Query 023124
Match_columns 287
No_of_seqs 100 out of 126
Neff 3.5
Searched_HMMs 46136
Date Fri Mar 29 08:36:43 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023124.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023124hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF11891 DUF3411: Domain of un 100.0 2E-39 4.4E-44 285.3 6.3 102 180-283 1-103 (180)
2 PLN03138 Protein TOC75; Provis 93.8 0.16 3.4E-06 54.6 7.0 21 2-22 5-25 (796)
3 COG4907 Predicted membrane pro 91.5 0.15 3.1E-06 52.4 2.9 6 32-37 548-553 (595)
4 TIGR02877 spore_yhbH sporulati 86.6 2.5 5.5E-05 42.1 7.5 15 119-133 112-126 (371)
5 PRK05325 hypothetical protein; 86.1 2.4 5.2E-05 42.5 7.1 14 120-133 101-114 (401)
6 PF04285 DUF444: Protein of un 84.7 2.9 6.2E-05 42.2 6.9 13 119-131 116-128 (421)
7 COG1512 Beta-propeller domains 83.3 1.2 2.6E-05 42.4 3.5 14 81-94 238-251 (271)
8 PHA00370 III attachment protei 79.1 4.7 0.0001 38.9 5.8 16 201-216 244-259 (297)
9 PF02084 Bindin: Bindin; Inte 77.0 6.4 0.00014 37.3 5.9 25 124-148 107-131 (238)
10 KOG3915 Transcription regulato 75.8 2.3 4.9E-05 44.1 2.9 9 219-227 204-212 (641)
11 PTZ00146 fibrillarin; Provisio 72.3 4.4 9.5E-05 39.0 3.8 10 218-227 202-211 (293)
12 PHA00370 III attachment protei 70.9 6.2 0.00013 38.2 4.4 14 153-166 213-226 (297)
13 TIGR01659 sex-lethal sex-letha 69.4 6.2 0.00013 38.3 4.1 36 28-63 237-272 (346)
14 PTZ00146 fibrillarin; Provisio 68.3 5.7 0.00012 38.2 3.6 8 158-165 136-143 (293)
15 KOG0921 Dosage compensation co 68.1 5.1 0.00011 44.7 3.6 21 64-84 1206-1226(1282)
16 PF02979 NHase_alpha: Nitrile 65.3 8.1 0.00018 35.5 3.8 43 145-187 17-65 (188)
17 PF04285 DUF444: Protein of un 57.1 11 0.00025 38.0 3.6 10 59-68 51-60 (421)
18 PRK05325 hypothetical protein; 56.8 12 0.00026 37.7 3.7 13 58-70 37-49 (401)
19 PF08671 SinI: Anti-repressor 53.3 10 0.00023 25.3 1.8 21 141-162 9-29 (30)
20 PRK05255 hypothetical protein; 45.4 1.4E+02 0.0031 26.8 8.2 17 173-189 107-124 (171)
21 PRK07772 single-stranded DNA-b 45.1 39 0.00085 30.6 4.7 6 7-12 30-35 (186)
22 PLN03134 glycine-rich RNA-bind 44.0 31 0.00067 29.3 3.7 8 29-36 79-86 (144)
23 KOG3074 Transcriptional regula 42.9 15 0.00034 35.1 1.8 15 116-130 45-59 (263)
24 PF07631 PSD4: Protein of unkn 42.5 96 0.0021 26.3 6.4 42 127-188 8-51 (128)
25 COG3028 Uncharacterized protei 41.4 77 0.0017 29.2 5.9 15 171-185 115-129 (187)
26 COG2718 Uncharacterized conser 38.8 50 0.0011 33.8 4.7 17 117-133 114-130 (423)
27 KOG0105 Alternative splicing f 37.5 28 0.0006 32.8 2.6 18 26-43 45-62 (241)
28 PRK07772 single-stranded DNA-b 36.3 47 0.001 30.1 3.8 11 57-67 74-84 (186)
29 TIGR02877 spore_yhbH sporulati 35.4 37 0.0008 34.1 3.2 14 57-70 48-61 (371)
30 COG2718 Uncharacterized conser 35.3 29 0.00062 35.4 2.5 11 102-112 103-113 (423)
31 PRK12799 motB flagellar motor 34.7 31 0.00066 35.1 2.6 26 218-243 26-51 (421)
32 KOG1456 Heterogeneous nuclear 34.5 31 0.00067 35.3 2.6 56 138-193 45-123 (494)
33 PF13677 MotB_plug: Membrane M 33.3 52 0.0011 24.3 3.0 27 217-243 15-41 (58)
34 TIGR03795 chp_BMA0021 conserve 31.8 31 0.00067 29.4 1.8 28 158-187 10-39 (114)
35 TIGR01323 nitrile_alph nitrile 29.9 52 0.0011 30.3 3.0 43 145-187 11-59 (185)
36 PF00813 FliP: FliP family; I 28.9 2.9E+02 0.0063 25.6 7.6 28 219-246 145-172 (194)
37 PF10415 FumaraseC_C: Fumarase 28.6 75 0.0016 23.4 3.1 37 123-162 14-50 (55)
38 PF06524 NOA36: NOA36 protein; 27.5 77 0.0017 31.1 3.8 7 59-65 224-230 (314)
39 PF02422 Keratin: Keratin; In 24.4 1.4E+02 0.0031 25.0 4.4 31 44-74 24-56 (98)
40 KOG3074 Transcriptional regula 24.4 47 0.001 31.9 1.8 10 225-234 159-168 (263)
41 TIGR00625 tfb2 Transcription f 24.0 79 0.0017 32.5 3.4 67 125-192 313-399 (448)
42 PF15207 TMEM240: TMEM240 fami 23.9 88 0.0019 28.3 3.3 26 214-240 83-108 (180)
43 PRK06925 flagellar motor prote 23.5 72 0.0016 29.0 2.8 26 217-242 13-38 (230)
44 TIGR03793 TOMM_pelo TOMM prope 23.2 50 0.0011 26.0 1.5 17 171-187 10-28 (77)
45 PRK09038 flagellar motor prote 22.9 75 0.0016 30.0 2.8 26 217-242 15-40 (281)
46 KOG0105 Alternative splicing f 22.8 1.9E+02 0.0041 27.4 5.3 12 72-83 74-85 (241)
47 PRK07734 motB flagellar motor 22.0 72 0.0016 29.5 2.5 26 217-242 17-42 (259)
48 KOG3570 MAPK-activating protei 21.6 1.7E+02 0.0036 33.6 5.3 71 18-94 40-122 (1588)
49 TIGR01659 sex-lethal sex-letha 20.9 1E+02 0.0022 30.0 3.4 6 27-32 194-199 (346)
50 PF05084 GRA6: Granule antigen 20.4 1.4E+02 0.0029 27.7 3.8 20 24-43 100-119 (215)
51 PF12244 DUF3606: Protein of u 20.2 1.9E+02 0.004 21.4 3.9 34 127-160 23-56 (57)
52 PRK06958 single-stranded DNA-b 20.1 1.1E+02 0.0023 27.9 3.1 11 57-67 73-83 (182)
No 1
>PF11891 DUF3411: Domain of unknown function (DUF3411); InterPro: IPR021825 This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is typically between 168 to 186 amino acids in length. This domain has a conserved RYQ sequence motif.
Probab=100.00 E-value=2e-39 Score=285.29 Aligned_cols=102 Identities=45% Similarity=0.742 Sum_probs=96.9
Q ss_pred hhhhcCcchhHHHhHHhhhhhhhhhhhhhhhccccchhhHHHHHHHHHHHHHHHHHhHhhcccccccCCCCcc-Ccchhh
Q 023124 180 DRMLADPSFLFKVGTEIVIDSCCATLAEFQKRGKDFWSEFELYLADLLVGLVVDIALVGMLAPYARIGQPSAS-SGLFGR 258 (287)
Q Consensus 180 ~RlLADP~FlfKl~~E~~i~i~~~~~~E~~~Rge~f~~ElDfV~adlv~~~i~nfaLV~lLAPt~s~g~~~~s-~g~~~~ 258 (287)
+||||||+|||||++||+||++|+++|||++|||+||+|||||++|+|+++|+||+||||||||+++++++++ .+ +.
T Consensus 1 ~RllADP~Fl~Kl~~E~~i~i~~~~~~e~~~R~e~f~~E~d~v~~d~v~~~i~n~~lv~llAPt~s~~~~~~~~~~--~~ 78 (180)
T PF11891_consen 1 ERLLADPSFLFKLAIEEVIGIGCATAAEYAKRGERFWNELDFVFSDVVVGSIVNFALVWLLAPTRSFGSPAASSPG--GG 78 (180)
T ss_pred CcccccchHHHHHHHHHHHHHHHHHHHHHHHcccchHHHHHHHHHHHHHHHHHHHHHHHhccchHhhCcccccccc--hH
Confidence 6999999999999999999999999999999999999999999999999999999999999999999998863 33 79
Q ss_pred HHhhhcCCCchhHHhhhhhhhhhhh
Q 023124 259 IQNACGSLPSSYMLLLLVIDRFHNE 283 (287)
Q Consensus 259 l~~~~~~LP~n~Fe~~~p~rrf~~~ 283 (287)
||+.+++||+|+||+.+|+|+|+..
T Consensus 79 ~~~~~~~~P~n~Fq~~~~g~~fsl~ 103 (180)
T PF11891_consen 79 LQKFLGSLPNNAFQKGYPGRSFSLA 103 (180)
T ss_pred HHHHHHhChHHHhccCCCCCcccHH
Confidence 9999999999999999999999754
No 2
>PLN03138 Protein TOC75; Provisional
Probab=93.77 E-value=0.16 Score=54.60 Aligned_cols=21 Identities=24% Similarity=0.176 Sum_probs=16.0
Q ss_pred CcccccccCCCCCCCCCCCCc
Q 023124 2 SACSSTFRLPNLPNISPQNHN 22 (287)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~~~ 22 (287)
++|.+.++-++++.-.||+..
T Consensus 5 ~~~~~~~~~~~~~~~~~~~~~ 25 (796)
T PLN03138 5 STMVSAAASTSLSSSRPQLSS 25 (796)
T ss_pred cccceeccCCCccCCCccccc
Confidence 578888888888887777654
No 3
>COG4907 Predicted membrane protein [Function unknown]
Probab=91.49 E-value=0.15 Score=52.45 Aligned_cols=6 Identities=0% Similarity=0.058 Sum_probs=2.5
Q ss_pred eecccC
Q 023124 32 SLRHST 37 (287)
Q Consensus 32 ~~~~s~ 37 (287)
-+||+-
T Consensus 548 i~h~ny 553 (595)
T COG4907 548 IFHNNY 553 (595)
T ss_pred EEecch
Confidence 344443
No 4
>TIGR02877 spore_yhbH sporulation protein YhbH. This protein family, typified by YhbH in Bacillus subtilis, is found in nearly every endospore-forming bacterium and in no other genome (but note that the trusted cutoff score is set high to exclude a single high-scoring sequence from Nitrosococcus oceani ATCC 19707, which is classified in the Gammaproteobacteria). The gene in Bacillus subtilis was shown to be in the regulon of the sporulation sigma factor, sigma-E, and its mutation was shown to create a sporulation defect.
Probab=86.58 E-value=2.5 Score=42.09 Aligned_cols=15 Identities=13% Similarity=0.155 Sum_probs=10.4
Q ss_pred ccccHHHHHHHHHhc
Q 023124 119 PILKFEEVMKEIELK 133 (287)
Q Consensus 119 ~ll~~~~Vl~ea~r~ 133 (287)
-=++.+|+++....-
T Consensus 112 ~e~s~eE~~~~lfEd 126 (371)
T TIGR02877 112 TEVTLEELFELLFED 126 (371)
T ss_pred EEecHHHHHHHHHhh
Confidence 347788888887543
No 5
>PRK05325 hypothetical protein; Provisional
Probab=86.14 E-value=2.4 Score=42.55 Aligned_cols=14 Identities=14% Similarity=0.199 Sum_probs=10.0
Q ss_pred cccHHHHHHHHHhc
Q 023124 120 ILKFEEVMKEIELK 133 (287)
Q Consensus 120 ll~~~~Vl~ea~r~ 133 (287)
=++.+|++......
T Consensus 101 els~eE~~~~lfEd 114 (401)
T PRK05325 101 EISLEELLDLLFED 114 (401)
T ss_pred EecHHHHHHHHHhh
Confidence 47788888877544
No 6
>PF04285 DUF444: Protein of unknown function (DUF444); InterPro: IPR006698 This entry is represented by Thermus phage phiYS40, Orf56. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches [].
Probab=84.69 E-value=2.9 Score=42.22 Aligned_cols=13 Identities=23% Similarity=0.031 Sum_probs=9.0
Q ss_pred ccccHHHHHHHHH
Q 023124 119 PILKFEEVMKEIE 131 (287)
Q Consensus 119 ~ll~~~~Vl~ea~ 131 (287)
--++.++++....
T Consensus 116 ~els~eE~~~llf 128 (421)
T PF04285_consen 116 FELSREEFLDLLF 128 (421)
T ss_pred EEEEHHHHHHHhH
Confidence 4577788777763
No 7
>COG1512 Beta-propeller domains of methanol dehydrogenase type [General function prediction only]
Probab=83.27 E-value=1.2 Score=42.37 Aligned_cols=14 Identities=50% Similarity=1.025 Sum_probs=5.5
Q ss_pred CCCCCCCCCCCCCC
Q 023124 81 GGDGGAGDSPGGGG 94 (287)
Q Consensus 81 ~G~Gg~g~~~~~gg 94 (287)
+|.|++|+.+|+++
T Consensus 238 ~g~g~~g~~gg~~~ 251 (271)
T COG1512 238 SGSGGSGGSGGGSS 251 (271)
T ss_pred CCCCCCCCCCCCCC
Confidence 34444433433333
No 8
>PHA00370 III attachment protein
Probab=79.14 E-value=4.7 Score=38.94 Aligned_cols=16 Identities=19% Similarity=0.270 Sum_probs=6.6
Q ss_pred hhhhhhhhhhccccch
Q 023124 201 CCATLAEFQKRGKDFW 216 (287)
Q Consensus 201 ~~~~~~E~~~Rge~f~ 216 (287)
.|.-+.+++---.+|.
T Consensus 244 ~C~~FV~~~geVYe~~ 259 (297)
T PHA00370 244 GCTPFVFAQGKVYEFI 259 (297)
T ss_pred CCCcceeeccchhhhh
Confidence 3444444444333333
No 9
>PF02084 Bindin: Bindin; InterPro: IPR000775 Bindin, the major protein component of the acrosome granule of sea urchin sperm, mediates species-specific adhesion of sperm to the egg surface during fertilisation [, ]. The protein coats the acrosomal process after externalisation by the acrosome reaction; it binds to sulphated, fucose-containing polysaccharides on the vitelline-layer receptor proteoglycans that cover the egg plasma membrane. Bindins from different genera show high levels of sequence similarity in both the mature bindin domain and in the probindin precursor region. The most highly conserved region is a 42-residue segment in the central portion of the mature bindin protein. This domain may be responsible for conserved functions of bindin, while the more highly divergent flanking regions may be responsible for its species-specific properties [].; GO: 0007342 fusion of sperm to egg plasma membrane
Probab=76.97 E-value=6.4 Score=37.25 Aligned_cols=25 Identities=16% Similarity=0.256 Sum_probs=16.5
Q ss_pred HHHHHHHHhcCCCchHHHHHHHHHc
Q 023124 124 EEVMKEIELKGVGLPDDMMEAAKTV 148 (287)
Q Consensus 124 ~~Vl~ea~r~~~sLPaDl~~Aa~~g 148 (287)
+.+.+-+.+|..+||-|+-+-++.|
T Consensus 107 ~~ikavLgaTKiDLPVDINDPYDlG 131 (238)
T PF02084_consen 107 EDIKAVLGATKIDLPVDINDPYDLG 131 (238)
T ss_pred HHHHHHhcccccccccccCChhhHH
Confidence 3344445788999998886655444
No 10
>KOG3915 consensus Transcription regulator dachshund, contains SKI/SNO domain [Transcription]
Probab=75.75 E-value=2.3 Score=44.12 Aligned_cols=9 Identities=44% Similarity=1.058 Sum_probs=4.1
Q ss_pred HHHHHHHHH
Q 023124 219 FELYLADLL 227 (287)
Q Consensus 219 lDfV~adlv 227 (287)
||+++-++|
T Consensus 204 fdlFLKhlV 212 (641)
T KOG3915|consen 204 FDLFLKHLV 212 (641)
T ss_pred HHHHHHHHh
Confidence 444444444
No 11
>PTZ00146 fibrillarin; Provisional
Probab=72.33 E-value=4.4 Score=39.01 Aligned_cols=10 Identities=20% Similarity=0.388 Sum_probs=6.8
Q ss_pred hHHHHHHHHH
Q 023124 218 EFELYLADLL 227 (287)
Q Consensus 218 ElDfV~adlv 227 (287)
.+|+||+|+.
T Consensus 202 ~vDvV~~Dva 211 (293)
T PTZ00146 202 MVDVIFADVA 211 (293)
T ss_pred CCCEEEEeCC
Confidence 3677777764
No 12
>PHA00370 III attachment protein
Probab=70.87 E-value=6.2 Score=38.15 Aligned_cols=14 Identities=14% Similarity=-0.090 Sum_probs=5.5
Q ss_pred HHHHHHHhhcCCcc
Q 023124 153 MFLLRYLDLQGSVW 166 (287)
Q Consensus 153 a~L~Rfl~L~~sp~ 166 (287)
++|...=+=+.+||
T Consensus 213 s~md~lg~g~gS~~ 226 (297)
T PHA00370 213 SEMDQLGEGDGSPL 226 (297)
T ss_pred hhhhhhcccCCcHH
Confidence 34443333344443
No 13
>TIGR01659 sex-lethal sex-lethal family splicing factor. This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661).
Probab=69.37 E-value=6.2 Score=38.30 Aligned_cols=36 Identities=19% Similarity=0.284 Sum_probs=17.5
Q ss_pred eeeEeecccCCCCcccccccccCCCCCCCCceeeec
Q 023124 28 TVFLSLRHSTATNPALCKLQCVGNNFDSTPKTIEIP 63 (287)
Q Consensus 28 ~~~~~~~~s~~~~~~~~~~~c~~~~~~~~p~~iei~ 63 (287)
..|++|.+-.--..|+..+...--+....+++|.+.
T Consensus 237 ~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l~V~~a 272 (346)
T TIGR01659 237 VAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRLA 272 (346)
T ss_pred EEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEEC
Confidence 457777665555555533332211223346665543
No 14
>PTZ00146 fibrillarin; Provisional
Probab=68.26 E-value=5.7 Score=38.24 Aligned_cols=8 Identities=25% Similarity=0.156 Sum_probs=3.5
Q ss_pred HHhhcCCc
Q 023124 158 YLDLQGSV 165 (287)
Q Consensus 158 fl~L~~sp 165 (287)
.|||=+.+
T Consensus 136 VLDLGaG~ 143 (293)
T PTZ00146 136 VLYLGAAS 143 (293)
T ss_pred EEEeCCcC
Confidence 34444443
No 15
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=68.09 E-value=5.1 Score=44.70 Aligned_cols=21 Identities=14% Similarity=0.287 Sum_probs=10.1
Q ss_pred CCcccccCCCCcccccCCCCC
Q 023124 64 GKITEESADCEPRIHSSGGDG 84 (287)
Q Consensus 64 g~it~ts~~~~~~~~~~~G~G 84 (287)
|+-....+..++....+.|+|
T Consensus 1206 GGYGgsa~~~~~~~Gagvg~G 1226 (1282)
T KOG0921|consen 1206 GGYGGSAPSARANYGAGVGNG 1226 (1282)
T ss_pred CCCCCCCCCCCCCccccccCC
Confidence 334444555555555444433
No 16
>PF02979 NHase_alpha: Nitrile hydratase, alpha chain; InterPro: IPR004232 Nitrile hydratases (4.2.1.84 from EC) are bacterial enzymes that catalyse the hydration of nitrile compounds to the corresponding amides. They are used as biocatalysts in acrylamide production, one of the few commercial scale bioprocesses, as well as in environmental remediation for the removal of nitriles from waste streams. Nitrile hydratases are composed of two subunits, alpha and beta, and are normally active as a tetramer, alpha(2)beta(2). Nitrile hydratases contain either a non-haem iron or a non-corrinoid cobalt centre, both types sharing a highly conserved peptide sequence in the alpha subunit (CXLCSC) that provides all the residues involved in coordinating the metal ion. Each type of nitrile hydratase specifically incorporated its metal with the help of activator proteins encoded by flanking regions of the nitrile hydratase genes that are necessary for metal insertion. The Fe-containing enzyme is photo-regulated: in the dark the enzyme is inactivated due to the association of nitric oxide (NO) to the iron, while in the light the enzyme is active by photo-dissociation of NO. The NO is held in place by a claw setting formed through specific oxygen atoms in two modified cysteines and a serine residue in the active site [, ]. The cobalt-containing enzyme is unaffected by NO, but was shown to undergo a similar effect with carbon monoxide [, ]. Fe- and cobalt-containing enzymes also display different inhibition patterns with nitrophenols. Thiocyanate hydrolase (SCNase) is a cobalt-containing metalloenzyme with a cysteine-sulphinic acid ligand that hydrolyses thiocyanate to carbonyl sulphide and ammonia []. The two enzymes, nitrile hydratase and SCNase, are homologous over regions corresponding to almost the entire coding regions of the genes: the beta and alpha subunits of thiocyanate hydrolase were homologous to the amino- and carboxyl-terminal halves of the beta subunit of nitrile hydratase, and the gamma subunit of thiocyanate hydrolase was homologous to the alpha subunit of nitrile hydratase []. This entry represents the structural domain of the alpha subunit of both iron- and cobalt-containing nitrile hydratases; the alpha subunit is a duplication of two structural repeats, each consisting of 4 layers, alpha/beta/beta/alpha []. This structure is also found in the related protein, the gamma subunit of thiocyanate hydrolase (SCNase).; GO: 0003824 catalytic activity, 0046914 transition metal ion binding, 0006807 nitrogen compound metabolic process; PDB: 2DPP_A 3HHT_A 1V29_A 2ZZD_I 2DXC_F 2DXB_F 2DD5_C 2DD4_C 2ZPH_A 2CYZ_A ....
Probab=65.29 E-value=8.1 Score=35.48 Aligned_cols=43 Identities=21% Similarity=0.164 Sum_probs=30.7
Q ss_pred HHHcCCCHHHHHHHHhhcCC---cch-hHHHHHHh--hhhhhhhhcCcc
Q 023124 145 AKTVGIRKMFLLRYLDLQGS---VWP-LGFLMRYC--FMLRDRMLADPS 187 (287)
Q Consensus 145 a~~g~is~a~L~Rfl~L~~s---p~~-l~~L~r~~--~g~r~RlLADP~ 187 (287)
++.|.|+++.+.++++...+ |-. .+-+.|++ +.||.|||+||.
T Consensus 17 ~ekg~~~~~~~~~~~~~~~~~~~P~~GarvVArAW~Dp~FK~rLLaD~~ 65 (188)
T PF02979_consen 17 IEKGLITPAEVDRIIETYESRVGPRNGARVVARAWTDPAFKARLLADPT 65 (188)
T ss_dssp HHTTSS-HHHHHHHHHHHHHTSSHHHHHHHHHHHHH-HHHHHHHHHSHH
T ss_pred HHcCCCCHHHHHHHHHHHHhccCccccceeehhhhCCHHHHHHHHHCHH
Confidence 45689999988888876553 321 25566666 999999999995
No 17
>PF04285 DUF444: Protein of unknown function (DUF444); InterPro: IPR006698 This entry is represented by Thermus phage phiYS40, Orf56. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches [].
Probab=57.12 E-value=11 Score=38.02 Aligned_cols=10 Identities=30% Similarity=0.368 Sum_probs=4.7
Q ss_pred eeeecCCccc
Q 023124 59 TIEIPGKITE 68 (287)
Q Consensus 59 ~iei~g~it~ 68 (287)
.|-||-+..+
T Consensus 51 ~V~IP~r~l~ 60 (421)
T PF04285_consen 51 KVSIPIRGLE 60 (421)
T ss_pred eEeecCCCCC
Confidence 3455544443
No 18
>PRK05325 hypothetical protein; Provisional
Probab=56.80 E-value=12 Score=37.67 Aligned_cols=13 Identities=23% Similarity=0.427 Sum_probs=7.6
Q ss_pred ceeeecCCccccc
Q 023124 58 KTIEIPGKITEES 70 (287)
Q Consensus 58 ~~iei~g~it~ts 70 (287)
..|-||-+++.+-
T Consensus 37 ~~v~IPi~~i~Ep 49 (401)
T PRK05325 37 EVVSIPIRDIDEP 49 (401)
T ss_pred ceEEecCCCCccc
Confidence 4556666666544
No 19
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=53.34 E-value=10 Score=25.26 Aligned_cols=21 Identities=19% Similarity=0.343 Sum_probs=14.4
Q ss_pred HHHHHHHcCCCHHHHHHHHhhc
Q 023124 141 MMEAAKTVGIRKMFLLRYLDLQ 162 (287)
Q Consensus 141 l~~Aa~~g~is~a~L~Rfl~L~ 162 (287)
|.+|.++| ++.+.+.+||..+
T Consensus 9 i~eA~~~G-ls~eeir~FL~~~ 29 (30)
T PF08671_consen 9 IKEAKESG-LSKEEIREFLEFN 29 (30)
T ss_dssp HHHHHHTT---HHHHHHHHHHH
T ss_pred HHHHHHcC-CCHHHHHHHHHhC
Confidence 45655555 9999999999875
No 20
>PRK05255 hypothetical protein; Provisional
Probab=45.35 E-value=1.4e+02 Score=26.85 Aligned_cols=17 Identities=35% Similarity=0.307 Sum_probs=12.0
Q ss_pred HHhhhhhhhhhc-Ccchh
Q 023124 173 RYCFMLRDRMLA-DPSFL 189 (287)
Q Consensus 173 r~~~g~r~RlLA-DP~Fl 189 (287)
+.+-.||+||++ |+.-+
T Consensus 107 h~lE~wRdrLi~~~d~al 124 (171)
T PRK05255 107 HKLERWRDRLLAEGDDAL 124 (171)
T ss_pred HHHHHHHHHHHhCCHHHH
Confidence 345799999999 55433
No 21
>PRK07772 single-stranded DNA-binding protein; Provisional
Probab=45.10 E-value=39 Score=30.59 Aligned_cols=6 Identities=17% Similarity=0.573 Sum_probs=2.9
Q ss_pred cccCCC
Q 023124 7 TFRLPN 12 (287)
Q Consensus 7 ~~~~~~ 12 (287)
+|||-.
T Consensus 30 ~FrVAv 35 (186)
T PRK07772 30 NFTVAS 35 (186)
T ss_pred EEEEEe
Confidence 455544
No 22
>PLN03134 glycine-rich RNA-binding protein 4; Provisional
Probab=43.98 E-value=31 Score=29.27 Aligned_cols=8 Identities=13% Similarity=0.389 Sum_probs=3.3
Q ss_pred eeEeeccc
Q 023124 29 VFLSLRHS 36 (287)
Q Consensus 29 ~~~~~~~s 36 (287)
-|++|.+-
T Consensus 79 aFV~F~~~ 86 (144)
T PLN03134 79 GFVNFNDE 86 (144)
T ss_pred EEEEECCH
Confidence 34444433
No 23
>KOG3074 consensus Transcriptional regulator of the PUR family, single-stranded-DNA-binding [Transcription]
Probab=42.90 E-value=15 Score=35.10 Aligned_cols=15 Identities=33% Similarity=0.202 Sum_probs=9.3
Q ss_pred cccccccHHHHHHHH
Q 023124 116 EFGPILKFEEVMKEI 130 (287)
Q Consensus 116 e~G~ll~~~~Vl~ea 130 (287)
--|++++-.||=+.+
T Consensus 45 ~rGRflKIaE~g~~~ 59 (263)
T KOG3074|consen 45 PRGRFLKIAEVGAGG 59 (263)
T ss_pred CCcceEEEEEeccCC
Confidence 467888776654433
No 24
>PF07631 PSD4: Protein of unknown function (DUF1592); InterPro: IPR013042 A region of similarity shared by several Rhodopirellula baltica cytochrome-like proteins that are predicted to be secreted. These proteins also contain IPR011478 from INTERPRO, IPR013036 from INTERPRO, IPR013039 from INTERPRO and IPR013043 from INTERPRO.
Probab=42.46 E-value=96 Score=26.26 Aligned_cols=42 Identities=24% Similarity=0.212 Sum_probs=28.2
Q ss_pred HHHHHhcCCCch-HHHHHHHHHcCCC-HHHHHHHHhhcCCcchhHHHHHHhhhhhhhhhcCcch
Q 023124 127 MKEIELKGVGLP-DDMMEAAKTVGIR-KMFLLRYLDLQGSVWPLGFLMRYCFMLRDRMLADPSF 188 (287)
Q Consensus 127 l~ea~r~~~sLP-aDl~~Aa~~g~is-~a~L~Rfl~L~~sp~~l~~L~r~~~g~r~RlLADP~F 188 (287)
-+..+-=-.+.| +.|.+||+.|.++ +++ ++.-.+|||+||.+
T Consensus 8 srLSYfLw~s~PD~~L~~aA~~g~L~~~~~--------------------l~~q~~RML~dpr~ 51 (128)
T PF07631_consen 8 SRLSYFLWGSPPDAELLDAAAAGELRTPEQ--------------------LRAQAERMLADPRA 51 (128)
T ss_pred HHHHHHHhcCCCCHHHHHHHHhCCCCCHHH--------------------HHHHHHHHHcCccH
Confidence 333344445667 6788999999885 332 33556799999986
No 25
>COG3028 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=41.35 E-value=77 Score=29.24 Aligned_cols=15 Identities=40% Similarity=0.616 Sum_probs=10.4
Q ss_pred HHHHhhhhhhhhhcC
Q 023124 171 LMRYCFMLRDRMLAD 185 (287)
Q Consensus 171 L~r~~~g~r~RlLAD 185 (287)
+.+++-.||+||+|+
T Consensus 115 ~lHklE~~RdrLia~ 129 (187)
T COG3028 115 LLHKLEQLRDRLIAE 129 (187)
T ss_pred HHHHHHHHHHHHHhc
Confidence 344457788888887
No 26
>COG2718 Uncharacterized conserved protein [Function unknown]
Probab=38.85 E-value=50 Score=33.76 Aligned_cols=17 Identities=24% Similarity=0.108 Sum_probs=10.8
Q ss_pred ccccccHHHHHHHHHhc
Q 023124 117 FGPILKFEEVMKEIELK 133 (287)
Q Consensus 117 ~G~ll~~~~Vl~ea~r~ 133 (287)
|=--.+.++++....+-
T Consensus 114 F~~~is~~e~~dllFed 130 (423)
T COG2718 114 FVFQISREEVLDLLFED 130 (423)
T ss_pred hheeeehhHHHHHHHHH
Confidence 33456777777776554
No 27
>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]
Probab=37.48 E-value=28 Score=32.78 Aligned_cols=18 Identities=17% Similarity=0.433 Sum_probs=10.0
Q ss_pred cceeeEeecccCCCCccc
Q 023124 26 PTTVFLSLRHSTATNPAL 43 (287)
Q Consensus 26 ~~~~~~~~~~s~~~~~~~ 43 (287)
|...|++|.|.---.-+.
T Consensus 45 ppfafVeFEd~RDAeDAi 62 (241)
T KOG0105|consen 45 PPFAFVEFEDPRDAEDAI 62 (241)
T ss_pred CCeeEEEecCccchhhhh
Confidence 555677777664433333
No 28
>PRK07772 single-stranded DNA-binding protein; Provisional
Probab=36.29 E-value=47 Score=30.08 Aligned_cols=11 Identities=9% Similarity=0.383 Sum_probs=4.8
Q ss_pred CceeeecCCcc
Q 023124 57 PKTIEIPGKIT 67 (287)
Q Consensus 57 p~~iei~g~it 67 (287)
.-.|.|.|++.
T Consensus 74 Gd~V~V~GrL~ 84 (186)
T PRK07772 74 GMRVIVTGRLK 84 (186)
T ss_pred CCEEEEEEEEE
Confidence 33444444443
No 29
>TIGR02877 spore_yhbH sporulation protein YhbH. This protein family, typified by YhbH in Bacillus subtilis, is found in nearly every endospore-forming bacterium and in no other genome (but note that the trusted cutoff score is set high to exclude a single high-scoring sequence from Nitrosococcus oceani ATCC 19707, which is classified in the Gammaproteobacteria). The gene in Bacillus subtilis was shown to be in the regulon of the sporulation sigma factor, sigma-E, and its mutation was shown to create a sporulation defect.
Probab=35.35 E-value=37 Score=34.09 Aligned_cols=14 Identities=29% Similarity=0.332 Sum_probs=8.1
Q ss_pred CceeeecCCccccc
Q 023124 57 PKTIEIPGKITEES 70 (287)
Q Consensus 57 p~~iei~g~it~ts 70 (287)
.-.|-||-++..+-
T Consensus 48 ~~~V~IPir~l~Ep 61 (371)
T TIGR02877 48 KKKIKVPIRGLKEY 61 (371)
T ss_pred CceEEccCCCCccc
Confidence 34566666666554
No 30
>COG2718 Uncharacterized conserved protein [Function unknown]
Probab=35.31 E-value=29 Score=35.40 Aligned_cols=11 Identities=55% Similarity=0.996 Sum_probs=5.3
Q ss_pred CCCCCCCCCCC
Q 023124 102 GGGGDGEGNDG 112 (287)
Q Consensus 102 gg~g~g~~~d~ 112 (287)
+|.|+|+++|+
T Consensus 103 ~~ag~~egED~ 113 (423)
T COG2718 103 QAAGDGEGEDE 113 (423)
T ss_pred CccCCCCCcch
Confidence 34445555543
No 31
>PRK12799 motB flagellar motor protein MotB; Reviewed
Probab=34.70 E-value=31 Score=35.07 Aligned_cols=26 Identities=15% Similarity=0.292 Sum_probs=23.9
Q ss_pred hHHHHHHHHHHHHHHHHHhHhhcccc
Q 023124 218 EFELYLADLLVGLVVDIALVGMLAPY 243 (287)
Q Consensus 218 ElDfV~adlv~~~i~nfaLV~lLAPt 243 (287)
.|=..++|+++++.+=|+|+|+++=+
T Consensus 26 aWkVAYADfvTlLMAFFlLLwsmSsv 51 (421)
T PRK12799 26 SWKIAYADFMTAMMAFFLVMWLLAVS 51 (421)
T ss_pred chhhhHHHHHHHHHHHHHHHHHhhcC
Confidence 69999999999999999999998743
No 32
>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]
Probab=34.51 E-value=31 Score=35.34 Aligned_cols=56 Identities=21% Similarity=0.226 Sum_probs=28.5
Q ss_pred hHHHHHHHHHcC---------CCHHHHHHHHhhcCCcch-------------hHHHHHHh-hhhhhhhhcCcchhHHHh
Q 023124 138 PDDMMEAAKTVG---------IRKMFLLRYLDLQGSVWP-------------LGFLMRYC-FMLRDRMLADPSFLFKVG 193 (287)
Q Consensus 138 PaDl~~Aa~~g~---------is~a~L~Rfl~L~~sp~~-------------l~~L~r~~-~g~r~RlLADP~FlfKl~ 193 (287)
-+|+.+|++..+ -...+|+.|=+++..-.- -..|+..- +.-.+|+--|++=+-||+
T Consensus 45 eadl~eal~~fG~i~yvt~~P~~r~alvefedi~~akn~Vnfaa~n~i~i~gq~Al~NyStsq~i~R~g~es~~pN~VL 123 (494)
T KOG1456|consen 45 EADLVEALSNFGPIAYVTCMPHKRQALVEFEDIEGAKNCVNFAADNQIYIAGQQALFNYSTSQCIERPGDESATPNKVL 123 (494)
T ss_pred hhHHHHHHhcCCceEEEEeccccceeeeeeccccchhhheehhccCcccccCchhhcccchhhhhccCCCCCCCCCeEE
Confidence 367777776643 234456666555543100 02333322 555667766666555554
No 33
>PF13677 MotB_plug: Membrane MotB of proton-channel complex MotA/MotB
Probab=33.27 E-value=52 Score=24.28 Aligned_cols=27 Identities=19% Similarity=0.198 Sum_probs=23.7
Q ss_pred hhHHHHHHHHHHHHHHHHHhHhhcccc
Q 023124 217 SEFELYLADLLVGLVVDIALVGMLAPY 243 (287)
Q Consensus 217 ~ElDfV~adlv~~~i~nfaLV~lLAPt 243 (287)
..|-+-++|+++.+.+=|+++|.++-.
T Consensus 15 ~~WlvtyaDlmTLLl~fFVlL~s~s~~ 41 (58)
T PF13677_consen 15 PRWLVTYADLMTLLLAFFVLLFSMSSV 41 (58)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 369999999999999999999987654
No 34
>TIGR03795 chp_BMA0021 conserved hypothetical protein, BMA_0021 family. Members of this protein family are found sparsely, mostly in members of the genus Burkholderia. Members often occur as tandem homologous genes, such as BMA_0021 and BMA_0022 in Burkholderia mallei ATCC 23344. The genes regularly are encoded near the so-called docking protein of TOMM (thiazole/oxazole-modified microcins) biosynthetic clusters, suggesting a role in bacteriocin biosynthesis. The function is unknown.
Probab=31.83 E-value=31 Score=29.39 Aligned_cols=28 Identities=25% Similarity=0.322 Sum_probs=20.9
Q ss_pred HHhhcCCcchhHHHHHHh--hhhhhhhhcCcc
Q 023124 158 YLDLQGSVWPLGFLMRYC--FMLRDRMLADPS 187 (287)
Q Consensus 158 fl~L~~sp~~l~~L~r~~--~g~r~RlLADP~ 187 (287)
||++.+ ..+|.+.+++ ..||+||++||.
T Consensus 10 ll~f~~--v~lraIA~AW~DpaFr~eLl~DPk 39 (114)
T TIGR03795 10 LLEFRA--VYLRAIALAWHSPEFKDELLADPV 39 (114)
T ss_pred HHHHHH--HHHHHHHHHhCCHHHHHHHHHCHH
Confidence 344443 3468888887 899999999995
No 35
>TIGR01323 nitrile_alph nitrile hydratase, alpha subunit. This model describes both iron- and cobalt-containing nitrile hydratase alpha chains. It excludes the thiocyanate hydrolase gamma subunit of Thiobacillus thioparus, a sequence that appears to have evolved from within the family of nitrile hydratase alpha subunits but which differs by several indels and a more rapid accumulation of point mutations.
Probab=29.94 E-value=52 Score=30.29 Aligned_cols=43 Identities=12% Similarity=-0.048 Sum_probs=30.6
Q ss_pred HHHcCCCHHHHHHHHhhcCC---cc-hhHHHHHHh--hhhhhhhhcCcc
Q 023124 145 AKTVGIRKMFLLRYLDLQGS---VW-PLGFLMRYC--FMLRDRMLADPS 187 (287)
Q Consensus 145 a~~g~is~a~L~Rfl~L~~s---p~-~l~~L~r~~--~g~r~RlLADP~ 187 (287)
++.|.|.++.+.+.++.... |. =.+-+.|++ +.||.|||+|..
T Consensus 11 ~eKGli~~~~id~~i~~~~~~~gP~nGA~vVArAW~Dp~fk~~Ll~d~~ 59 (185)
T TIGR01323 11 KSKGLIPEGAVDQLTSLYENEWGPENGAKVVAKAWVDPEFRALLLKDAT 59 (185)
T ss_pred HHcCCCCHHHHHHHHHHHHhccCCcchhhhhhHHhcCHHHHHHHHhChH
Confidence 45688888888777765443 31 125566777 999999999984
No 36
>PF00813 FliP: FliP family; InterPro: IPR005838 Secretion of virulence factors in Gram-negative bacteria involves transportation of the protein across two membranes to reach the cell exterior []. There have been four secretion systems described in animal enteropathogens such as Salmonella and Yersinia, with further sequence similarities in plant pathogens like Ralstonia and Erwinia. The type III secretion system is of great interest as it is used to transport virulence factors from the pathogen directly into the host cell [] and is only triggered when the bacterium comes into close contact with the host. The protein subunits of the system are very similar to those of bacterial flagellar biosynthesis []. However, while the latter forms a ring structure to allow secretion of flagellin and is an integral part of the flagellum itself [], type III subunits in the outer membrane translocate secreted proteins through a channel-like structure. It is believed that the family of type III inner membrane proteins are used as structural moieties in a complex with several other subunits [], including the ATPase necessary for driving the secretion system. One such set of inner membrane proteins, termed "P" here for nomenclature purposes, includes the Salmonella and Shigella SpaP, the Yersinia YscR, the Erwinia HrcR, and the Xanthamonas Pro2 genes [], as well as several FliP flagellar biosynthesis genes []. FliP is an ~30Kd protein containing three or four transmembrane (TM) regions.; GO: 0009306 protein secretion, 0016020 membrane
Probab=28.85 E-value=2.9e+02 Score=25.57 Aligned_cols=28 Identities=21% Similarity=0.268 Sum_probs=23.9
Q ss_pred HHHHHHHHHHHHHHHHHhHhhccccccc
Q 023124 219 FELYLADLLVGLVVDIALVGMLAPYARI 246 (287)
Q Consensus 219 lDfV~adlv~~~i~nfaLV~lLAPt~s~ 246 (287)
+=|++.|++++.|+=.+=+-|+.|+.-.
T Consensus 145 lPFlvIDlvVasiLmamGMmMl~P~~IS 172 (194)
T PF00813_consen 145 LPFLVIDLVVASILMAMGMMMLPPVTIS 172 (194)
T ss_pred HHHHHHHHHHHHHHHHhhhhhcCchHHH
Confidence 5688899999999999999999998643
No 37
>PF10415 FumaraseC_C: Fumarase C C-terminus; InterPro: IPR018951 Fumarase C catalyses the stereo-specific interconversion of fumarate to L-malate as part of the Krebs cycle. The full-length protein forms a tetramer with visible globular shape. FumaraseC_C is the C-terminal 65 residues referred to as domain 3. The core of the molecule consists of a bundle of 20 alpha-helices from the five-helix bundle of domain 2. The projections from the core of the tetramer are generated from domains 1 and 3 of each subunit []. This entry does not appear to be part of either the active site or the activation site but is helical in structure forming a little bundle. ; GO: 0016829 lyase activity, 0006099 tricarboxylic acid cycle; PDB: 3RRP_A 3OCE_D 3OCF_D 3E04_B 3GTD_A 3R6V_F 3R6Q_F 1J3U_B 1FUR_A 1YFE_A ....
Probab=28.62 E-value=75 Score=23.36 Aligned_cols=37 Identities=19% Similarity=0.118 Sum_probs=27.1
Q ss_pred HHHHHHHHHhcCCCchHHHHHHHHHcCCCHHHHHHHHhhc
Q 023124 123 FEEVMKEIELKGVGLPDDMMEAAKTVGIRKMFLLRYLDLQ 162 (287)
Q Consensus 123 ~~~Vl~ea~r~~~sLPaDl~~Aa~~g~is~a~L~Rfl~L~ 162 (287)
..+|-++|.+++.++..-. .+.|.++++++.+.|+.+
T Consensus 14 aa~iAk~A~~~g~svre~v---~~~g~lt~ee~d~ll~p~ 50 (55)
T PF10415_consen 14 AAEIAKEALAEGRSVREVV---LEEGLLTEEELDELLDPE 50 (55)
T ss_dssp HHHHHHHHHHHT--HHHHH---HHTTSS-HHHHHHHTSHH
T ss_pred HHHHHHHHHHcCCCHHHHH---HHcCCCCHHHHHHHcCHH
Confidence 4678889999999886544 467889999999998865
No 38
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=27.54 E-value=77 Score=31.12 Aligned_cols=7 Identities=0% Similarity=0.359 Sum_probs=2.9
Q ss_pred eeeecCC
Q 023124 59 TIEIPGK 65 (287)
Q Consensus 59 ~iei~g~ 65 (287)
-+-||-+
T Consensus 224 dLSmStR 230 (314)
T PF06524_consen 224 DLSMSTR 230 (314)
T ss_pred cceeeee
Confidence 3444433
No 39
>PF02422 Keratin: Keratin; InterPro: IPR003461 Keratins are a well known group of intermediate filament proteins. Like actin filaments, keratins are flexible but provide a firm cell skeleton. Unlike actin, however, no known keratins are associated with motor functions. This family represents avian keratin proteins [], found in feathers, scale and claw. The avian keratins (F-ker, S-ker, C-ker and B-ker) are a complex mixture of very similar polypeptides.; GO: 0005200 structural constituent of cytoskeleton, 0005882 intermediate filament
Probab=24.40 E-value=1.4e+02 Score=25.04 Aligned_cols=31 Identities=23% Similarity=0.509 Sum_probs=20.6
Q ss_pred ccccccCCCC--CCCCceeeecCCcccccCCCC
Q 023124 44 CKLQCVGNNF--DSTPKTIEIPGKITEESADCE 74 (287)
Q Consensus 44 ~~~~c~~~~~--~~~p~~iei~g~it~ts~~~~ 74 (287)
|..||--+.- ...||-|.++|-|.-+.++..
T Consensus 24 Cv~QcpdS~vvIqPppvVVTlPGPILSs~pQ~~ 56 (98)
T PF02422_consen 24 CVRQCPDSEVVIQPPPVVVTLPGPILSSFPQPS 56 (98)
T ss_pred HHhhCCCceEEEcCCCEEEeccCcccccCCccc
Confidence 4777763321 235788899999988776443
No 40
>KOG3074 consensus Transcriptional regulator of the PUR family, single-stranded-DNA-binding [Transcription]
Probab=24.36 E-value=47 Score=31.92 Aligned_cols=10 Identities=40% Similarity=0.547 Sum_probs=4.0
Q ss_pred HHHHHHHHHH
Q 023124 225 DLLVGLVVDI 234 (287)
Q Consensus 225 dlv~~~i~nf 234 (287)
|+|+-++.||
T Consensus 159 daLaelle~~ 168 (263)
T KOG3074|consen 159 DALAELLEDF 168 (263)
T ss_pred HHHHHHHHHh
Confidence 3333344443
No 41
>TIGR00625 tfb2 Transcription factor tfb2. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=24.01 E-value=79 Score=32.53 Aligned_cols=67 Identities=13% Similarity=0.133 Sum_probs=44.8
Q ss_pred HHHHHHHhcCCCch---------HHHHHHHHHcCCCHHHHHHHHhhcCCcchhH--------HHHHH---hhhhhhhhhc
Q 023124 125 EVMKEIELKGVGLP---------DDMMEAAKTVGIRKMFLLRYLDLQGSVWPLG--------FLMRY---CFMLRDRMLA 184 (287)
Q Consensus 125 ~Vl~ea~r~~~sLP---------aDl~~Aa~~g~is~a~L~Rfl~L~~sp~~l~--------~L~r~---~~g~r~RlLA 184 (287)
++++.--+-...+| ..+++|.+.| |+..|+.+||.-.+.|...+ -++.. |..=|+|+-.
T Consensus 313 ~il~lF~~~~~r~pnlvvg~iTr~Sv~~A~~~G-ITa~qIi~fl~~~ahp~~~~~~~~~lP~tv~dQi~lWe~e~~R~~~ 391 (448)
T TIGR00625 313 ALIALFSELLARFPNMVVGQITRESIRRALANG-ITAQQIIHYLRTHAHPQMRKEQTPVLPPTIVDQIRLWELERDRLRF 391 (448)
T ss_pred HHHHHHHHHHhcCCceEEEEecHHHHHHHHHcC-CCHHHHHHHHHhcCChhhhccCCCCCChHHHHHHHHHHHHhcceEe
Confidence 45555444444444 4567888777 99999999999888764211 23333 3444889999
Q ss_pred CcchhHHH
Q 023124 185 DPSFLFKV 192 (287)
Q Consensus 185 DP~FlfKl 192 (287)
.|.||||=
T Consensus 392 ~~~~l~~~ 399 (448)
T TIGR00625 392 TEGVLYND 399 (448)
T ss_pred ecceeeee
Confidence 98888764
No 42
>PF15207 TMEM240: TMEM240 family
Probab=23.94 E-value=88 Score=28.27 Aligned_cols=26 Identities=35% Similarity=0.365 Sum_probs=21.1
Q ss_pred cchhhHHHHHHHHHHHHHHHHHhHhhc
Q 023124 214 DFWSEFELYLADLLVGLVVDIALVGML 240 (287)
Q Consensus 214 ~f~~ElDfV~adlv~~~i~nfaLV~lL 240 (287)
--++|+|+++ -++++.+..-+||||=
T Consensus 83 vtkqeidlml-glllgfcisw~l~wmd 108 (180)
T PF15207_consen 83 VTKQEIDLML-GLLLGFCISWFLVWMD 108 (180)
T ss_pred chHHHHHHHH-HHHHHHHHHHHHHHHh
Confidence 3478999987 4788888899999983
No 43
>PRK06925 flagellar motor protein MotS; Reviewed
Probab=23.51 E-value=72 Score=28.99 Aligned_cols=26 Identities=15% Similarity=0.257 Sum_probs=23.8
Q ss_pred hhHHHHHHHHHHHHHHHHHhHhhccc
Q 023124 217 SEFELYLADLLVGLVVDIALVGMLAP 242 (287)
Q Consensus 217 ~ElDfV~adlv~~~i~nfaLV~lLAP 242 (287)
.+|-.-++|++|.+.+=|+|+|.++=
T Consensus 13 ~~W~vtyaD~~TlLlafFvlL~s~s~ 38 (230)
T PRK06925 13 PKWMVTFSDLITLILVFFILLFSMSQ 38 (230)
T ss_pred cchhhhHHHHHHHHHHHHHHHHHhhc
Confidence 47999999999999999999999874
No 44
>TIGR03793 TOMM_pelo TOMM propeptide domain. This model represents a domain that is conserved among a large number of putative thiazole/oxazole-modified microcins (TOMM). Oddly, most of this seqence region appears homologous to nitrile hydratase subunits. This family is expanded especially in Pelotomaculum thermopropionicum SI.
Probab=23.25 E-value=50 Score=26.02 Aligned_cols=17 Identities=12% Similarity=0.380 Sum_probs=13.4
Q ss_pred HHHHh--hhhhhhhhcCcc
Q 023124 171 LMRYC--FMLRDRMLADPS 187 (287)
Q Consensus 171 L~r~~--~g~r~RlLADP~ 187 (287)
+.|++ +.||.||++||.
T Consensus 10 varAw~Dp~Fr~~Ll~DPr 28 (77)
T TIGR03793 10 IAKAWEDEAFKQALLTNPK 28 (77)
T ss_pred HHHHHcCHHHHHHHHHCHH
Confidence 34444 899999999995
No 45
>PRK09038 flagellar motor protein MotD; Reviewed
Probab=22.91 E-value=75 Score=29.98 Aligned_cols=26 Identities=12% Similarity=0.163 Sum_probs=23.7
Q ss_pred hhHHHHHHHHHHHHHHHHHhHhhccc
Q 023124 217 SEFELYLADLLVGLVVDIALVGMLAP 242 (287)
Q Consensus 217 ~ElDfV~adlv~~~i~nfaLV~lLAP 242 (287)
.+|-.-++|+++++.+=|+|+|.++=
T Consensus 15 ~~WlvtYAD~mTLLlaFFVlL~smS~ 40 (281)
T PRK09038 15 ERWLVSYADFITLLFAFFVVMYAISS 40 (281)
T ss_pred cchhhhHHHHHHHHHHHHHHHHHHhc
Confidence 37999999999999999999998873
No 46
>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]
Probab=22.83 E-value=1.9e+02 Score=27.43 Aligned_cols=12 Identities=8% Similarity=0.097 Sum_probs=6.7
Q ss_pred CCCcccccCCCC
Q 023124 72 DCEPRIHSSGGD 83 (287)
Q Consensus 72 ~~~~~~~~~~G~ 83 (287)
+.++|.+-++..
T Consensus 74 rLRVEfprggr~ 85 (241)
T KOG0105|consen 74 RLRVEFPRGGRS 85 (241)
T ss_pred eEEEEeccCCCc
Confidence 455666655553
No 47
>PRK07734 motB flagellar motor protein MotB; Reviewed
Probab=22.05 E-value=72 Score=29.52 Aligned_cols=26 Identities=19% Similarity=0.203 Sum_probs=23.7
Q ss_pred hhHHHHHHHHHHHHHHHHHhHhhccc
Q 023124 217 SEFELYLADLLVGLVVDIALVGMLAP 242 (287)
Q Consensus 217 ~ElDfV~adlv~~~i~nfaLV~lLAP 242 (287)
..|-.-++|++|++.+=|+|+|.++=
T Consensus 17 ~~W~vtYAD~vTlLlaFFvlL~s~s~ 42 (259)
T PRK07734 17 ESWLIPYADLLTLLLALFIVLFAMSS 42 (259)
T ss_pred CcchhhHHHHHHHHHHHHHHHHHHhh
Confidence 36999999999999999999999873
No 48
>KOG3570 consensus MAPK-activating protein DENN [Signal transduction mechanisms]
Probab=21.57 E-value=1.7e+02 Score=33.56 Aligned_cols=71 Identities=21% Similarity=0.291 Sum_probs=37.5
Q ss_pred CCCCc-ccccc--eeeEeecccCCCCcccccccccCCCCCCCCceeeecCCccccc---------CCCCcccccCCCCCC
Q 023124 18 PQNHN-IVMPT--TVFLSLRHSTATNPALCKLQCVGNNFDSTPKTIEIPGKITEES---------ADCEPRIHSSGGDGG 85 (287)
Q Consensus 18 ~~~~~-~~~~~--~~~~~~~~s~~~~~~~~~~~c~~~~~~~~p~~iei~g~it~ts---------~~~~~~~~~~~G~Gg 85 (287)
|..|. ..+|+ ++||.=.--+...|+.-. -+|-+-|-..+.-|++--. ...+.++.+-.|.||
T Consensus 40 ~~DH~dFpLP~Dvv~FCQPEGCtsv~~Rr~~------~rD~tsFVF~LTdKDsgktRYGICvNFYrsf~~r~s~~~g~~g 113 (1588)
T KOG3570|consen 40 LEDHTEFPLPPDVVFFCQPEGCLSVRQRRMS------LRDDTSFVFTLTDKDTGVTRYGICVNFYRSFQKRISKEKGEGG 113 (1588)
T ss_pred ccccccCCCCCCeEEEeCCccccchhhhhhc------ccCCceEEEEEecccCcceeeEEEeeeehhhhhccchhccccc
Confidence 44453 34554 678876666655665522 2234445555555554322 345556666667776
Q ss_pred CCCCCCCCC
Q 023124 86 AGDSPGGGG 94 (287)
Q Consensus 86 ~g~~~~~gg 94 (287)
.|..|+-|+
T Consensus 114 ag~Rg~~g~ 122 (1588)
T KOG3570|consen 114 AGSRGKEGT 122 (1588)
T ss_pred cccCCCCCC
Confidence 666544333
No 49
>TIGR01659 sex-lethal sex-lethal family splicing factor. This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661).
Probab=20.91 E-value=1e+02 Score=30.02 Aligned_cols=6 Identities=17% Similarity=0.733 Sum_probs=2.9
Q ss_pred ceeeEe
Q 023124 27 TTVFLS 32 (287)
Q Consensus 27 ~~~~~~ 32 (287)
+++|+.
T Consensus 194 ~~lfV~ 199 (346)
T TIGR01659 194 TNLYVT 199 (346)
T ss_pred ceeEEe
Confidence 445554
No 50
>PF05084 GRA6: Granule antigen protein (GRA6); InterPro: IPR008119 Toxoplasma gondii is an obligate intracellular apicomplexan protozoan parasite, with a complex lifestyle involving varied hosts []. It has two phases of growth: an intestinal phase in feline hosts, and an extra-intestinal phase in other mammals. Oocysts from infected cats develop into tachyzoites, and eventually, bradyzoites and zoitocysts in the extraintestinal host []. Transmission of the parasite occurs through contact with infected cats or raw/undercooked meat; in immunocompromised individuals, it can cause severe and often lethal toxoplasmosis. Acute infection in healthy humans can sometimes also cause tissue damage []. The protozoan utilises a variety of secretory and antigenic proteins to invade a host and gain access to the intracellular environment []. These originate from distinct organelles in the T. gondii cell termed micronemes, rhoptries, and dense granules. They are released at specific times during invasion to ensure the proteins are allocated to their correct target destinations []. Dense granule antigens (GRAs) are released from the T. gondii tachyzoite while still encapsulated in a host vacuole. Gra6, one of these moieties, is associated with the parasitophorous vacuole []. It possesses a hydrophobic central region flanked by two hydrophilic domains, and is present as a single copy gene in the Toxoplasma gondii genome []. Gra6 shares a similar function with Gra2, in that it is rapidly targeted to a network of membranous tubules that connect with the vacuolar membrane []. Indeed, these two proteins, together with Gra4, form a multimeric complex that stabilises the parasite within the vacuole.
Probab=20.35 E-value=1.4e+02 Score=27.74 Aligned_cols=20 Identities=30% Similarity=0.328 Sum_probs=9.3
Q ss_pred cccceeeEeecccCCCCccc
Q 023124 24 VMPTTVFLSLRHSTATNPAL 43 (287)
Q Consensus 24 ~~~~~~~~~~~~s~~~~~~~ 43 (287)
|-|..|.-+=+.+-..-|.+
T Consensus 100 V~P~~V~~~E~~s~a~~~~~ 119 (215)
T PF05084_consen 100 VDPFPVLANEGKSEARGPSQ 119 (215)
T ss_pred CCccccccccccCccccchH
Confidence 34444444444444444444
No 51
>PF12244 DUF3606: Protein of unknown function (DUF3606); InterPro: IPR022037 This family of proteins is found in bacteria. Proteins in this family are typically between 58 and 85 amino acids in length. There is a single completely conserved residue G that may be functionally important.
Probab=20.21 E-value=1.9e+02 Score=21.37 Aligned_cols=34 Identities=18% Similarity=0.183 Sum_probs=28.2
Q ss_pred HHHHHhcCCCchHHHHHHHHHcCCCHHHHHHHHh
Q 023124 127 MKEIELKGVGLPDDMMEAAKTVGIRKMFLLRYLD 160 (287)
Q Consensus 127 l~ea~r~~~sLPaDl~~Aa~~g~is~a~L~Rfl~ 160 (287)
++-|.++.--=++.|++|++.-|-+.+.+.+||.
T Consensus 23 v~ywa~~~gvt~~~L~~AV~~vG~~~~~V~~~L~ 56 (57)
T PF12244_consen 23 VRYWAKRFGVTEEQLREAVRAVGNSRAAVRAYLG 56 (57)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHCcCHHHHHHHHc
Confidence 4566666666689999999999999999999984
No 52
>PRK06958 single-stranded DNA-binding protein; Provisional
Probab=20.06 E-value=1.1e+02 Score=27.87 Aligned_cols=11 Identities=27% Similarity=0.516 Sum_probs=4.8
Q ss_pred CceeeecCCcc
Q 023124 57 PKTIEIPGKIT 67 (287)
Q Consensus 57 p~~iei~g~it 67 (287)
.-.|.|+|++.
T Consensus 73 Gs~V~VeGrL~ 83 (182)
T PRK06958 73 GSSVYIEGRIR 83 (182)
T ss_pred CCEEEEEEEEE
Confidence 33444444443
Done!