHHHHHHHHHHHHHHHHHHhccchhHHHHHHHHHHhhhccCCcccc
Confidence 9999999887 2222 1233567889999999999865522332 55555555
Q ss_pred -----cCH---HHHHHHHHHhh
Q 048140 320 -----MNP---NMIEKIEELRK 333 (334)
Q Consensus 320 -----~~P---~vi~rl~~lk~ 333 (334)
|.| .+++|+..|.+
T Consensus 351 ~~~~~~~~~~~~~~~r~~~le~ 372 (504)
T PRK14963 351 AAVAPPAPAPADLTQRLNRLEK 372 (504)
T ss_pred ccccccCCCHHHHHHHHHHHHH
Confidence 444 47888887753
No 21
>PF10540 Membr_traf_MHD: Munc13 (mammalian uncoordinated) homology domain; InterPro: IPR019558 Mammalian uncoordinated homology 13 (Munc13) proteins constitute a family of three highly homologous molecules (Munc13-1, Munc13-2 and Munc13-3) with homology to Caenorhabditis elegans unc-13p. Munc13 proteins contain a phorbol ester-binding C1 domain and two C2 domains, which are Ca2+/phospholipid binding domains. Sequence analyses have uncovered two regions called Munc13 homology domains 1 (MHD1) and 2 (MHD2) that are arranged between two flanking C2 domains. MHD1 and MHD2 domains are present in a wide variety of proteins from Arabidopsis thaliana (Mouse-ear cress), C. elegans, Drosophila melanogaster (Fruit fly), Mus musculus (Mouse), Rattus norvegicus (Rat) and Homo sapiens (Human), some of which may function in a Munc13-like manner to regulate membrane trafficking. The MHD1 and MHD2 domains are predicted to be alpha-helical. ; PDB: 3SWH_A.
Probab=38.13 E-value=98 Score=26.84 Aligned_cols=81 Identities=23% Similarity=0.316 Sum_probs=42.0
Q ss_pred chhhhHHHHHHHHHHHHHHHhhhhhcC--ch--hHHHHHHHhccCChHHHHhhhhhhcCCCccccccCcccccCChHHHH
Q 048140 219 SNMMKEEVKDILYHLYMTARGNLQRLM--PK--EVRILKYLLTIEDPEERLCGLKDAFTPGEEIEGKDVDTLYTTPEMLH 294 (334)
Q Consensus 219 S~~~k~EvKDIm~hLY~~ak~~l~r~~--Pk--EvrilkyLL~IeDP~er~~aL~~AFtPG~e~e~~d~d~LyttP~~L~ 294 (334)
++..++=.+-||.++++..-.++...+ |+ ..++...+-+ ..+.+...-.+|.... .--..=..|+
T Consensus 20 ~~L~~~~f~~vl~~lW~~vl~~l~~llvlP~ls~~~~~~~~~~------~~~~~~~~~~~~~~~~-----Lt~~q~~~l~ 88 (137)
T PF10540_consen 20 SNLEKENFKRVLKELWKVVLETLEELLVLPPLSDKPMLGLLQS------AVSSLSSHGIGGSQRP-----LTPKQCDRLF 88 (137)
T ss_dssp HHS-HHHHHHHHHHHHHHHHHHHHHHTTS-G------------------GG-TTS------------------TCHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcchhHHHHHHHH------HHHHHHhhcccccCCC-----CCHHHHHHHH
Confidence 345667789999999999999999988 54 4444444444 2222222211221111 1112235799
Q ss_pred HHHHHHHHHhhhcccc
Q 048140 295 ALMKTLVDAYNFSREG 310 (334)
Q Consensus 295 ~~i~~ilday~~~~~~ 310 (334)
.|++.+.+=||....|
T Consensus 89 ~~L~~L~~FFhA~G~G 104 (137)
T PF10540_consen 89 KWLDTLKDFFHAEGNG 104 (137)
T ss_dssp HHHHHHHHHHHCCCTS
T ss_pred HHHHHHHHHHhCCCCC
Confidence 9999999999997655
No 22
>KOG4559 consensus Uncharacterized conserved protein [Function unknown]
Probab=37.78 E-value=74 Score=27.76 Aligned_cols=22 Identities=32% Similarity=0.448 Sum_probs=14.8
Q ss_pred HHHhhhhhhhHHHHHHHHHHhh
Q 048140 156 VQAYDTTTESIEALNAAELKFQ 177 (334)
Q Consensus 156 veAyD~a~~d~~~L~~A~~kf~ 177 (334)
++--|.+.++.+.|++|..+|+
T Consensus 95 lqQIDaiddst~kLEaAa~~Ld 116 (120)
T KOG4559|consen 95 LQQIDAIDDSTDKLEAAAAKLD 116 (120)
T ss_pred HHHHHHHhhHHHHHHHHHHHHH
Confidence 3344666677777888887765
No 23
>PF01213 CAP_N: Adenylate cyclase associated (CAP) N terminal; InterPro: IPR013992 Cyclase-associated proteins (CAPs) are highly conserved actin-binding proteins present in a wide range of organisms including yeast, fly, plants, and mammals. CAPs are multifunctional proteins that contain several structural domains. CAP is involved in species-specific signalling pathways [, , , ]. In Drosophila, CAP functions in Hedgehog-mediated eye development and in establishing oocyte polarity. In Dictyostelium (slim mold), CAP is involved in microfilament reorganisation near the plasma membrane in a PIP2-regulated manner and is required to perpetuate the cAMP relay signal to organise fruitbody formation. In plants, CAP is involved in plant signalling pathways required for co-ordinated organ expansion. In yeast, CAP is involved in adenylate cyclase activation, as well as in vesicle trafficking and endocytosis. In both yeast and mammals, CAPs appear to be involved in recycling G-actin monomers from ADF/cofilins for subsequent rounds of filament assembly [, ]. In mammals, there are two different CAPs (CAP1 and CAP2) that share 64% amino acid identity. All CAPs appear to contain a C-terminal actin-binding domain that regulates actin remodelling in response to cellular signals and is required for normal cellular morphology, cell division, growth and locomotion in eukaryotes. CAP directly regulates actin filament dynamics and has been implicated in a number of complex developmental and morphological processes, including mRNA localisation and the establishment of cell polarity. Actin exists both as globular (G) (monomeric) actin subunits and assembled into filamentous (F) actin. In cells, actin cycles between these two forms. Proteins that bind F-actin often regulate F-actin assembly and its interaction with other proteins, while proteins that interact with G-actin often control the availability of unpolymerised actin. CAPs bind G-actin. In addition to actin-binding, CAPs can have additional roles, and may act as bifunctional proteins. In Saccharomyces cerevisiae (Baker's yeast), CAP is a component of the adenylyl cyclase complex (Cyr1p) that serves as an effector of Ras during normal cell signalling. S. cerevisiae CAP functions to expose adenylate cyclase binding sites to Ras, thereby enabling adenylate cyclase to be activated by Ras regulatory signals. In Schizosaccharomyces pombe (Fission yeast), CAP is also required for adenylate cyclase activity, but not through the Ras pathway. In both organisms, the N-terminal domain is responsible for adenylate cyclase activation, but the S cerevisiae and S. pombe N-termini cannot complement one another. Yeast CAPs are unique among the CAP family of proteins, because they are the only ones to directly interact with and activate adenylate cyclase []. S. cerevisiae CAP has four major domains. In addition to the N-terminal adenylate cyclase-interacting domain, and the C-terminal actin-binding domain, it possesses two other domains: a proline-rich domain that interacts with Src homology 3 (SH3) domains of specific proteins, and a domain that is responsible for CAP oligomerisation to form multimeric complexes (although oligomerisation appears to involve the N- and C-terminal domains as well). The proline-rich domain interacts with profilin, a protein that catalyses nucleotide exchange on G-actin monomers and promotes addition to barbed ends of filamentous F-actin []. Since CAP can bind profilin via a proline-rich domain, and G-actin via a C-terminal domain, it has been suggested that a ternary G-actin/CAP/profilin complex could be formed. This entry represents the N-terminal domain of CAP proteins. This domain has an all-alpha structure consisting of six helices in a bundle with a left-handed twist and an up-and-down topology [].; GO: 0003779 actin binding, 0007010 cytoskeleton organization; PDB: 1TJF_B 1S0P_A.
Probab=36.94 E-value=1.1e+02 Score=30.47 Aligned_cols=56 Identities=27% Similarity=0.444 Sum_probs=34.9
Q ss_pred HHHHHHHHHHhhhhcHHHHHHHHHHHHHHcCCchhhHHHhhhccCCChHHHHHHHHHHHHh
Q 048140 75 KHKLLRLGRKLKEIDEDVQSHNELLEVIEAAPSEVSQIVSRRCKDFTQEFFEHLHTVAESY 135 (334)
Q Consensus 75 k~kl~~L~Rklk~ide~~~~hneLLe~i~~~p~eie~iVArrRkdFT~eFF~hL~~~~ea~ 135 (334)
..+++.++-+-|+=|.. ...+||.=|.+.=.+|..+=.++| ...||.||..+.|+.
T Consensus 85 qr~~L~~as~~kKP~~~--~~~~lL~Pl~~~i~~i~~~ke~nR---~s~~fNHLsavsEgi 140 (312)
T PF01213_consen 85 QRKFLLVASKCKKPDQS--ELQELLKPLSEAIQKIQEFKEKNR---GSKFFNHLSAVSEGI 140 (312)
T ss_dssp HHHHHHHHHHBE---HH--HHHHHCHHHHHHHHHHHHHHHTTT---TSTTHHHHHHHHCGG
T ss_pred HHHHHHHHHccCCCChh--hHHHHHHHHHHHHHHHHHHHhccC---CCchHHHHHHHHHhh
Confidence 35677778888877766 455555555444444444444444 467999999999987
No 24
>PF09537 DUF2383: Domain of unknown function (DUF2383); InterPro: IPR019052 This entry represents a functionally uncharacterised ferritin like domain.; PDB: 3FSE_B.
Probab=36.93 E-value=47 Score=26.79 Aligned_cols=78 Identities=13% Similarity=0.182 Sum_probs=45.1
Q ss_pred HHHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHhhhhhCCcchHHHHHHHHHHHHhcc----CCHHHHHHHHHHHHHhhh
Q 048140 143 DDIAKLGKLCVAAVQAYDTTTESIEALNAAELKFQDIINSPSVDAACRKIDSLAEKNQ----LDSALVLMITKAWSAAKE 218 (334)
Q Consensus 143 ~~La~L~~~claaveAyD~a~~d~~~L~~A~~kf~dILnS~Sldaa~~KId~LAe~~e----LDsaLvLli~kA~aAAKe 218 (334)
+.|..|-..|..++++|+.+.+..+. ..=+..|+++.+.- ...+..|.++...-- =++++.-.+..+|...|.
T Consensus 4 ~~Ln~Ll~~~~d~~~~Y~~a~~~~~~-~~lk~~f~~~~~~~--~~~~~~L~~~i~~~Gg~p~~~gs~~g~~~r~~~~ik~ 80 (111)
T PF09537_consen 4 EALNDLLKGLHDGIEGYEKAAEKAED-PELKSLFQEFAQER--QQHAEELQAEIQELGGEPEESGSFKGALHRAWMDIKS 80 (111)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHH--S-HHHHHHHHHHHHHH--HHHHHHHHHHHHHTT--H----HHCHHHH-TTTHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCC-HHHHHHHHHHHHHH--HHHHHHHHHHHHHcCCCcCcccCHHHHHHHHHHHHHH
Confidence 46777888899999999999988653 33344555555443 233334444443333 345888888888888887
Q ss_pred chhhh
Q 048140 219 SNMMK 223 (334)
Q Consensus 219 S~~~k 223 (334)
+-...
T Consensus 81 ~~~~~ 85 (111)
T PF09537_consen 81 ALGGD 85 (111)
T ss_dssp S----
T ss_pred HhcCC
Confidence 55553
No 25
>TIGR02284 conserved hypothetical protein. Members of this protein family are found mostly in the Proteobacteria, although one member is found in the the marine planctomycete Pirellula sp. strain 1. The function is unknown.
Probab=36.91 E-value=2.3e+02 Score=24.56 Aligned_cols=106 Identities=15% Similarity=0.209 Sum_probs=58.6
Q ss_pred HHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHhhhhhCCcc--hHHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhchh
Q 048140 144 DIAKLGKLCVAAVQAYDTTTESIEALNAAELKFQDIINSPS--VDAACRKIDSLAEKNQLDSALVLMITKAWSAAKESNM 221 (334)
Q Consensus 144 ~La~L~~~claaveAyD~a~~d~~~L~~A~~kf~dILnS~S--ldaa~~KId~LAe~~eLDsaLvLli~kA~aAAKeS~~ 221 (334)
.|..|=..|..++++|+.+.++.+.- .-+..|+.+-..-. ..+....|..|-..-+=++++.-.+..+|.+.|.+=.
T Consensus 4 ~Ln~Lie~~~D~~~gY~~aae~v~~~-~lk~~f~~~~~~~~~~~~eL~~~v~~lGg~p~~~gs~~g~lhr~w~~lks~~~ 82 (139)
T TIGR02284 4 SLNDLIEISIDGKDGFEESAEEVKDP-ELATLFRRIAGEKSAIVSELQQVVASLGGKPEDHGSMVGSLHQFWGKIRATLT 82 (139)
T ss_pred HHHHHHHHcccHHHHHHHHHHHCCCH-HHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCcHHHHHHHHHHHHHHHHc
Confidence 45566667788999999999885422 22344444433221 2222223333332333578899999999997766433
Q ss_pred ------hhHHHHHHHHHHHHHHHhhhhhc-CchhHH
Q 048140 222 ------MKEEVKDILYHLYMTARGNLQRL-MPKEVR 250 (334)
Q Consensus 222 ------~k~EvKDIm~hLY~~ak~~l~r~-~PkEvr 250 (334)
+=+++..-=-+.-.+.+..|..- .|+++|
T Consensus 83 ~~~d~aiL~~~e~gEd~~~~~y~~aL~~~~l~~~~r 118 (139)
T TIGR02284 83 PNDDYVVLEEAERGEDRAKKAYDETLADQDTPAAAR 118 (139)
T ss_pred CCChHHHHHHHHHhHHHHHHHHHHHHhcCCCChHHH
Confidence 12223222234444455556554 777765
No 26
>KOG0796 consensus Spliceosome subunit [RNA processing and modification]
Probab=36.58 E-value=3e+02 Score=28.00 Aligned_cols=123 Identities=20% Similarity=0.260 Sum_probs=65.4
Q ss_pred CChHHHHHHHHHHHHhcCChhhHHHHHHHHHHHHHHHH-HhhhhhhhHHHHHHHHHHhhhhhCCcchHHHHHHHHHHHHh
Q 048140 120 FTQEFFEHLHTVAESYYNDPAKQDDIAKLGKLCVAAVQ-AYDTTTESIEALNAAELKFQDIINSPSVDAACRKIDSLAEK 198 (334)
Q Consensus 120 FT~eFF~hL~~~~ea~~d~~dr~~~La~L~~~claave-AyD~a~~d~~~L~~A~~kf~dILnS~Sldaa~~KId~LAe~ 198 (334)
|--+|+++|...+..+ +++ +.+.-.++...+| --+.+...++.+..-..+ +...-++|.+|.+.
T Consensus 80 ~E~d~~~~l~~~v~d~----~rr--i~~~kerL~e~~ee~~~e~~~k~~~v~~l~e~---------I~~~l~~~E~LG~e 144 (319)
T KOG0796|consen 80 YEWDALEILERFVADV----DRR--IEKAKERLAETVEERSEEAARKAEKVHELEEK---------IGKLLEKAEELGEE 144 (319)
T ss_pred hhHHHHHHHHHHHHHH----HHH--HHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHH---------HHHHHHHHHHHhhc
Confidence 5556899998888887 444 2333333333332 111111112222222233 34445688899999
Q ss_pred ccCCHHHHHHHHHHHHHhhhchhhhH-HHHHHHHHHHHHHHhhhhhcCchhH-HHHHHHhccCChHHHH
Q 048140 199 NQLDSALVLMITKAWSAAKESNMMKE-EVKDILYHLYMTARGNLQRLMPKEV-RILKYLLTIEDPEERL 265 (334)
Q Consensus 199 ~eLDsaLvLli~kA~aAAKeS~~~k~-EvKDIm~hLY~~ak~~l~r~~PkEv-rilkyLL~IeDP~er~ 265 (334)
|.+|-|- .+-++.+..+. |-.++.-.-+.++-++..-+++=+| -|----|++.|-..|+
T Consensus 145 G~Veeaq--------~~~~e~E~lk~~e~e~~~~~~~~~~~~~~~~~qkl~VCeVCGa~L~~~D~d~Rl 205 (319)
T KOG0796|consen 145 GNVEEAQ--------KAMKEVEELKAKEKEEAEESYNTTMPGASAQQQKLRVCEVCGAFLSVNDADRRL 205 (319)
T ss_pred CCHHHHH--------HHHHHHHHHHHHHHHHHHHHHccCcchhhhhhhhhhHHHhhhHHHhccchHHHH
Confidence 9988663 33333333333 3334444444555555544554443 4556678888888875
No 27
>PF08376 NIT: Nitrate and nitrite sensing; InterPro: IPR013587 The nitrate and nitrite-sensing (NIT) domain is a (~250 aa) sensor domain found in various receptor components of signal transduction pathways from different bacterial lineages []. The NIT domain is predicted to be all alpha-helical in structure []. Proteins containing a NIT domain belong to one of four known classes of prokaryotic signal transduction proteins: intracellular transcription anti-termination regulators, sensor histidine kinases, methyl-accepting chemotaxis proteins, diguanylate cyclases/phosphodiesterases. NIT-containing receptors regulate cellular functions such as gene expression (transcription anti-terminators and histidine kinases), cell motility (chemotaxis receptors), and enzyme activity (diguanylate cyclases/phosphodiesterases), in response to changes in nitrate and/or nitrite concentrations. The NIT domain is found as both an extracellular and an intracellular sensor. The NIT domain can be found in combination with other signalling domains, such as ANTAR, HAMP (IPR003660 from INTERPRO), MCP, Hemerythrins (IPR002063 from INTERPRO), CHASE (IPR006189 from INTERPRO), GGDEF (IPR000160 from INTERPRO), PAS (IPR000014 from INTERPRO), EAL (IPR001633 from INTERPRO), HK (IPR005467 from INTERPRO), GAF, REC and Hpt (IPR008207 from INTERPRO).; PDB: 4AKK_A.
Probab=36.21 E-value=3e+02 Score=24.23 Aligned_cols=203 Identities=17% Similarity=0.164 Sum_probs=106.3
Q ss_pred HHHHHhhhhcHHHHHHHHHHHHHHcCCchhhHHHhhhccCCChHHHHHHHHHHHHhcCChhhHHHHHHHHHHHHHHHHHh
Q 048140 80 RLGRKLKEIDEDVQSHNELLEVIEAAPSEVSQIVSRRCKDFTQEFFEHLHTVAESYYNDPAKQDDIAKLGKLCVAAVQAY 159 (334)
Q Consensus 80 ~L~Rklk~ide~~~~hneLLe~i~~~p~eie~iVArrRkdFT~eFF~hL~~~~ea~~d~~dr~~~La~L~~~claaveAy 159 (334)
.|...-..+|.-+..+...+..+...+.+- .+=.++..+...+..=+.-|..+....-...+++..|
T Consensus 29 ~l~~qr~~tD~a~~~~~~~~~~~~~~~~~~-------------~~~~~~~~~~~~l~~L~~~R~~vd~~~~~~~~~~~~Y 95 (247)
T PF08376_consen 29 ELKAQRAATDRAIAELRRALADIDDSDSDE-------------ELRDRLQEILNALDQLPQLRQQVDNRSIDPDEAFDAY 95 (247)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHCTT--HH--------------HHHHHHHHHHHGGGHHHHHHHHHHT-S-HHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHhccccccch-------------hHHHHHHHHHHHHHhHHHHHHHHhcCCCChHHHHHHH
Confidence 366667788888888888888766554211 1222333333333111222444444444556677777
Q ss_pred hhhhhhHHHHHHHHHHhhhhhCCcchHHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhchhhhHHHHHHHHH--HHHHH
Q 048140 160 DTTTESIEALNAAELKFQDIINSPSVDAACRKIDSLAEKNQLDSALVLMITKAWSAAKESNMMKEEVKDILYH--LYMTA 237 (334)
Q Consensus 160 D~a~~d~~~L~~A~~kf~dILnS~Sldaa~~KId~LAe~~eLDsaLvLli~kA~aAAKeS~~~k~EvKDIm~h--LY~~a 237 (334)
...... |..--..+......|.+-..-.-+-.|+..+|.=+--=.+++-++++-+ ...++...++.- .|...
T Consensus 96 ~~~i~~---ll~~~~~l~~~~~d~~l~~~~~a~~~l~~a~E~~~~era~~~~~l~~~~---~~~~~~~~~~~~~~~~~~~ 169 (247)
T PF08376_consen 96 TELIDS---LLDLIDALAQQSDDPELARQLRALTALLRAKEYAGQERALLAGALAAGR---LSPEELRQFASLIARQRAA 169 (247)
T ss_dssp HHHHHH---HHTHHHHHHCC---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT------HHHHHHHHHHHHHHHHH
T ss_pred HHHHHH---HHHHHHHHHhccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcC---CCHHHHHHHHHHHHHHHHH
Confidence 766665 3333334444445566666666677777777765555555666666532 344444444432 23456
Q ss_pred HhhhhhcCchhHHH-HHHHhccCChHHHHhhhhhhcCCCccccccCccccc-CChHHHHHHHHHHHHHhhhc
Q 048140 238 RGNLQRLMPKEVRI-LKYLLTIEDPEERLCGLKDAFTPGEEIEGKDVDTLY-TTPEMLHALMKTLVDAYNFS 307 (334)
Q Consensus 238 k~~l~r~~PkEvri-lkyLL~IeDP~er~~aL~~AFtPG~e~e~~d~d~Ly-ttP~~L~~~i~~ilday~~~ 307 (334)
..++....|++.+- +.-+++- +.-.++..+.+.+.-++. +. .++ .+|..........++.+...
T Consensus 170 l~~f~~~a~~~~~~~~~~~~~~-~~~~~~~~~~~~i~~~~~----~~-~~~~~~~~~W~~~~t~~id~l~~v 235 (247)
T PF08376_consen 170 LESFQAAASPEQRALYDALLSS-PAVQRVQRLRDQILSNGP----GG-GLSPIDAEEWFAAATARIDALRQV 235 (247)
T ss_dssp HHHHHHHS-HHHHHHHHHHS------HHHHHHHHHHHCS---------S-TTHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHhCCHHHHHHHHHHHhh-HHHHHHHHHHHHHhhccc----CC-CCCCCCHHHHHHHHHHHHHHHHHH
Confidence 67777777776654 4444443 666677778776655433 11 244 67777777777777776654
No 28
>PF04048 Sec8_exocyst: Sec8 exocyst complex component specific domain; InterPro: IPR007191 Sec8 is a component of the exocyst complex involved in the docking of exocystic vesicles with a fusion site on the plasma membrane. The exocyst complex is composed of Sec3, Sec5, Sec6, Sec8, Sec10, Sec15, Exo70 and Exo84.; GO: 0006904 vesicle docking involved in exocytosis, 0015031 protein transport, 0000145 exocyst
Probab=35.86 E-value=77 Score=27.48 Aligned_cols=80 Identities=16% Similarity=0.247 Sum_probs=47.2
Q ss_pred HHHHHHHHHcCCchhhHHHhhhccCCChHHHHHHHHHHHHhc----CChhhHHHHHHHHHHHHHHHHHhhhhhhhHHHHH
Q 048140 95 HNELLEVIEAAPSEVSQIVSRRCKDFTQEFFEHLHTVAESYY----NDPAKQDDIAKLGKLCVAAVQAYDTTTESIEALN 170 (334)
Q Consensus 95 hneLLe~i~~~p~eie~iVArrRkdFT~eFF~hL~~~~ea~~----d~~dr~~~La~L~~~claaveAyD~a~~d~~~L~ 170 (334)
+.++-+.....+..+..+|..+...|+.- +.+|+ .-.+-++.+..+-..|.++-..--+-..++..|.
T Consensus 42 ~~~f~~~~~~~~~~L~~vV~eh~q~Fn~s--------I~sy~~i~~~i~~sq~~i~~lK~~L~~ak~~L~~~~~eL~~L~ 113 (142)
T PF04048_consen 42 YQEFEELKKRIEKALQEVVNEHYQGFNSS--------IGSYSQILSSISESQERIRELKESLQEAKSLLGCRREELKELW 113 (142)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHH
Confidence 33444444455567777888777777754 22221 1123355566666666666666666666777777
Q ss_pred HHHHHhhhhhCC
Q 048140 171 AAELKFQDIINS 182 (334)
Q Consensus 171 ~A~~kf~dILnS 182 (334)
....++..+|..
T Consensus 114 ~~s~~~~~mi~i 125 (142)
T PF04048_consen 114 QRSQEYKEMIEI 125 (142)
T ss_pred HHHHHHHHHHHH
Confidence 777776666654
No 29
>PF11570 E2R135: Coiled-coil receptor-binding R-domain of colicin E2; InterPro: IPR024566 Bacteriocins are protein antibiotics that kill bacteria closely related to the producing species. Colicins are a subgroup of bacteriocins that are produced by and target Escherichia coli. The lethal action of most colicins is exerted either by formation of a pore in the cytoplasmic membrane of the target cell, or by an enzymatic nuclease digestion mechanism. Most colicins are able to translocate the outer membrane by a two-receptor system, where one receptor is used for the initial binding and the second for translocation. The initial binding is to cell surface receptors such as the porins OmpF, FepA, BtuB, Cir and FhuA. The presence of specific periplasmic proteins, such as TolA, TolB, TolC, or TonB, are required for translocation across the membrane []. Colicins are composed of domains with distinct functional roles. In general they contain a central R (receptor) domain that mediates receptor binding, an N-terminal T (translocation) domain that mediates translocation of the protein from the outer membrane receptor to the colicin's target within the cell, and a C-terminal C (catalytic) domain that performs the catalytic cleavage []. This entry represents the central R domain found in colicin-E2 and other colicins.; PDB: 2YSU_B 1UJW_B 2B5U_C 1JCH_A.
Probab=34.23 E-value=85 Score=28.25 Aligned_cols=43 Identities=30% Similarity=0.326 Sum_probs=31.3
Q ss_pred hHHHHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHhhhhhCCcchHHHHHHHHHHHHhccCCH
Q 048140 141 KQDDIAKLGKLCVAAVQAYDTTTESIEALNAAELKFQDIINSPSVDAACRKIDSLAEKNQLDS 203 (334)
Q Consensus 141 r~~~La~L~~~claaveAyD~a~~d~~~L~~A~~kf~dILnS~Sldaa~~KId~LAe~~eLDs 203 (334)
....++++..++-+++.+|-..-.- +++|..|..+ |+.|++++
T Consensus 20 a~~~I~~~q~r~a~a~~~~~~r~se-------------------ldqA~~~~~e-ae~k~~~~ 62 (136)
T PF11570_consen 20 ADEDIATLQERQASAEQALNGRRSE-------------------LDQANKKVKE-AEIKQDEF 62 (136)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHH-------------------HHHHHHHHHH-HHHHHCCC
T ss_pred HHHHHHHHHHHHHHHHHHHhhHHHH-------------------HHHHHHHHHH-HHhccccc
Confidence 4567889999999999887654443 6666677777 77777664
No 30
>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD. This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence.
Probab=32.75 E-value=36 Score=27.92 Aligned_cols=29 Identities=24% Similarity=0.209 Sum_probs=25.1
Q ss_pred hHHHHHHHhccCChHHHHhhhhhhcCCCc
Q 048140 248 EVRILKYLLTIEDPEERLCGLKDAFTPGE 276 (334)
Q Consensus 248 EvrilkyLL~IeDP~er~~aL~~AFtPG~ 276 (334)
=--++..||++.||+|-..-|++-|||-+
T Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~l~t~~e 33 (88)
T TIGR02531 5 LDELFDAILTLKNREECYRFFDDIATINE 33 (88)
T ss_pred HHHHHHHHHhCCCHHHHHHHHHHhCCHHH
Confidence 34578899999999999999999999854
No 31
>PRK15084 formate hydrogenlyase maturation protein HycH; Provisional
Probab=31.98 E-value=46 Score=29.81 Aligned_cols=53 Identities=19% Similarity=0.303 Sum_probs=44.8
Q ss_pred HHHHHHHhhhhhCCcchHHHHHHHHHHHHhcc--CCHHHHHHHHHHHHHhhhchh
Q 048140 169 LNAAELKFQDIINSPSVDAACRKIDSLAEKNQ--LDSALVLMITKAWSAAKESNM 221 (334)
Q Consensus 169 L~~A~~kf~dILnS~Sldaa~~KId~LAe~~e--LDsaLvLli~kA~aAAKeS~~ 221 (334)
|.---+.|.+++++..-+.|-+|+..+.+=|| +||+=+.++..|...+..+.+
T Consensus 49 L~~~~e~y~~wi~~l~~~eArrKl~gl~kfgEI~I~~~H~~~L~~A~~~~~~~~~ 103 (133)
T PRK15084 49 LTCPLDEYLAWIATLEEGEARRKMEGVPKFGEIVIDSSHVALLARAFDEAAAAQT 103 (133)
T ss_pred hcCCHHHHHHHHHhCChHHHHHHHhCcCceeEEEECHHHHHHHHHHHhhhccccC
Confidence 33344678888888877899999999999999 899999999999998876655
No 32
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=31.76 E-value=1.1e+02 Score=21.99 Aligned_cols=56 Identities=13% Similarity=0.195 Sum_probs=41.3
Q ss_pred hhhcCchhHHHHHHHhccCChHHHHhhhhhhcCCCccccccCcccccCChHHHHHHHHHHHHHhhhccccchHH
Q 048140 241 LQRLMPKEVRILKYLLTIEDPEERLCGLKDAFTPGEEIEGKDVDTLYTTPEMLHALMKTLVDAYNFSREGSLLK 314 (334)
Q Consensus 241 l~r~~PkEvrilkyLL~IeDP~er~~aL~~AFtPG~e~e~~d~d~LyttP~~L~~~i~~ilday~~~~~~tl~~ 314 (334)
+.+..|.|++||++|..=-++.|--..| ..+|.-+...+..+..-++......++.
T Consensus 1 ~~~LT~~E~~vl~~l~~G~~~~eIA~~l------------------~is~~tV~~~~~~i~~Kl~~~~~~~l~~ 56 (58)
T PF00196_consen 1 FPSLTERELEVLRLLAQGMSNKEIAEEL------------------GISEKTVKSHRRRIMKKLGVKNRAELIA 56 (58)
T ss_dssp SGSS-HHHHHHHHHHHTTS-HHHHHHHH------------------TSHHHHHHHHHHHHHHHHT-SSHHHHHH
T ss_pred CCccCHHHHHHHHHHHhcCCcchhHHhc------------------CcchhhHHHHHHHHHHHhCCCCHHHHHh
Confidence 3568899999999999988888876654 6788888888888888887765544443
No 33
>cd07908 Mn_catalase_like Manganese catalase-like protein, ferritin-like diiron-binding domain. This uncharacterized bacterial protein family has a ferritin-like domain similar to that of the manganese catalase protein of Lactobacillus plantarum and the bll3758 protein of Bradyrhizobium japonicum. Ferritin-like, diiron-carboxylate proteins participate in a range of functions including iron regulation, mono-oxygenation, and reactive radical production. These proteins are characterized by the fact that they catalyze dioxygen-dependent oxidation-hydroxylation reactions within diiron centers; one exception is manganese catalase, which catalyzes peroxide-dependent oxidation-reduction within a dimanganese center. Diiron-carboxylate proteins are further characterized by the presence of duplicate metal ligands, glutamates and histidines (ExxH) and two additional glutamates within a four-helix bundle. Outside of these conserved residues there is little obvious homology. Members include bacterio
Probab=31.67 E-value=1.6e+02 Score=25.16 Aligned_cols=46 Identities=17% Similarity=0.320 Sum_probs=32.7
Q ss_pred chhhhhhhhhhhHHHhHHhhhhccCHHHHHHHHHHHHHhhhhcHHHHHHHHHHHHH
Q 048140 47 FSKEWNNLRSNFFKRCQDRADAEVDPEMKHKLLRLGRKLKEIDEDVQSHNELLEVI 102 (334)
Q Consensus 47 fs~eW~~~R~~ff~Rc~~rA~~e~Dp~~k~kl~~L~Rklk~ide~~~~hneLLe~i 102 (334)
-+.||..+-.+||.+...+ ..+|..+..|..++. +|+ +|.+.|..+
T Consensus 25 ~~~E~~ai~~Y~y~~~~~~---~~~~~~k~~f~~lA~------eE~-~H~~~l~~~ 70 (154)
T cd07908 25 TNSELTAISQYIYQHLISE---EKYPEIAETFLGIAI------VEM-HHLEILGQL 70 (154)
T ss_pred cchHHHHHHHHHHHHHHcc---CCCHHHHHHHHHHHH------HHH-HHHHHHHHH
Confidence 4689999999999877654 368888888777764 555 555555444
No 34
>KOG3030 consensus Lipid phosphate phosphatase and related enzymes of the PAP2 family [Lipid transport and metabolism]
Probab=31.15 E-value=11 Score=37.49 Aligned_cols=17 Identities=29% Similarity=0.626 Sum_probs=14.9
Q ss_pred hhhhhhhHHHhHHhhhh
Q 048140 52 NNLRSNFFKRCQDRADA 68 (334)
Q Consensus 52 ~~~R~~ff~Rc~~rA~~ 68 (334)
-++|||||.|||=....
T Consensus 134 GRlRP~Fl~vC~P~~~~ 150 (317)
T KOG3030|consen 134 GRLRPHFLDVCQPDGTD 150 (317)
T ss_pred cCCCCCeeccccCCccC
Confidence 47899999999988866
No 35
>PF08900 DUF1845: Domain of unknown function (DUF1845); InterPro: IPR014996 Members of this protein family, such as PFL4669, are found in integrating conjugative elements (ICE) of the PFGI-1 class as in Pseudomonas fluorescens.
Probab=30.66 E-value=4.6e+02 Score=24.61 Aligned_cols=108 Identities=21% Similarity=0.267 Sum_probs=73.9
Q ss_pred hhhHHHhH--HhhhhccCHHHHHHHHHHHHHhhhhcHHHHHHHHHHHHHHcC-CchhhHHHhhhccCCChHHHHHHHHHH
Q 048140 56 SNFFKRCQ--DRADAEVDPEMKHKLLRLGRKLKEIDEDVQSHNELLEVIEAA-PSEVSQIVSRRCKDFTQEFFEHLHTVA 132 (334)
Q Consensus 56 ~~ff~Rc~--~rA~~e~Dp~~k~kl~~L~Rklk~ide~~~~hneLLe~i~~~-p~eie~iVArrRkdFT~eFF~hL~~~~ 132 (334)
|+|+.++. .++...+||=-=..|+++-.+|.++.++|+...+-|+.+... |..+.--......-++.+.|
T Consensus 40 ~~~~~~~~~i~~~a~~DdPyAD~~L~~iEe~i~~~~~~l~~~~~~l~~~l~~~p~~i~i~~~~s~~P~~~~l~------- 112 (217)
T PF08900_consen 40 PGFASRLNRIWRDARQDDPYADWWLLRIEEKINEARQELQELIARLDALLAELPKGISISEIQSVQPVDVPLF------- 112 (217)
T ss_pred HHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCccccccccCCCccceeE-------
Confidence 56777776 466778999999999999999999999999999999887766 65543333233222222211
Q ss_pred HHhcCChhhHHHHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHhhhhhCCcchH
Q 048140 133 ESYYNDPAKQDDIAKLGKLCVAAVQAYDTTTESIEALNAAELKFQDIINSPSVD 186 (334)
Q Consensus 133 ea~~d~~dr~~~La~L~~~claaveAyD~a~~d~~~L~~A~~kf~dILnS~Sld 186 (334)
--.-+|-.|+-.+.-||...-- .-.+....+++....+
T Consensus 113 -----------~~splGy~~v~LL~~yD~L~~~-----v~~a~h~glis~~~~~ 150 (217)
T PF08900_consen 113 -----------FRSPLGYRCVYLLVDYDQLARK-----VLTAWHYGLISRQERE 150 (217)
T ss_pred -----------ecCHHHHHHHHHHHHHHHHHHH-----HHHHHHHhCCChHHHH
Confidence 1135788999999999976544 2334455666655433
No 36
>cd03313 enolase Enolase: Enolases are homodimeric enzymes that catalyse the reversible dehydration of 2-phospho-D-glycerate to phosphoenolpyruvate as part of the glycolytic and gluconeogenesis pathways. The reaction is facilitated by the presence of metal ions.
Probab=30.09 E-value=1.7e+02 Score=29.75 Aligned_cols=83 Identities=24% Similarity=0.268 Sum_probs=51.5
Q ss_pred HHHHHHHHHHHHHHHhhhhhcCchh-HHHH---HHHhccCChHHHHhhhhhhc-----CCCcccc-cc---------Ccc
Q 048140 224 EEVKDILYHLYMTARGNLQRLMPKE-VRIL---KYLLTIEDPEERLCGLKDAF-----TPGEEIE-GK---------DVD 284 (334)
Q Consensus 224 ~EvKDIm~hLY~~ak~~l~r~~PkE-vril---kyLL~IeDP~er~~aL~~AF-----tPG~e~e-~~---------d~d 284 (334)
.|+.......|++.|.-+...-+.- ..+= -+--+++++++++.++.+|+ +||+.+. += +.-
T Consensus 171 ~ea~~~~~~~~~~lK~~l~~~~g~~~~~vgdeGg~~p~~~~d~~~l~~i~eAi~~~g~~~G~dv~i~lD~aas~~~~~~~ 250 (408)
T cd03313 171 SEALRMGAEVYHTLKKVLKKKGGLLATNVGDEGGFAPNLSSNEEALDLLVEAIEKAGYEPGKKIAIALDVAASEFYDEGK 250 (408)
T ss_pred HHHHHHHHHHHHHHHHHHHhhcCccccccccccCcCCCCCChHHHHHHHHHHHHHhcCCCCCeEEEEEehhhhhhcccCc
Confidence 5667777777887774443221000 0000 00015788999999999999 8998665 11 122
Q ss_pred ccc-------CChHHHHHHHHHHHHHhhh
Q 048140 285 TLY-------TTPEMLHALMKTLVDAYNF 306 (334)
Q Consensus 285 ~Ly-------ttP~~L~~~i~~ilday~~ 306 (334)
|-| .||+++...+..+++.|..
T Consensus 251 y~~~~~~~~~~t~~eai~~~~~l~e~~~i 279 (408)
T cd03313 251 YVYDSDEGKKLTSEELIDYYKELVKKYPI 279 (408)
T ss_pred ceeccCCCcccCHHHHHHHHHHHHHhCCc
Confidence 223 5889999989988887764
No 37
>TIGR03042 PS_II_psbQ_bact photosystem II protein PsbQ. This protein through the member sll1638 from Synechocystis sp. PCC 6803, was shown to be part of the cyanobacteria photosystem II. It is homologous to (but quite diverged from) the chloroplast PsbQ protein, called oxygen-evolving enhancer protein 3 (OEE3). We designate this cyanobacteria protein PsbQ by homology.
Probab=28.56 E-value=2.7e+02 Score=25.10 Aligned_cols=92 Identities=14% Similarity=0.216 Sum_probs=52.9
Q ss_pred CHHHHHHHHHHHHHhhhhcHHHHHHHHHHHHHHcCCchhhHHHhhhccCCChHH--------HHHHHHHHHHhcCChhhH
Q 048140 71 DPEMKHKLLRLGRKLKEIDEDVQSHNELLEVIEAAPSEVSQIVSRRCKDFTQEF--------FEHLHTVAESYYNDPAKQ 142 (334)
Q Consensus 71 Dp~~k~kl~~L~Rklk~ide~~~~hneLLe~i~~~p~eie~iVArrRkdFT~eF--------F~hL~~~~ea~~d~~dr~ 142 (334)
.|.....+-+-++.+++.-|+|.. +...|.+.-=-|+.-| =.-|+.++.+. -+++|
T Consensus 31 sp~~l~~i~~~~~~i~~~~~r~~e--------------Lk~lI~kk~W~~vrn~irgp~g~Lr~dl~~l~~sl--~p~dq 94 (142)
T TIGR03042 31 SPAQLAQIQRQAEGIEAAKDRLPE--------------LASLVAKEDWVFTRNLIHGPMGEVRREMTYLNQSL--LPKDQ 94 (142)
T ss_pred CHHHHHHHHHHHHHHHHHHHhhHH--------------HHHHHhhcchHHHHHHHhccHHHHHHHHHHHHHcc--CHHhH
Confidence 366666655555555555554443 3333333322222222 22345555554 47788
Q ss_pred HHHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHhhhh
Q 048140 143 DDIAKLGKLCVAAVQAYDTTTESIEALNAAELKFQDI 179 (334)
Q Consensus 143 ~~La~L~~~claaveAyD~a~~d~~~L~~A~~kf~dI 179 (334)
.++.+|...+...++.-|.|..... --.|+..|+.+
T Consensus 95 k~a~~L~~~Lf~~L~~LD~AA~~kd-~~~a~k~Y~~a 130 (142)
T TIGR03042 95 KEALALAKELKDDLEKLDEAARLQD-GPQAQKAYQKA 130 (142)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcC-HHHHHHHHHHH
Confidence 8899999999998888888877654 44444444443
No 38
>COG3937 Uncharacterized conserved protein [Function unknown]
Probab=27.19 E-value=3.3e+02 Score=23.78 Aligned_cols=47 Identities=23% Similarity=0.488 Sum_probs=31.0
Q ss_pred HHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhchhhhHHHHHHHHHHHH---HHHhhhhhcCchhHHHH
Q 048140 186 DAACRKIDSLAEKNQLDSALVLMITKAWSAAKESNMMKEEVKDILYHLYM---TARGNLQRLMPKEVRIL 252 (334)
Q Consensus 186 daa~~KId~LAe~~eLDsaLvLli~kA~aAAKeS~~~k~EvKDIm~hLY~---~ak~~l~r~~PkEvril 252 (334)
+-+.+-||+|+++|+|+.. |+|.++--|-+ .+++.+...+|--++++
T Consensus 24 ek~~klvDelVkkGeln~e--------------------Eak~~vddl~~q~k~~~~e~e~K~~r~i~~m 73 (108)
T COG3937 24 EKVQKLVDELVKKGELNAE--------------------EAKRFVDDLLRQAKEAQGELEEKIPRKIEEM 73 (108)
T ss_pred HHHHHHHHHHHHcCCCCHH--------------------HHHHHHHHHHHHHHHHhhhHHHhhhHHHHHH
Confidence 4455678999999999864 66655555544 45556666666666554
No 39
>PF12041 DELLA: Transcriptional regulator DELLA protein N terminal; InterPro: IPR021914 Gibberellins are plant hormones which have great impact on growth signalling. DELLA proteins are transcriptional regulators of growth related proteins which are downregulated when gibberellins bind to their receptor GID1. GID1 forms a complex with DELLA proteins and signals them towards 26S proteasome. The N-terminal of DELLA proteins contains conserved DELLA and VHYNP motifs which are important for GID1 binding and proteolysis of the DELLA proteins [].; PDB: 2ZSH_B 2ZSI_B.
Probab=26.65 E-value=42 Score=27.35 Aligned_cols=47 Identities=15% Similarity=0.208 Sum_probs=28.6
Q ss_pred hHHHHhhhhhhcC--CCccccccCcccccCChHHHHHHHHHHHHHhhhc
Q 048140 261 PEERLCGLKDAFT--PGEEIEGKDVDTLYTTPEMLHALMKTLVDAYNFS 307 (334)
Q Consensus 261 P~er~~aL~~AFt--PG~e~e~~d~d~LyttP~~L~~~i~~ilday~~~ 307 (334)
-.+|+.-|+.+.. |.+.+..-..|..---|..|-.||+.||.-+..+
T Consensus 19 VAQkLEqLE~vmg~~~~d~ls~lasDTVhyNPSDLs~WvesMLsEln~~ 67 (73)
T PF12041_consen 19 VAQKLEQLEMVMGNAQEDGLSQLASDTVHYNPSDLSSWVESMLSELNPP 67 (73)
T ss_dssp HHHHHHHHHHHHTT---------HCCHCCS-TTBHHHHHHHHHHC----
T ss_pred HHHHHHHHHHHHcccccchHHHhhhhhhccChHHHHHHHHHHHHhcCCC
Confidence 3567777787776 7777777777888889999999999999887654
No 40
>PF07450 HycH: Formate hydrogenlyase maturation protein HycH; InterPro: IPR010005 This family contains the bacterial formate hydrogenlyase maturation protein HycH, which is approximately 140 residues long. This may be required for the conversion of a precursor form of the large subunit of hydrogenlyase 3 into a mature form [].
Probab=25.50 E-value=94 Score=27.80 Aligned_cols=53 Identities=21% Similarity=0.236 Sum_probs=44.2
Q ss_pred HHHHHHHhhhhhCCcchHHHHHHHHHHHHhcc--CCHHHHHHHHHHHHHhhhchh
Q 048140 169 LNAAELKFQDIINSPSVDAACRKIDSLAEKNQ--LDSALVLMITKAWSAAKESNM 221 (334)
Q Consensus 169 L~~A~~kf~dILnS~Sldaa~~KId~LAe~~e--LDsaLvLli~kA~aAAKeS~~ 221 (334)
|.---+.|.+++....-+.|-+|+..+.+=|| +||+=+.++..|...+..+..
T Consensus 47 l~cp~~~y~~wi~~lp~~eArrKl~gl~kfGEI~Id~~H~~~L~~al~~~~~~~~ 101 (131)
T PF07450_consen 47 LECPLEEYERWIAQLPEGEARRKLEGLLKFGEIEIDSEHVALLAPALDELAPSFT 101 (131)
T ss_pred ccCCHHHHHHHHHhCCcHHHHHHHhCCCceeEEEECHHHHHHHHHHHHHhhhcCC
Confidence 33345678888888666799999999999999 899999999999988876655
No 41
>PF11269 DUF3069: Protein of unknown function (DUF3069); InterPro: IPR021422 This family of proteins with unknown function appear to be restricted to Gammaproteobacteria. ; PDB: 2PV4_A.
Probab=25.26 E-value=4.9e+02 Score=23.16 Aligned_cols=91 Identities=9% Similarity=0.211 Sum_probs=54.4
Q ss_pred chhhHHHhhhccCCCh-HHHHHHHHHHHHhcCChhhHHHHHHHHH-HHHHHHHHhhhhhhhHHHHHHHHHHhhhhhCCcc
Q 048140 107 SEVSQIVSRRCKDFTQ-EFFEHLHTVAESYYNDPAKQDDIAKLGK-LCVAAVQAYDTTTESIEALNAAELKFQDIINSPS 184 (334)
Q Consensus 107 ~eie~iVArrRkdFT~-eFF~hL~~~~ea~~d~~dr~~~La~L~~-~claaveAyD~a~~d~~~L~~A~~kf~dILnS~S 184 (334)
.-|++.=+.-+.=+.. +=|.-|..+++|+ -+ |.+++. ... +.=|.+.+.. .=+....-|+.+|...
T Consensus 28 ~aWdalPaSAqnvldnfeqFHalv~isqA~-~~------l~~~ae~~~~---~~~e~~~~~~-~~EY~~~lld~vl~~~- 95 (121)
T PF11269_consen 28 EAWDALPASAQNVLDNFEQFHALVSISQAW-AG------LSRMAEFDIS---ELPEDMEEEE-EQEYRAQLLDRVLHNC- 95 (121)
T ss_dssp HHHHHS-HHHHTSS-H-HHHHHHH-HHHHH-HH------HHHH----HH---HHHHTTTTS--HHHHHH-HHHHHHHTH-
T ss_pred HHHHHCcHHHHHHhhhHHHHHHHHHHHHHH-Hc------chHHhhchhh---cCccchhHHH-HHHHHHHHHHHHHHHH-
Confidence 5789999999999999 9899999999998 22 222222 111 1112222221 1344455677777654
Q ss_pred hHHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhchhhhHHHHHHH
Q 048140 185 VDAACRKIDSLAEKNQLDSALVLMITKAWSAAKESNMMKEEVKDIL 230 (334)
Q Consensus 185 ldaa~~KId~LAe~~eLDsaLvLli~kA~aAAKeS~~~k~EvKDIm 230 (334)
++++|++|+ .|+.-..|+++.+.||
T Consensus 96 lKd~vKqLK---------------------KAR~d~~mk~~f~~V~ 120 (121)
T PF11269_consen 96 LKDMVKQLK---------------------KARRDPSMKNSFKEVF 120 (121)
T ss_dssp HHHHHHHHH---------------------HHTT-HHHHHHHHHHH
T ss_pred HHHHHHHHH---------------------HHccCHHHHHHHHHHh
Confidence 777776664 5777888899998887
No 42
>KOG0240 consensus Kinesin (SMY1 subfamily) [Cytoskeleton]
Probab=25.13 E-value=6.2e+02 Score=27.93 Aligned_cols=126 Identities=13% Similarity=0.214 Sum_probs=83.7
Q ss_pred HHHHHHHHHHHhhhhcHHHHHHHHHHHHHHcCCchhhHHHhhhccCCChHHHHHHHHHHHHhcCChhhHHHHHHHHHHHH
Q 048140 74 MKHKLLRLGRKLKEIDEDVQSHNELLEVIEAAPSEVSQIVSRRCKDFTQEFFEHLHTVAESYYNDPAKQDDIAKLGKLCV 153 (334)
Q Consensus 74 ~k~kl~~L~Rklk~ide~~~~hneLLe~i~~~p~eie~iVArrRkdFT~eFF~hL~~~~ea~~d~~dr~~~La~L~~~cl 153 (334)
....+-+|.+.+-.-|+++..-..|.+.++..-.+=++..+..|.+.+.= |.++...-+ +.+...++....-+.+-
T Consensus 419 ~~e~~~~L~qqlD~kd~~~n~~sqL~~~lk~q~~~qee~~s~~~~~~e~~-q~e~~~~Q~---~~e~~~~e~~e~~~al~ 494 (607)
T KOG0240|consen 419 LTERIESLYQQLDQKDDQINKQSQLMEKLKEQLLDQEELLSSTRRLYEDI-QQELSEIQE---ENEAAKDEVKEVLTALE 494 (607)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHH-HHHHHHHHH---HHHHHHHHHHHHHHHHH
Confidence 34556677777888999999999999999866544444444444444433 233443333 22334445777788888
Q ss_pred HHHHHhhhhhhhHH---H--HHHHHHHhhhhhCCcchHHHHHHHHHHHHhccCCH
Q 048140 154 AAVQAYDTTTESIE---A--LNAAELKFQDIINSPSVDAACRKIDSLAEKNQLDS 203 (334)
Q Consensus 154 aaveAyD~a~~d~~---~--L~~A~~kf~dILnS~Sldaa~~KId~LAe~~eLDs 203 (334)
+.+.+||..++.++ . +..+-..++...++++.-...--+..+...+++-.
T Consensus 495 el~~~~~~~~~~~~~~~~~n~~sel~sl~~~~~~~~~r~~~~~~~l~~~~~~~~~ 549 (607)
T KOG0240|consen 495 ELAVNYDQKSEEKESKLSQNLKSELQSLQEPSEHQSKRITELLSELRKDLGEIGW 549 (607)
T ss_pred HHHHhhhHHHHHHhhhhhhhhHHHHHhhhhcccchhHHHHHHHHHHHhhhccccc
Confidence 99999999988866 2 45666778888888887666666666666666543
No 43
>PRK10512 selenocysteinyl-tRNA-specific translation factor; Provisional
Probab=24.99 E-value=3.8e+02 Score=28.86 Aligned_cols=74 Identities=14% Similarity=0.025 Sum_probs=52.0
Q ss_pred cCchhHHHHHHHhccCChHHHHhhhhhhcCCCccccccCcccccCChHHHHHHHHHHHHHhhhccccchHHHHHhhcC
Q 048140 244 LMPKEVRILKYLLTIEDPEERLCGLKDAFTPGEEIEGKDVDTLYTTPEMLHALMKTLVDAYNFSREGSLLKEAKDMMN 321 (334)
Q Consensus 244 ~~PkEvrilkyLL~IeDP~er~~aL~~AFtPG~e~e~~d~d~LyttP~~L~~~i~~ilday~~~~~~tl~~eA~~l~~ 321 (334)
..|+.++=|---|++ |+..-...|..+-.-|--+.-. +.+|.+|+.+.+.++.+.+.+..+ ++-.+.++|+++.
T Consensus 504 ~~p~~~~~~~~~l~~-~~~~~~~~l~~l~~~g~lv~l~--~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~r~~~g 577 (614)
T PRK10512 504 DEPWWVRDLAKETGT-DEQAMRLTLRQAAQQGIITAIV--KDRYYRNDRIVQFANMIRELDQEC-GSTCAADFRDRLG 577 (614)
T ss_pred cCCCCHHHHHHHhCC-CHHHHHHHHHHHHHCCCEEEec--CCEEECHHHHHHHHHHHHHHHhhC-CcEeHHHHHHHhC
Confidence 467776544334454 4666688888888888555433 589999999998888877776444 5667788888765
No 44
>cd07316 terB_like_DjlA N-terminal tellurium resistance protein terB-like domain of heat shock DnaJ-like proteins. Tellurium resistance terB-like domain of the DnaJ-like DjlA proteins. This family represents the terB-like domain of DjlA-like proteins, a subgroup of heat shock DnaJ-like proteins. Escherichia coli DjlA is a type III membrane protein with a small N-terminal transmembrane region and DnaJ-like domain on the extreme C-terminus. Overproduction has been shown to activate the RcsC pathway, which regulates the production of the capsular exopolysaccharide colanic acid. The specific function of this domain is unknown.
Probab=24.95 E-value=3.4e+02 Score=21.22 Aligned_cols=45 Identities=13% Similarity=0.028 Sum_probs=29.1
Q ss_pred hhhhccCHHHHHHHHHHHHHhhhhcHHHHHHHHHHHHHHcCCchh
Q 048140 65 RADAEVDPEMKHKLLRLGRKLKEIDEDVQSHNELLEVIEAAPSEV 109 (334)
Q Consensus 65 rA~~e~Dp~~k~kl~~L~Rklk~ide~~~~hneLLe~i~~~p~ei 109 (334)
+||-.-++..++.+.++.+.+...+.+.+.--+++...+.++.++
T Consensus 11 ~aDG~v~~~E~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 (106)
T cd07316 11 KADGRVSEAEIQAARALMDQMGLDAEARREAIRLFNEGKESDFGL 55 (106)
T ss_pred hccCCcCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhCcCCCCH
Confidence 567788899999988888887654344555445554444444443
No 45
>PF12348 CLASP_N: CLASP N terminal; InterPro: IPR024395 This domain is found in the N-terminal region of CLIP-associated proteins (CLASPs), which are widely conserved microtubule plus-end-tracking proteins that regulate the stability of dynamic microtubules [, ]. The domain is also found in other proteins involved in microtubule binding, including STU1, MOR1 and spindle pole body component Alp14.; PDB: 2QK2_A.
Probab=24.10 E-value=5e+02 Score=22.93 Aligned_cols=148 Identities=16% Similarity=0.183 Sum_probs=72.4
Q ss_pred ccCCChHHHHHHHHHHHHh-cCChhhHHHHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHhhhhhCCcc---hHHHHHHH
Q 048140 117 CKDFTQEFFEHLHTVAESY-YNDPAKQDDIAKLGKLCVAAVQAYDTTTESIEALNAAELKFQDIINSPS---VDAACRKI 192 (334)
Q Consensus 117 RkdFT~eFF~hL~~~~ea~-~d~~dr~~~La~L~~~claaveAyD~a~~d~~~L~~A~~kf~dILnS~S---ldaa~~KI 192 (334)
..++.+.|+.+|+.++..+ ..-.+.|-.+++.+-.|++.+-.+-...-+.. ++.---.+=+.+.+++ -++|...|
T Consensus 40 ~~~~~~~~~~~l~~~~~~i~~~l~d~Rs~v~~~A~~~l~~l~~~l~~~~~~~-~~~~l~~Ll~~~~~~~~~i~~~a~~~L 118 (228)
T PF12348_consen 40 PEDFPPDFVECLRQLLDAIIKQLSDLRSKVSKTACQLLSDLARQLGSHFEPY-ADILLPPLLKKLGDSKKFIREAANNAL 118 (228)
T ss_dssp -----HHHHHHHH---HHHHH-S-HH---HHHHHHHHHHHHHHHHGGGGHHH-HHHHHHHHHHGGG---HHHHHHHHHHH
T ss_pred ccccHHHHHHHHHHhHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHhHhHHHH-HHHHHHHHHHHHccccHHHHHHHHHHH
Confidence 5788899999998444433 23456677777777777766543332221111 2222223333444443 58889999
Q ss_pred HHHHHhccCCHHH-HHHHHHHHHHhhhchhhhHHHHHHHHHHHHHHH---hhhhhc--CchhHHHHHHHhccCChHHHHh
Q 048140 193 DSLAEKNQLDSAL-VLMITKAWSAAKESNMMKEEVKDILYHLYMTAR---GNLQRL--MPKEVRILKYLLTIEDPEERLC 266 (334)
Q Consensus 193 d~LAe~~eLDsaL-vLli~kA~aAAKeS~~~k~EvKDIm~hLY~~ak---~~l~r~--~PkEvrilkyLL~IeDP~er~~ 266 (334)
..|.+.-...+.+ +..+..+. .-.|+....++=..+.++-.... ..+... .|.=+..|..+|+=.||+=|-.
T Consensus 119 ~~i~~~~~~~~~~~~~~l~~~~--~~Kn~~vR~~~~~~l~~~l~~~~~~~~~l~~~~~~~~l~~~l~~~l~D~~~~VR~~ 196 (228)
T PF12348_consen 119 DAIIESCSYSPKILLEILSQGL--KSKNPQVREECAEWLAIILEKWGSDSSVLQKSAFLKQLVKALVKLLSDADPEVREA 196 (228)
T ss_dssp HHHHTTS-H--HHHHHHHHHHT--T-S-HHHHHHHHHHHHHHHTT-----GGG--HHHHHHHHHHHHHHHTSS-HHHHHH
T ss_pred HHHHHHCCcHHHHHHHHHHHHH--hCCCHHHHHHHHHHHHHHHHHccchHhhhcccchHHHHHHHHHHHCCCCCHHHHHH
Confidence 9999988755555 55555433 44567777777777777666655 333322 2444556666666666666654
Q ss_pred h
Q 048140 267 G 267 (334)
Q Consensus 267 a 267 (334)
+
T Consensus 197 A 197 (228)
T PF12348_consen 197 A 197 (228)
T ss_dssp H
T ss_pred H
Confidence 4
No 46
>PF09537 DUF2383: Domain of unknown function (DUF2383); InterPro: IPR019052 This entry represents a functionally uncharacterised ferritin like domain.; PDB: 3FSE_B.
Probab=24.01 E-value=1.2e+02 Score=24.44 Aligned_cols=36 Identities=19% Similarity=0.482 Sum_probs=20.0
Q ss_pred hhHHHhHHhhhhccCHHHHHHHHHHHHHhhhhcHHHHHH
Q 048140 57 NFFKRCQDRADAEVDPEMKHKLLRLGRKLKEIDEDVQSH 95 (334)
Q Consensus 57 ~ff~Rc~~rA~~e~Dp~~k~kl~~L~Rklk~ide~~~~h 95 (334)
..|.++-+++. ||..|.-|..++..-+..-.+++.+
T Consensus 18 ~~Y~~a~~~~~---~~~lk~~f~~~~~~~~~~~~~L~~~ 53 (111)
T PF09537_consen 18 EGYEKAAEKAE---DPELKSLFQEFAQERQQHAEELQAE 53 (111)
T ss_dssp HHHHHHHHH-----SHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHCC---CHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34555544444 7888887777666555444444443
No 47
>PF11588 DUF3243: Protein of unknown function (DUF3243); InterPro: IPR021637 This family of proteins with unknown function includes uncharacterised proteins ymfJ and yflH. The family appears to be restricted to Firmicutes.; PDB: 3D0W_B.
Probab=23.97 E-value=1.8e+02 Score=24.11 Aligned_cols=55 Identities=24% Similarity=0.344 Sum_probs=38.1
Q ss_pred HHHHHHHHhhhchhhhHHHHHHHHHHHHHHHhhhhhcCch---hHHHHHHHhccCChHHHHh
Q 048140 208 MITKAWSAAKESNMMKEEVKDILYHLYMTARGNLQRLMPK---EVRILKYLLTIEDPEERLC 266 (334)
Q Consensus 208 li~kA~aAAKeS~~~k~EvKDIm~hLY~~ak~~l~r~~Pk---EvrilkyLL~IeDP~er~~ 266 (334)
.|..+...|+..-+.++-+.++.|++.. .|+..++| |-|+||-|=.+-|++||..
T Consensus 13 ~Lg~~v~~ae~~Gms~e~i~~~A~~iGd----yLA~~vdP~N~EerlLkELW~va~e~Eq~~ 70 (81)
T PF11588_consen 13 FLGDRVEQAEKLGMSEETIANLAYQIGD----YLAKNVDPKNPEERLLKELWDVADEEEQHA 70 (81)
T ss_dssp HHHHHHHHHHHHHHHTT----HHHHHHH----HHHT-----SHHHHHHHHHHHC--HHHHHH
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHHH----HHHhcCCCCCHHHHHHHHHHHhCCHHHHHH
Confidence 4677888999999998889999998875 66666664 7899999999999999864
No 48
>PF06810 Phage_GP20: Phage minor structural protein GP20; InterPro: IPR009636 This family consists of several phage minor structural protein Gp20 sequences and prophage sequences of around 180 residues in length. The function of this family is unknown.; GO: 0005198 structural molecule activity
Probab=23.74 E-value=5.3e+02 Score=23.03 Aligned_cols=43 Identities=12% Similarity=0.210 Sum_probs=27.6
Q ss_pred HHHHhhhhhhhHHHHHHHHHHhhhhhCCcchHHHHHHHHHHHHhc
Q 048140 155 AVQAYDTTTESIEALNAAELKFQDIINSPSVDAACRKIDSLAEKN 199 (334)
Q Consensus 155 aveAyD~a~~d~~~L~~A~~kf~dILnS~Sldaa~~KId~LAe~~ 199 (334)
..+.||..-.++...+..-..|++ +..+.++.-.+|.+|-.++
T Consensus 25 ~~~e~~~~k~ql~~~d~~i~~Lk~--~~~d~eeLk~~i~~lq~~~ 67 (155)
T PF06810_consen 25 VKEERDNLKTQLKEADKQIKDLKK--SAKDNEELKKQIEELQAKN 67 (155)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHh--ccCCHHHHHHHHHHHHHHH
Confidence 355666666665555555555555 5677777777887776655
No 49
>PF12397 U3snoRNP10: U3 small nucleolar RNA-associated protein 10 ; InterPro: IPR022125 This domain family is found in eukaryotes, and is approximately 120 amino acids in length. The family is found in association with PF08146 from PFAM. This family is the protein associated with U3 snoRNA which is involved in the processing of pre-rRNA.
Probab=23.33 E-value=4.2e+02 Score=21.71 Aligned_cols=84 Identities=20% Similarity=0.268 Sum_probs=59.3
Q ss_pred hHHHHHH-HHHHHHhccCCHHHHHHHHHHHHHhhhchhhhHHHHHHHHHHHHHHHhhhhhcCchhHHHHHHHhccCChHH
Q 048140 185 VDAACRK-IDSLAEKNQLDSALVLMITKAWSAAKESNMMKEEVKDILYHLYMTARGNLQRLMPKEVRILKYLLTIEDPEE 263 (334)
Q Consensus 185 ldaa~~K-Id~LAe~~eLDsaLvLli~kA~aAAKeS~~~k~EvKDIm~hLY~~ak~~l~r~~PkEvrilkyLL~IeDP~e 263 (334)
...+|=- |-.||.+..|++.++--+-++....-.......+.--.+-+||.. +++. ...| .+.+|+|+.+.+..+
T Consensus 23 ~~~a~ymIl~~La~k~~L~~~~l~~l~~~i~~~~~~~~~~~~~l~~L~~l~q~-q~~~-~~lp--~~~~~~l~~~~~l~~ 98 (121)
T PF12397_consen 23 LQAAAYMILSVLASKVPLSDEVLNALMESILKNWTQETVQRQALICLIVLCQS-QENV-DSLP--RKVFKALLKLPDLIE 98 (121)
T ss_pred HHHHHHHHHHHHHhhcCCcHHHHHHHHHHHHhccccchhHHHHHHHHHHHHHc-cccc-ccCC--HHHHHHHHcCccHHH
Confidence 4444433 456888999999999999999888776665556677778888821 1111 1233 568999999999998
Q ss_pred HHhhhhhhc
Q 048140 264 RLCGLKDAF 272 (334)
Q Consensus 264 r~~aL~~AF 272 (334)
.+..|.+-+
T Consensus 99 ~L~~l~~~~ 107 (121)
T PF12397_consen 99 LLSELSEKY 107 (121)
T ss_pred HHHHHHhcC
Confidence 888886544
No 50
>PF09371 Tex_N: Tex-like protein N-terminal domain; InterPro: IPR018974 This presumed domain is found at the N terminus of Q45388 from SWISSPROT. This protein defines a novel family of prokaryotic transcriptional accessory factors []. ; PDB: 2OCE_A 3BZK_A 3BZC_A.
Probab=23.13 E-value=1.5e+02 Score=27.57 Aligned_cols=51 Identities=14% Similarity=0.231 Sum_probs=24.0
Q ss_pred HHHhhhccCCChHH-HHHHHHHHHHhcCChhhHHHHHHHHHHHHHHHHHhhhhhhh
Q 048140 111 QIVSRRCKDFTQEF-FEHLHTVAESYYNDPAKQDDIAKLGKLCVAAVQAYDTTTES 165 (334)
Q Consensus 111 ~iVArrRkdFT~eF-F~hL~~~~ea~~d~~dr~~~La~L~~~claaveAyD~a~~d 165 (334)
-+|||+||+-||.- -..|+.+.+.| .....|.+=...++.+++.=...+..
T Consensus 26 PFIARYRKe~TG~Lde~~lR~i~~~~----~~~~~L~~Rk~~il~~i~eqgkLt~e 77 (193)
T PF09371_consen 26 PFIARYRKEMTGGLDEVQLREIQDRY----EYLRELEKRKESILKSIEEQGKLTPE 77 (193)
T ss_dssp HHHHHH-HHHHTS--HHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHTT---HH
T ss_pred chhhhhhhhhhCCCCHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHcccCCHH
Confidence 47899999999863 23344444444 33333433344444444444433333
No 51
>cd05509 Bromo_gcn5_like Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates acetylation of histones at lysine residues; such acetylation is generally correlated with the activation of transcription. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=23.01 E-value=1.6e+02 Score=23.65 Aligned_cols=47 Identities=19% Similarity=0.243 Sum_probs=38.2
Q ss_pred cccCChHHHHHHHHHHHH-HhhhccccchHHHHHhhcCHHHHHHHHHH
Q 048140 285 TLYTTPEMLHALMKTLVD-AYNFSREGSLLKEAKDMMNPNMIEKIEEL 331 (334)
Q Consensus 285 ~LyttP~~L~~~i~~ild-ay~~~~~~tl~~eA~~l~~P~vi~rl~~l 331 (334)
.-|.|+.++..-|.-|.. |...|.+|+.+-.+..-+.-.+.++|+.|
T Consensus 54 ~~Y~s~~~f~~Dv~li~~Na~~yN~~~s~~~~~a~~l~~~f~~~~~~~ 101 (101)
T cd05509 54 GYYVTLEEFVADLKLIFDNCRLYNGPDTEYYKCANKLEKFFWKKLKEL 101 (101)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHhhC
Confidence 349999999999999987 56667779988888888888888877654
No 52
>PF06160 EzrA: Septation ring formation regulator, EzrA ; InterPro: IPR010379 During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerises into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation [].; GO: 0000921 septin ring assembly, 0005940 septin ring, 0016021 integral to membrane
Probab=22.49 E-value=7.7e+02 Score=26.17 Aligned_cols=63 Identities=14% Similarity=0.283 Sum_probs=50.8
Q ss_pred chhhhhhhhhhhHHHhHHhhhhccCHHHHHHHHHHHHHhhhhcHHHHHHHHHHHHHHcCCchh
Q 048140 47 FSKEWNNLRSNFFKRCQDRADAEVDPEMKHKLLRLGRKLKEIDEDVQSHNELLEVIEAAPSEV 109 (334)
Q Consensus 47 fs~eW~~~R~~ff~Rc~~rA~~e~Dp~~k~kl~~L~Rklk~ide~~~~hneLLe~i~~~p~ei 109 (334)
...+|..|-..-|+-|......-++-..+.++.+-...++.+++.++...+-+..|+..=.++
T Consensus 65 w~~~w~~i~~~~~~~ie~~L~~ae~~~~~~rf~ka~~~i~~~~~~l~~~e~~i~~i~~~l~~L 127 (560)
T PF06160_consen 65 WRQKWDEIVTKQLPEIEEQLFEAEEYADKYRFKKAKQAIKEIEEQLDEIEEDIKEILDELDEL 127 (560)
T ss_pred HHHHHHHHHHHhhHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 467999999888999999998888888899999998888888888887777666665443333
No 53
>PF01503 PRA-PH: Phosphoribosyl-ATP pyrophosphohydrolase; InterPro: IPR021130 Phosphoribosyl-ATP pyrophosphatase, 3.6.1.31 from EC catalyses the second step in the histidine biosynthetic pathway: 5-phosphoribosyl-ATP + H2O = 5-phosphoribosyl-AMP + PPi The Neurospora crassa enzyme also catalyzes the reactions of histidinol dehydrogenase (1.1.1.23 from EC) and phosphoribosyl-AMP cyclohydrolase (3.5.4.19 from EC). This entry also includes the Bacillus subtilis Cof proteins, which catalyze the hydrolysis of 4-amino-2-methyl-5-hydroxymethylpyrimidine pyrophosphate to 4-amino-2-methyl-5-hydroxymethylpyrimidine phosphate []. ; PDB: 2A7W_K 3NL9_A 1YXB_D 1YVW_A 2YFD_C 2YFC_B 2YF3_C 2YF4_A 2YEU_E 2YF9_A ....
Probab=21.99 E-value=1.7e+02 Score=22.90 Aligned_cols=27 Identities=33% Similarity=0.496 Sum_probs=19.4
Q ss_pred HHHhh--hchhhhHHHHHHHHHHHHHHHh
Q 048140 213 WSAAK--ESNMMKEEVKDILYHLYMTARG 239 (334)
Q Consensus 213 ~aAAK--eS~~~k~EvKDIm~hLY~~ak~ 239 (334)
+.|++ ...-..+|+-|+|||+|-.+..
T Consensus 39 ~~A~~~~d~~~~~~e~aDlly~~~~~~~~ 67 (83)
T PF01503_consen 39 IEAAKNGDKEEVADELADLLYHLLGLLAS 67 (83)
T ss_dssp HHHHHCSHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHcCCHHHHHHHHHHHHHHHHHHHHH
Confidence 34444 4455678999999999987653
No 54
>PF13949 ALIX_LYPXL_bnd: ALIX V-shaped domain binding to HIV ; PDB: 2XS1_A 2XS8_A 2R03_A 2R02_A 2OEX_B 2OEV_A 2OJQ_A 2R05_A.
Probab=21.73 E-value=6.6e+02 Score=23.41 Aligned_cols=59 Identities=25% Similarity=0.434 Sum_probs=33.8
Q ss_pred HHHHHHHHHHHHHhhhhcHHHHHHHHHHHHHHc-CC-chhhHHHhh-hc---cCCChHHHHHHHH
Q 048140 72 PEMKHKLLRLGRKLKEIDEDVQSHNELLEVIEA-AP-SEVSQIVSR-RC---KDFTQEFFEHLHT 130 (334)
Q Consensus 72 p~~k~kl~~L~Rklk~ide~~~~hneLLe~i~~-~p-~eie~iVAr-rR---kdFT~eFF~hL~~ 130 (334)
|.....+..|-+.|.++++=...-+.++..++. .. .++..++.. .+ .+|..=|=+||.-
T Consensus 137 ~~~~~~i~~L~~ll~~l~~l~~eR~~~~~~lk~~~~~d~i~~~l~~~~~~~~~~~~~lf~~eL~k 201 (296)
T PF13949_consen 137 PQVSEVIRQLRELLNKLEELKKEREELLEQLKEKLQNDDISKLLSELNKNGSADFEALFEEELKK 201 (296)
T ss_dssp GSS-HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHSSS--HHHHHHHHHHH
T ss_pred cchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccHHHHHHHhhccCCccHHHHHHHHHHH
Confidence 444555666666777777777777888888886 33 455655552 22 3566556556554
No 55
>PRK04778 septation ring formation regulator EzrA; Provisional
Probab=21.64 E-value=5.1e+02 Score=27.38 Aligned_cols=209 Identities=14% Similarity=0.207 Sum_probs=111.9
Q ss_pred chhhhhhhhhhhHHHhHHhhhhccCHHHHHHHHHHHHHhhhhcHHHHHHHHHHHHHHcCCchhhHHHhhhccCCC--hHH
Q 048140 47 FSKEWNNLRSNFFKRCQDRADAEVDPEMKHKLLRLGRKLKEIDEDVQSHNELLEVIEAAPSEVSQIVSRRCKDFT--QEF 124 (334)
Q Consensus 47 fs~eW~~~R~~ff~Rc~~rA~~e~Dp~~k~kl~~L~Rklk~ide~~~~hneLLe~i~~~p~eie~iVArrRkdFT--~eF 124 (334)
+..+|+.|-.+-|+-|....-...+-..+.++.+-.+.+..+++.|+...+-+..|+..=++|-..=.++|...+ .+=
T Consensus 69 w~~~~~~i~~~~~~~ie~~l~~ae~~~~~~~f~~a~~~~~~~~~~l~~~e~~~~~i~~~l~~l~~~e~~nr~~v~~l~~~ 148 (569)
T PRK04778 69 WRQKWDEIVTNSLPDIEEQLFEAEELNDKFRFRKAKHEINEIESLLDLIEEDIEQILEELQELLESEEKNREEVEQLKDL 148 (569)
T ss_pred HHHHHHHHHHhhhhhHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 468999999999999999999988888999999998888888888887776666665433333222223332222 233
Q ss_pred HHHHHHHHHHhc----CC----hhhHHHHHHHHHHHH---------HHHHHhhhhhhhHHHHHHHHHHhhhhhC-----C
Q 048140 125 FEHLHTVAESYY----ND----PAKQDDIAKLGKLCV---------AAVQAYDTTTESIEALNAAELKFQDIIN-----S 182 (334)
Q Consensus 125 F~hL~~~~ea~~----d~----~dr~~~La~L~~~cl---------aaveAyD~a~~d~~~L~~A~~kf~dILn-----S 182 (334)
|+.++-.+-+.+ .. +++...|+..=+... .|=+-++.+-+....|...-....+++. -
T Consensus 149 y~~~rk~ll~~~~~~G~a~~~le~~l~~~e~~f~~f~~l~~~Gd~~~A~e~l~~l~~~~~~l~~~~~~iP~l~~~~~~~~ 228 (569)
T PRK04778 149 YRELRKSLLANRFSFGPALDELEKQLENLEEEFSQFVELTESGDYVEAREILDQLEEELAALEQIMEEIPELLKELQTEL 228 (569)
T ss_pred HHHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 445544443332 11 111222222222222 2222333333333333333333333332 1
Q ss_pred cc-hHHHHHHHHHHHHhcc-CC----HHHHHHHHHHHHH----hhh-----chhhhHHHHHHHHHHHHH------HHhhh
Q 048140 183 PS-VDAACRKIDSLAEKNQ-LD----SALVLMITKAWSA----AKE-----SNMMKEEVKDILYHLYMT------ARGNL 241 (334)
Q Consensus 183 ~S-ldaa~~KId~LAe~~e-LD----saLvLli~kA~aA----AKe-----S~~~k~EvKDIm~hLY~~------ak~~l 241 (334)
|. +++.-.-+..|.+.|= |+ ++=+--|.+.+.. .+. ...--+++.+-+-+||.. |+...
T Consensus 229 P~ql~el~~gy~~m~~~gy~~~~~~i~~~i~~l~~~i~~~~~~l~~l~l~~~~~~~~~i~~~Id~Lyd~lekE~~A~~~v 308 (569)
T PRK04778 229 PDQLQELKAGYRELVEEGYHLDHLDIEKEIQDLKEQIDENLALLEELDLDEAEEKNEEIQERIDQLYDILEREVKARKYV 308 (569)
T ss_pred hHHHHHHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHHHHHHHHhcChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 22 5666666788888884 33 2334444444444 221 222223455555666653 55556
Q ss_pred hhcCchhHHHHHHH
Q 048140 242 QRLMPKEVRILKYL 255 (334)
Q Consensus 242 ~r~~PkEvrilkyL 255 (334)
.+.+|+--+-|.|+
T Consensus 309 ek~~~~l~~~l~~~ 322 (569)
T PRK04778 309 EKNSDTLPDFLEHA 322 (569)
T ss_pred HHhhHHHHHHHHHH
Confidence 66666655555443
No 56
>PF13514 AAA_27: AAA domain
Probab=21.44 E-value=1.3e+03 Score=26.57 Aligned_cols=132 Identities=17% Similarity=0.218 Sum_probs=67.5
Q ss_pred cCHHHHHHHHHHHHHhhhhcHHHHHHHHHHHHHHcCC----chhhHHHhhhccCCChHHH-HHHHHHHHHhcCChhhHHH
Q 048140 70 VDPEMKHKLLRLGRKLKEIDEDVQSHNELLEVIEAAP----SEVSQIVSRRCKDFTQEFF-EHLHTVAESYYNDPAKQDD 144 (334)
Q Consensus 70 ~Dp~~k~kl~~L~Rklk~ide~~~~hneLLe~i~~~p----~eie~iVArrRkdFT~eFF-~hL~~~~ea~~d~~dr~~~ 144 (334)
..|..-...+...+.+.....++..+..-++.+...- ..+..++.+.-.++...-. ..+..+...+......+..
T Consensus 723 ~~~~~~~~~l~~l~~l~~~~~~~~~~~~ri~~~~~~~~~f~~~~~~L~~~l~~~~~~~~~~~~~~~L~~~l~~a~~~~~~ 802 (1111)
T PF13514_consen 723 ASPEEALEALELLEELREALAEIRELRRRIEQMEADLAAFEEQVAALAERLGPDLPEDPAEEALEALRARLEEAREAQEE 802 (1111)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcccccCcHHHHHHHHHHHHHHHHHHHHH
Confidence 3565555555555556655555555555555554332 3344444444444333211 2333333333233344566
Q ss_pred HHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHhhhhhCCcchHHHHHHHHHHHHhccC
Q 048140 145 IAKLGKLCVAAVQAYDTTTESIEALNAAELKFQDIINSPSVDAACRKIDSLAEKNQL 201 (334)
Q Consensus 145 La~L~~~claaveAyD~a~~d~~~L~~A~~kf~dILnS~Sldaa~~KId~LAe~~eL 201 (334)
+.++...+-.+-+.++.+...+..+......+-....+.|.++....+....+..++
T Consensus 803 ~~~l~~~~~~~~~~~~~~~~~l~~~~~~l~~L~~~a~~~~~e~l~~~~~~~~~~~~l 859 (1111)
T PF13514_consen 803 RERLQEQLEELEEELEQAEEELEELEAELAELLEQAGVEDEEELREAEERAEERREL 859 (1111)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHH
Confidence 666777777777777777666444444333333344556666665555555444444
No 57
>cd07177 terB_like tellurium resistance terB-like protein. This family consists of tellurium resistance terB proteins, N-terminal domain of heat shock DnaJ-like proteins, N-terminal domain of Mo-dependent nitrogenase-like proteins, C-terminal domain of ABC transporter ATP-binding proteins, C-terminal domain of serine/threonine protein kinase, and many hypothetical bacterial proteins. The function of this family is unknown.
Probab=21.17 E-value=3.7e+02 Score=20.29 Aligned_cols=85 Identities=22% Similarity=0.232 Sum_probs=51.9
Q ss_pred hhhccCHHHHHHHHHHHHHhhhh-cHHHHHHHHHHHHHHc---CCchhhHHHhhhcc-CCChHHHHHHHHHHHHhc-CCh
Q 048140 66 ADAEVDPEMKHKLLRLGRKLKEI-DEDVQSHNELLEVIEA---APSEVSQIVSRRCK-DFTQEFFEHLHTVAESYY-NDP 139 (334)
Q Consensus 66 A~~e~Dp~~k~kl~~L~Rklk~i-de~~~~hneLLe~i~~---~p~eie~iVArrRk-dFT~eFF~hL~~~~ea~~-d~~ 139 (334)
||-+-+|..+..+..+.+.+-.. ..+.+.-.+++..... .+..+..++..... +--..++..+..++.+=+ =++
T Consensus 12 aDG~i~~~E~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~l~~~~~ia~aDG~~~~ 91 (104)
T cd07177 12 ADGRVDEEEIAAIEALLRRLPLLDAEERAELIALLEEPLAEAGDLAALAALLKELPDAELREALLAALWEVALADGELDP 91 (104)
T ss_pred hcCCCCHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHhcccHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhccCCCH
Confidence 68889999999999888887652 2344555555555554 34455554443332 333466777777766653 234
Q ss_pred hhHHHHHHHHH
Q 048140 140 AKQDDIAKLGK 150 (334)
Q Consensus 140 dr~~~La~L~~ 150 (334)
.++.-|.+++.
T Consensus 92 ~E~~~l~~l~~ 102 (104)
T cd07177 92 EERALLRRLAD 102 (104)
T ss_pred HHHHHHHHHHh
Confidence 56666666654
No 58
>PF11363 DUF3164: Protein of unknown function (DUF3164); InterPro: IPR021505 This entry is represented by Bacteriophage B3, Orf6. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=21.04 E-value=1.3e+02 Score=28.01 Aligned_cols=28 Identities=25% Similarity=0.373 Sum_probs=15.9
Q ss_pred chhHHHHHHHhccCChH--HHHhhhhhhcCC
Q 048140 246 PKEVRILKYLLTIEDPE--ERLCGLKDAFTP 274 (334)
Q Consensus 246 PkEvrilkyLL~IeDP~--er~~aL~~AFtP 274 (334)
|+.|--|+-| .|+||+ +-..++.+|..|
T Consensus 138 ~~rIl~Lrrl-~i~D~~w~~am~aI~dsi~v 167 (195)
T PF11363_consen 138 TSRILGLRRL-EIDDERWQEAMDAIKDSIQV 167 (195)
T ss_pred HHHHHHHHhc-cCCCHHHHHHHHHHHhceEe
Confidence 4445555555 788874 334556666554
No 59
>PF01347 Vitellogenin_N: Lipoprotein amino terminal region; InterPro: IPR001747 This entry represents a conserved region found in several lipid transport proteins, including vitellogenin, microsomal triglyceride transfer protein and apolipoprotein B-100 []. Vitellinogen precursors provide the major egg yolk proteins that are a source of nutrients during early development of oviparous vertebrates and invertebrates. Vitellinogen precursors are multi-domain apolipoproteins that are cleaved into distinct yolk proteins. Different vitellinogen precursors exist, which are composed of variable combinations of yolk protein components; however, the cleavage sites are conserved. In vertebrates, a complete vitellinogen is composed of an N-terminal signal peptide for export, followed by four regions that can be cleaved into yolk proteins: lipovitellin-1, phosvitin, lipovitellin-2, and a von Willebrand factor type D domain (YGP40) [, ]. Microsomal triglyceride transfer protein (MTTP) is an endoplasmic reticulum lipid transfer protein involved in the biosynthesis and lipid loading of apolipoprotein B. MTTP is also involved in the late stage of CD1d trafficking in the lysosomal compartment, CD1d being the MHC I-like lipid antigen presenting molecule []. Apolipoprotein B can exist in two forms: B-100 and B-48. Apoliporotein B-100 is present on several lipoproteins, including very low-density lipoproteins (VLDL), intermediate density lipoproteins (IDL) and low density lipoproteins (LDL), and can assemble VLDL particles in the liver []. Apolipoprotein B-100 has been linked to the development of atherosclerosis.; GO: 0005319 lipid transporter activity, 0006869 lipid transport; PDB: 1LSH_A.
Probab=20.99 E-value=5.6e+02 Score=26.51 Aligned_cols=54 Identities=24% Similarity=0.395 Sum_probs=34.6
Q ss_pred HHHHHHHhhhchhhhHHHHHHHHHHHHHHHhhhhhcCchhHHHHHHHhccCC-hH-HHHhhh
Q 048140 209 ITKAWSAAKESNMMKEEVKDILYHLYMTARGNLQRLMPKEVRILKYLLTIED-PE-ERLCGL 268 (334)
Q Consensus 209 i~kA~aAAKeS~~~k~EvKDIm~hLY~~ak~~l~r~~PkEvrilkyLL~IeD-P~-er~~aL 268 (334)
+...||--+-.....++|.+|++.+|.-. .-|.|+||.-|++=+.- |. ..+..+
T Consensus 542 ~~Ai~Alr~~~~~~~~~v~~~l~~I~~n~------~e~~EvRiaA~~~lm~~~P~~~~l~~i 597 (618)
T PF01347_consen 542 VAAIQALRRLAKHCPEKVREILLPIFMNT------TEDPEVRIAAYLILMRCNPSPSVLQRI 597 (618)
T ss_dssp HHHHHTTTTGGGT-HHHHHHHHHHHHH-T------TS-HHHHHHHHHHHHHT---HHHHHHH
T ss_pred HHHHHHHHHHhhcCcHHHHHHHHHHhcCC------CCChhHHHHHHHHHHhcCCCHHHHHHH
Confidence 33444444456777889999999999754 45899999999877765 53 334433
No 60
>COG2206 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]
Probab=20.65 E-value=2e+02 Score=28.30 Aligned_cols=60 Identities=20% Similarity=0.245 Sum_probs=39.3
Q ss_pred HHHHHHHHHHHhhhhhhhHHHHHHHHHHhhhhhCCcchHHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhc
Q 048140 148 LGKLCVAAVQAYDTTTESIEALNAAELKFQDIINSPSVDAACRKIDSLAEKNQLDSALVLMITKAWSAAKES 219 (334)
Q Consensus 148 L~~~claaveAyD~a~~d~~~L~~A~~kf~dILnS~Sldaa~~KId~LAe~~eLDsaLvLli~kA~aAAKeS 219 (334)
|.+++++.+-+||.++.+ .-|. ..-|.++|-+-|.. ...+++||.+|..+-++..--...
T Consensus 258 l~aRIiAVADvydAlts~--------RpYk---ka~s~~~Al~~l~~-~~~~~fDp~vv~~~~~~~~~~~~~ 317 (344)
T COG2206 258 LEARIIAVADVYDALTSD--------RPYK---KAKSPEEALEELRK-NSGGKFDPKVVDAFLKALSKYPIG 317 (344)
T ss_pred hHhHHHHHhhHHHHHhcC--------CCCc---ccCCHHHHHHHHHH-hcCCCCCHHHHHHHHHHHhhcCCc
Confidence 668889999999988854 1111 12345554444444 445679999999998887654443
No 61
>PF03869 Arc: Arc-like DNA binding domain; InterPro: IPR005569 Arc repressor act by the cooperative binding of two Arc repressor dimers to a 21-base-pair operator site. Each Arc dimer uses an antiparallel beta-sheet to recognise bases in the major groove [].; GO: 0003677 DNA binding; PDB: 3QOQ_D 1MNT_B 1QTG_B 1BDV_A 1PAR_C 1BDT_C 1ARR_B 1MYL_F 1MYK_A 1NLA_B ....
Probab=20.58 E-value=1.1e+02 Score=22.45 Aligned_cols=33 Identities=27% Similarity=0.416 Sum_probs=24.8
Q ss_pred ccCChHHHHHHHHHHHHHhhhccccchHHHHHhhcCHHHHHHHHH
Q 048140 286 LYTTPEMLHALMKTLVDAYNFSREGSLLKEAKDMMNPNMIEKIEE 330 (334)
Q Consensus 286 LyttP~~L~~~i~~ilday~~~~~~tl~~eA~~l~~P~vi~rl~~ 330 (334)
-.--|++|+.+|+..-..=+.| ||-+||++|+.
T Consensus 8 ~lRlP~~l~~~lk~~A~~~gRS------------~NsEIv~~L~~ 40 (50)
T PF03869_consen 8 NLRLPEELKEKLKERAEENGRS------------MNSEIVQRLEE 40 (50)
T ss_dssp EEECEHHHHHHHHHHHHHTTS-------------HHHHHHHHHHH
T ss_pred eeECCHHHHHHHHHHHHHhCCC------------hHHHHHHHHHH
Confidence 3446999999999988877776 66677877764
No 62
>PF09675 Chlamy_scaf: Chlamydia-phage Chp2 scaffold (Chlamy_scaf); InterPro: IPR014131 Members of this entry are encoded by genes in chlamydiaphage such as Vp3. These viruses have around eight genes and infect obligately intracellular bacterial pathogens of the genus Chlamydia. This protein is annotated as VP3 or structural protein (as if a protein of mature viral particles), however, it is displaced from procapsids as DNA is packaged, and therefore is more correctly described as a scaffolding protein.
Probab=20.47 E-value=75 Score=27.83 Aligned_cols=48 Identities=29% Similarity=0.519 Sum_probs=36.6
Q ss_pred HHHHHHHHHHcCCchhhHHHhhhccCCCh---HHHHHHHHHHHHhcCChhhHHHHHHHH
Q 048140 94 SHNELLEVIEAAPSEVSQIVSRRCKDFTQ---EFFEHLHTVAESYYNDPAKQDDIAKLG 149 (334)
Q Consensus 94 ~hneLLe~i~~~p~eie~iVArrRkdFT~---eFF~hL~~~~ea~~d~~dr~~~La~L~ 149 (334)
.|.+-|..+.+..+-.+.+=|.-|..|.. +||+++ ++++-.+++.+||
T Consensus 32 DyqeAln~V~e~~eaFd~LPa~iRe~F~N~P~efl~f~--------~dp~N~ee~~~Lg 82 (114)
T PF09675_consen 32 DYQEALNMVAEANEAFDELPAHIRERFNNDPEEFLEFL--------NDPKNYEEAIKLG 82 (114)
T ss_pred hHHHHHHHHHHHHHHHHHchHHHHHHhCCCHHHHHHHH--------hCccCHHHHHHhc
Confidence 45666666666666677888888999976 898866 5777788888888
No 63
>PRK13441 F0F1 ATP synthase subunit delta; Provisional
Probab=20.45 E-value=2.9e+02 Score=24.52 Aligned_cols=43 Identities=12% Similarity=0.224 Sum_probs=27.3
Q ss_pred hhHHHHHHHHHHhhhhhCCcchHHHHHH--HHHHHH--hccCCHHHH
Q 048140 164 ESIEALNAAELKFQDIINSPSVDAACRK--IDSLAE--KNQLDSALV 206 (334)
Q Consensus 164 ~d~~~L~~A~~kf~dILnS~Sldaa~~K--Id~LAe--~~eLDsaLv 206 (334)
++...+..+-..+.++|.+|++....++ |+++.. .+.+|+.++
T Consensus 29 ~~l~~~~~~~~~~~~~l~~p~i~~~~K~~~l~~~~~~~~~~~~~~~~ 75 (180)
T PRK13441 29 EFLDLVCQIYESAKEFFDNPIVKPEKKVSLIKEIMKEFGQEMDEFFE 75 (180)
T ss_pred HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhccccCHHHH
Confidence 3333444444456789999998876665 777764 345776553
No 64
>PF05478 Prominin: Prominin; InterPro: IPR008795 The prominins are an emerging family of proteins that, among the multispan membrane proteins, display a novel topology. Mouse and Homo sapiens prominin and (Mus musculus) prominin-like 1 (PROML1) are predicted to contain five membrane spanning domains, with an N-terminal domain exposed to the extracellular space followed by four, alternating small cytoplasmic and large extracellular, loops and a cytoplasmic C-terminal domain []. The exact function of prominin is unknown although in humans defects in PROM1, the gene coding for prominin, cause retinal degeneration [].; GO: 0016021 integral to membrane
Probab=20.09 E-value=9.7e+02 Score=26.60 Aligned_cols=83 Identities=25% Similarity=0.329 Sum_probs=66.8
Q ss_pred Cccchhhhhcc---------hhhhhhhhhhhHHHhHHhhhhccCHHHHHHHHHHHHHhhhhcHHHHHHHHHHHHHHcCCc
Q 048140 37 TPTDWRRLLVF---------SKEWNNLRSNFFKRCQDRADAEVDPEMKHKLLRLGRKLKEIDEDVQSHNELLEVIEAAPS 107 (334)
Q Consensus 37 ~~~dWr~llaf---------s~eW~~~R~~ff~Rc~~rA~~e~Dp~~k~kl~~L~Rklk~ide~~~~hneLLe~i~~~p~ 107 (334)
+|.+=+.+++- +..-+++-++.+.+++........|.. ..+..++..++++.+.|+.=+..+..+++..+
T Consensus 192 ~~~qi~~l~~~ny~~~~~~v~~~L~~~~~~lg~~i~~~l~~~~~~~L-~~i~~l~~~~~~~~~~L~~v~~~~~~L~~~~~ 270 (806)
T PF05478_consen 192 TPQQIDHLLVQNYSELKDHVSSDLDNIGSLLGGDIQDQLGSNVYPAL-DSILDLAQAMQETKELLQNVNSSLKDLQEYQS 270 (806)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHhccchhhHHHHHHHhhhhHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 55555555543 566778889999999999999999988 78889999999999999999999999998777
Q ss_pred hhhHHHhhhccCC
Q 048140 108 EVSQIVSRRCKDF 120 (334)
Q Consensus 108 eie~iVArrRkdF 120 (334)
.++.-+...|.+.
T Consensus 271 qL~~~L~~vK~~L 283 (806)
T PF05478_consen 271 QLRDGLRGVKRDL 283 (806)
T ss_pred HHHHHHHHHHHHH
Confidence 7776666655443
Done!