Query gi|254780721|ref|YP_003065134.1| pilus component protein [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 329
No_of_seqs 154 out of 1349
Neff 8.6
Searched_HMMs 39220
Date Sun May 29 23:16:00 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780721.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG4965 TadB Flp pilus assembl 100.0 1.5E-30 3.7E-35 220.3 32.5 167 155-325 110-279 (309)
2 COG2064 TadC Flp pilus assembl 100.0 3.7E-23 9.3E-28 171.3 35.6 313 12-327 5-319 (320)
3 PRK06041 flagellar assembly pr 99.6 6.2E-12 1.6E-16 97.0 27.9 136 156-294 298-434 (547)
4 PRK06041 flagellar assembly pr 99.5 8.3E-10 2.1E-14 83.0 28.2 138 164-302 57-195 (547)
5 pfam00482 GSPII_F Bacterial ty 99.4 2.8E-11 7.2E-16 92.7 14.7 123 186-314 1-123 (125)
6 PRK10573 type IV pilin biogene 99.2 4.7E-09 1.2E-13 78.0 17.4 110 182-300 262-372 (397)
7 PRK10573 type IV pilin biogene 99.2 2.4E-07 6.1E-12 66.7 25.9 46 229-274 274-319 (397)
8 COG1955 FlaJ Archaeal flagella 99.1 3.1E-07 7.8E-12 66.0 23.6 120 168-290 288-408 (527)
9 COG1459 PulF Type II secretory 99.1 6E-08 1.5E-12 70.7 18.1 112 181-300 261-372 (397)
10 COG1955 FlaJ Archaeal flagella 98.9 6E-06 1.5E-10 57.5 21.9 136 164-301 35-171 (527)
11 COG1459 PulF Type II secretory 98.9 1.1E-05 2.8E-10 55.7 29.8 55 218-275 266-320 (397)
12 TIGR02120 GspF general secreti 98.8 3.5E-07 9E-12 65.6 14.3 134 161-302 246-392 (414)
13 TIGR02120 GspF general secreti 98.5 0.00014 3.5E-09 48.5 22.4 148 174-329 69-216 (414)
14 pfam09548 Spore_III_AB Stage I 96.7 0.046 1.2E-06 31.8 22.0 106 151-265 7-124 (170)
15 PRK08307 stage III sporulation 95.7 0.15 3.9E-06 28.3 22.6 106 151-265 9-126 (172)
16 TIGR02833 spore_III_AB stage I 93.8 0.45 1.1E-05 25.2 17.5 147 150-313 6-166 (170)
17 PRK03072 heat shock protein Ht 82.4 3.1 7.8E-05 19.7 5.9 12 198-209 220-231 (289)
18 PRK02391 heat shock protein Ht 77.5 4.4 0.00011 18.7 6.2 11 198-208 229-239 (297)
19 PRK05457 heat shock protein Ht 72.6 5.8 0.00015 17.9 5.0 12 34-45 51-62 (289)
20 PRK01345 heat shock protein Ht 71.7 6.1 0.00016 17.7 4.9 11 199-209 218-228 (314)
21 PRK03001 heat shock protein Ht 69.9 6.7 0.00017 17.5 5.0 13 198-210 216-228 (284)
22 PRK03982 heat shock protein Ht 67.8 7.4 0.00019 17.2 5.1 13 198-210 221-233 (288)
23 pfam12169 DNA_pol3_gamma3 DNA 65.9 8 0.0002 16.9 5.4 83 179-263 26-108 (143)
24 PRK08475 F0F1 ATP synthase sub 62.3 9.3 0.00024 16.5 8.7 52 138-189 19-70 (170)
25 TIGR02606 antidote_CC2985 puta 62.1 9.4 0.00024 16.5 5.8 46 248-294 7-53 (77)
26 KOG3533 consensus 56.8 12 0.00029 15.9 4.3 72 243-328 2500-2571(2706)
27 pfam04799 Fzo_mitofusin fzo-li 48.4 16 0.0004 15.0 13.8 72 161-246 60-136 (171)
28 pfam12046 DUF3529 Protein of u 47.4 12 0.00031 15.8 1.8 63 110-182 75-139 (173)
29 pfam00745 GlutR_dimer Glutamyl 44.1 18 0.00046 14.6 9.8 91 177-276 5-95 (101)
30 pfam06697 DUF1191 Protein of u 42.2 19 0.00049 14.4 2.8 17 166-182 232-248 (275)
31 TIGR00814 stp serine transport 41.2 20 0.00051 14.3 3.9 87 237-327 276-379 (419)
32 pfam04228 Zn_peptidase Putativ 41.2 20 0.00051 14.3 3.8 14 97-110 102-115 (292)
33 TIGR02203 MsbA_lipidA lipid A 40.4 21 0.00052 14.2 8.1 47 141-193 178-224 (603)
34 pfam12072 DUF3552 Domain of un 36.6 23 0.0006 13.9 6.8 16 231-246 144-159 (201)
35 PRK04897 heat shock protein Ht 36.3 24 0.00061 13.8 6.0 13 197-209 240-252 (298)
36 TIGR01477 RIFIN variant surfac 32.7 27 0.00069 13.5 3.2 20 251-270 309-328 (395)
37 PRK12482 flagellar motor prote 30.7 29 0.00074 13.2 20.4 108 123-230 175-284 (287)
38 PRK01844 hypothetical protein; 30.6 29 0.00075 13.2 4.3 20 150-169 11-30 (72)
39 PRK05289 UDP-N-acetylglucosami 29.8 30 0.00077 13.1 5.8 30 231-260 222-251 (261)
40 TIGR02029 AcsF magnesium-proto 29.2 31 0.00079 13.1 4.5 70 178-250 75-145 (344)
41 pfam03918 CcmH Cytochrome C bi 27.4 33 0.00084 12.9 4.7 16 104-120 68-83 (145)
42 PRK10862 SoxR reducing system 26.9 34 0.00086 12.8 7.5 43 121-167 82-124 (158)
43 pfam04246 RseC_MucC Positive r 26.6 34 0.00087 12.8 7.4 44 121-168 75-118 (135)
44 KOG3385 consensus 25.8 35 0.0009 12.7 6.7 31 284-314 84-114 (118)
45 PRK08374 homoserine dehydrogen 25.2 26 0.00067 13.5 0.6 54 191-244 140-195 (316)
46 pfam03564 DUF1759 Protein of u 25.1 36 0.00093 12.6 11.3 121 181-309 6-131 (146)
47 COG0398 Uncharacterized conser 25.1 36 0.00093 12.6 10.8 76 96-174 36-113 (223)
48 COG4980 GvpP Gas vesicle prote 24.8 37 0.00094 12.6 5.1 28 218-247 62-89 (115)
49 pfam03649 UPF0014 Uncharacteri 24.6 37 0.00095 12.5 3.5 28 217-244 151-178 (250)
50 PRK13455 F0F1 ATP synthase sub 24.3 38 0.00096 12.5 10.2 44 145-189 29-73 (184)
51 PRK03427 cell division protein 23.4 39 0.001 12.4 2.5 21 8-28 1-21 (331)
52 TIGR02857 CydD ABC transporter 22.8 40 0.001 12.3 18.9 106 112-228 118-227 (570)
53 pfam05659 RPW8 Arabidopsis bro 22.5 41 0.001 12.3 13.5 63 180-245 29-91 (147)
54 pfam03323 GerA Bacillus/Clostr 22.4 41 0.001 12.3 2.2 50 154-208 279-328 (468)
55 TIGR03224 benzo_boxA benzoyl-C 22.3 29 0.00075 13.2 0.4 56 166-221 342-399 (411)
56 TIGR00701 TIGR00701 conserved 22.3 41 0.0011 12.2 2.4 21 174-194 121-141 (151)
57 PRK12461 UDP-N-acetylglucosami 21.6 42 0.0011 12.2 6.0 30 231-260 219-249 (256)
58 PRK13721 conjugal transfer ATP 21.4 43 0.0011 12.1 5.3 33 258-290 827-859 (864)
59 TIGR02362 dhaK1b probable dihy 21.2 27 0.00068 13.5 -0.0 19 252-270 153-171 (328)
60 PRK01265 heat shock protein Ht 20.6 45 0.0011 12.0 8.5 12 198-209 236-247 (326)
61 TIGR02332 HpaX 4-hydroxyphenyl 20.4 45 0.0011 12.0 3.9 53 238-290 248-309 (412)
62 COG5249 RER1 Golgi protein inv 20.4 45 0.0011 12.0 2.8 21 236-258 99-119 (180)
63 COG1826 TatA Sec-independent p 20.2 39 0.00099 12.4 0.6 17 9-25 4-20 (94)
No 1
>COG4965 TadB Flp pilus assembly protein TadB [Intracellular trafficking and secretion]
Probab=100.00 E-value=1.5e-30 Score=220.29 Aligned_cols=167 Identities=22% Similarity=0.305 Sum_probs=155.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCC
Q ss_conf 99999999999999999999999999999999999999997499689999999984077877899999999999965999
Q gi|254780721|r 155 LIGYVGFCAPSVWISNLVQKRQSSIKRAWPDALDLLLICVESGISIDQALRRVAEDIGGQSVPLSEEMLLTIAELSFLPN 234 (329)
Q Consensus 155 ~~~~~g~~~P~~~l~~~~~~r~~~i~~~lP~~ld~l~~~~~aG~~l~~Al~~va~e~~~~~~~l~~e~~~~~~~~~~G~~ 234 (329)
.+.+.+..+|.++++++++||.+++.+|||+++|++++.++||+|+.+|++.+++|.++ |++.||..+.++++.|.|
T Consensus 110 ~~~~~~~llp~~~~~~~~~rr~krf~~qlP~aLdlivr~l~aG~~l~dAl~~~~~e~~~---Pl~~ef~~i~~~~~~G~~ 186 (309)
T COG4965 110 VALIGAALLPRLVLRSRRARRLKRFGQQLPEALDLIVRALRAGAPLPDALRLAAKETPE---PLGTEFTLITDRQQLGID 186 (309)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCC---CHHHHHHHHHHHHHCCCC
T ss_conf 99999999999999999999999999976699999998865799879999999860898---567899999999983998
Q ss_pred HHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-
Q ss_conf 8999999998639958999999999999719958999999999999999999999998433369999999999999999-
Q gi|254780721|r 235 RQVAFENFYNRTQMDCVRNATQALIQSDRYGTSIGDSLRVLVSETRSERLMEAEKKAASLGPKLTVPMIIFFLPVLILV- 313 (329)
Q Consensus 235 ~~~Al~~~a~r~~~~~~~~~~~~l~~~~~~G~~l~~~L~~~a~~~r~~~~~~~e~~a~~~~~k~~~~~il~~~p~~~~~- 313 (329)
.++|+.++.+|++.+|+++|+..+..+.++|||++|.|++++..+|||++++.|.+|.++|+||++ +|+..+|+++..
T Consensus 187 ~~~a~~~~~er~p~~el~fl~ivi~iq~~~GGnL~e~l~~ls~vireRkk~~~Kv~AlsaEaRmSA-~Il~~lP~~v~~l 265 (309)
T COG4965 187 LPAALLRMYERYPLEELYFLAIVISIQSRHGGNLSELLDNLSRVIRERKKMKAKVRALSAEARMSA-WILGALPLLVGLL 265 (309)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHH
T ss_conf 469999999837823688999999988762878999999999999999999999998634111688-9999835999999
Q ss_pred --HHHHHHHHHHHH
Q ss_conf --997799999999
Q gi|254780721|r 314 --IIGPAILSIIDT 325 (329)
Q Consensus 314 --~~~P~~~~~~~~ 325 (329)
.++|.+++.+.+
T Consensus 266 i~~~~P~~l~~lw~ 279 (309)
T COG4965 266 IYLLSPDYLSFLWT 279 (309)
T ss_pred HHHCCCHHHHHHHC
T ss_conf 99819378999835
No 2
>COG2064 TadC Flp pilus assembly protein TadC [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=99.95 E-value=3.7e-23 Score=171.34 Aligned_cols=313 Identities=31% Similarity=0.393 Sum_probs=231.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 89999999999999999999999607660899999999877887654432100012456775654457899998520000
Q gi|254780721|r 12 TELAVAITTAVSIFSLIYAVVIPSLGSGELEKRMKSVAVEREILRKQQITSLQKDSASSRLRTRDSKSLRNFVKKLNLKA 91 (329)
Q Consensus 12 ~~lli~il~~i~v~~~i~~l~~~~~~~~~~~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 91 (329)
.......+.+...+............+.......+......+............... .....................
T Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~ 82 (320)
T COG2064 5 AELYLTFLVARPLFALAILVVMAVLKRKELLLLLKGVDREIPRIILLSLIRLLIGSV--SIRELLAFLLRKIISGLLLFF 82 (320)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHH--CCCHHHHHHHHHHHHHHHHHH
T ss_conf 789999998999999999999998264017999987898700566899998864311--002057899999999988877
Q ss_pred CCCCHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 12556999999967999867589999999999999999999-99999732001215899999999999999999999999
Q gi|254780721|r 92 ILVDENIVNKLRAAGFRSEYSLNILLVVRLVVPIIFLILGI-IWIFGYDKLLEYPFQLRVGAVILIGYVGFCAPSVWISN 170 (329)
Q Consensus 92 ~~~~~~l~~~L~~AG~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~P~~~l~~ 170 (329)
.........++.+++++.......+..........+..... ++..........+.......++.....|++.|....+.
T Consensus 83 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~g~~~p~i~~~~ 162 (320)
T COG2064 83 GGEDSKPRFKLVEALYRLELALPLFLFALLLALFLGVLLSLPILLLVLGSFIILPLSDFLAIALLISLLGLPLPFILFSL 162 (320)
T ss_pred HHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCCCHHHHHHH
T ss_conf 76677898889999998850340899999999999999999999999987300229999999999988144207899999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCHH
Q ss_conf 99999999999999999999999974996899999999840778778999999999999659998999999998639958
Q gi|254780721|r 171 LVQKRQSSIKRAWPDALDLLLICVESGISIDQALRRVAEDIGGQSVPLSEEMLLTIAELSFLPNRQVAFENFYNRTQMDC 250 (329)
Q Consensus 171 ~~~~r~~~i~~~lP~~ld~l~~~~~aG~~l~~Al~~va~e~~~~~~~l~~e~~~~~~~~~~G~~~~~Al~~~a~r~~~~~ 250 (329)
..++|.+++++++|+++|.+..|.++|+++.+|++.++++..+. +++++|+..+..++++|.+.++|+.+++.+.++.+
T Consensus 163 ~~~~r~~~i~~~~p~~l~~~~~~~~~G~~l~~al~~va~~~~~~-~~l~~~~~~~~~~~~~g~~~~~al~~~~~~~~~~~ 241 (320)
T COG2064 163 ALKKRLKEIARELPDFLRLMAVCLEAGLSLADALKRVADELYGQ-RILAEELARTTAELSLGLSIEEALIRLAVRLGSDE 241 (320)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCC-HHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHH
T ss_conf 99862135899889999999999882878999999998733233-88999999999998769977999999987443499
Q ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999999997199589999999999-9999999999999843336999999999999999999779999999973
Q gi|254780721|r 251 VRNATQALIQSDRYGTSIGDSLRVLVSE-TRSERLMEAEKKAASLGPKLTVPMIIFFLPVLILVIIGPAILSIIDTMK 327 (329)
Q Consensus 251 ~~~~~~~l~~~~~~G~~l~~~L~~~a~~-~r~~~~~~~e~~a~~~~~k~~~~~il~~~p~~~~~~~~P~~~~~~~~~~ 327 (329)
.+.+++.+.++.+.|+++.+.|+..+.+ .++.+....+++..+.+.++..++++|++|+.+.+.+.|..+++...+.
T Consensus 242 ~~~~~~~l~~~~~~g~~l~~~l~~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~~~i~~~~~v~~~~~~~~~~~~~~ 319 (320)
T COG2064 242 VKRVVSLLTQALESGGSLADALRVLSMELSRETRLKLGEIRAGKIGVGILLPLILVIIPVLLFVVILPAILGIASSGG 319 (320)
T ss_pred HHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf 999999999998833209999999999999998899998899988879999999999999999999888999998615
No 3
>PRK06041 flagellar assembly protein J; Reviewed
Probab=99.64 E-value=6.2e-12 Score=97.05 Aligned_cols=136 Identities=13% Similarity=0.097 Sum_probs=116.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-CCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCC
Q ss_conf 9999999999999999999999999999999999999997-499689999999984077877899999999999965999
Q gi|254780721|r 156 IGYVGFCAPSVWISNLVQKRQSSIKRAWPDALDLLLICVE-SGISIDQALRRVAEDIGGQSVPLSEEMLLTIAELSFLPN 234 (329)
Q Consensus 156 ~~~~g~~~P~~~l~~~~~~r~~~i~~~lP~~ld~l~~~~~-aG~~l~~Al~~va~e~~~~~~~l~~e~~~~~~~~~~G~~ 234 (329)
+..+..++|.-++.++..++.++.++++|+|+..+..... .|.++.++++.+.+. ..+++.++.++..+++++|.+
T Consensus 298 ai~~~pll~~G~~~~~eE~~I~rrD~~fP~FIRsLGss~~a~G~t~~~aL~~L~~~---dfG~L~~~I~~LykRL~~~id 374 (547)
T PRK06041 298 ALVGTPLAPLGYVARRDEGNIIRRDENFPAFIRSLGSSVSAKGGTLTDALKYLDKK---DFGPLTPDINELYKRLNLRLD 374 (547)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHH---CCCCCCHHHHHHHHHHHCCCC
T ss_conf 99999999999999999988887662128999998777442477699999996552---465566889999999875898
Q ss_pred HHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 899999999863995899999999999971995899999999999999999999999843
Q gi|254780721|r 235 RQVAFENFYNRTQMDCVRNATQALIQSDRYGTSIGDSLRVLVSETRSERLMEAEKKAASL 294 (329)
Q Consensus 235 ~~~Al~~~a~r~~~~~~~~~~~~l~~~~~~G~~l~~~L~~~a~~~r~~~~~~~e~~a~~~ 294 (329)
.+.||+.|...+++.-++.|......+.+.|||-.++-+..|+.+.+-...|.++.-...
T Consensus 375 ~~~aW~~F~~etgS~LI~~fs~if~~~~~lGG~p~~vgeiiS~n~~~iv~LR~kR~q~~~ 434 (547)
T PRK06041 375 SKKAWRKFIADTGSYLIQKFSEIFRDAVELGGDPDVVGEIISSNFLEIVLLRMKRYQSVS 434 (547)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 788999887543549999999999999984999899999998889999999999999998
No 4
>PRK06041 flagellar assembly protein J; Reviewed
Probab=99.49 E-value=8.3e-10 Score=82.99 Aligned_cols=138 Identities=13% Similarity=0.036 Sum_probs=122.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHH-CCCCHHHHHHHH
Q ss_conf 9999999999999999999999999999999749968999999998407787789999999999996-599989999999
Q gi|254780721|r 164 PSVWISNLVQKRQSSIKRAWPDALDLLLICVESGISIDQALRRVAEDIGGQSVPLSEEMLLTIAELS-FLPNRQVAFENF 242 (329)
Q Consensus 164 P~~~l~~~~~~r~~~i~~~lP~~ld~l~~~~~aG~~l~~Al~~va~e~~~~~~~l~~e~~~~~~~~~-~G~~~~~Al~~~ 242 (329)
-..|.+.+..+|++++++++|.++..|.....++++..+-++..+++ ++.++++++|++++...++ +|.+..+|.+..
T Consensus 57 a~~yP~~~~~~~~~~I~~~m~~~iT~M~~LSt~~~~r~~if~~Ls~~-~ey~G~la~e~~kI~~Lv~~w~~sl~eA~r~~ 135 (547)
T PRK06041 57 AIGYPKIKLDSKRLKINNDLLFFITYMAVLSTADLDRDEIFRYLSEE-KEYLGQLSKEFKKIYVLVKKWNYSLAEACRFL 135 (547)
T ss_pred HHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHC-CHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHH
T ss_conf 99730888754899888630899999999982699989999998843-12206889999999999998681689999999
Q ss_pred HHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 986399589999999999997199589999999999999999999999984333699999
Q gi|254780721|r 243 YNRTQMDCVRNATQALIQSDRYGTSIGDSLRVLVSETRSERLMEAEKKAASLGPKLTVPM 302 (329)
Q Consensus 243 a~r~~~~~~~~~~~~l~~~~~~G~~l~~~L~~~a~~~r~~~~~~~e~~a~~~~~k~~~~~ 302 (329)
|+|+|++.+++|.+-+..+.+.|.++.+.|+.-.+...+.....-|..-..+..--.++.
T Consensus 136 A~rtpS~~~~dFLdRlA~si~SG~~~~eFL~~Eq~~~~~~y~~~ye~~LesLd~~~e~Yv 195 (547)
T PRK06041 136 AKRTPSDRLSDFLDRLAYSIDSGEPLKEFLKQEQDTVMEIYKTFYERALESLDKWKDAYV 195 (547)
T ss_pred HHCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 762997799999999998886699879999999999999999999999999999999999
No 5
>pfam00482 GSPII_F Bacterial type II secretion system protein F domain. The original family covered both the regions found by the current model. The splitting of the family has allowed the related FlaJ_arch (archaeal FlaJ family) to be merged with it. Proteins with this domain in form a platform for the type II secretion machinery, as well as the type IV pili and the archaeal flagellae. This domain seems to show some similarity to pfam00664, but this may just be due to similarities in the TM helices (personal obs: C Yeats).
Probab=99.39 E-value=2.8e-11 Score=92.71 Aligned_cols=123 Identities=23% Similarity=0.266 Sum_probs=109.2
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf 99999999974996899999999840778778999999999999659998999999998639958999999999999719
Q gi|254780721|r 186 ALDLLLICVESGISIDQALRRVAEDIGGQSVPLSEEMLLTIAELSFLPNRQVAFENFYNRTQMDCVRNATQALIQSDRYG 265 (329)
Q Consensus 186 ~ld~l~~~~~aG~~l~~Al~~va~e~~~~~~~l~~e~~~~~~~~~~G~~~~~Al~~~a~r~~~~~~~~~~~~l~~~~~~G 265 (329)
+++.++.++++|+|+.+|++.++++. .+++++++++.+.++++.|.+..+++. +.+.++++.++..+..+.+.|
T Consensus 1 fl~~l~~~~~sG~~l~~al~~~~~~~--~~~~l~~~~~~i~~~l~~G~~~~~al~----~~~~~~~~~~~~~~~~~~~~g 74 (125)
T pfam00482 1 FLRQLATLLRAGLPLLEALEILAEEA--ENGPLREELKRIRERLREGGSLSEALA----RTPLSEFPPLLVALIAAGESG 74 (125)
T ss_pred CHHHHHHHHHCCCCHHHHHHHHHHHC--CCHHHHHHHHHHHHHHHCCCHHHHHHH----HCCCCCCCHHHHHHHHHHHHC
T ss_conf 98989999986998999999998664--898999999999999980860999997----667112999999999999875
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 9589999999999999999999999984333699999999999999999
Q gi|254780721|r 266 TSIGDSLRVLVSETRSERLMEAEKKAASLGPKLTVPMIIFFLPVLILVI 314 (329)
Q Consensus 266 ~~l~~~L~~~a~~~r~~~~~~~e~~a~~~~~k~~~~~il~~~p~~~~~~ 314 (329)
|++.+.|+..++.++++++.+.+..+...+..+.+++.+++++++++++
T Consensus 75 g~l~~~l~~~a~~~~~~~~~~~~~~~~~~~~~~~i~~~~~i~~~~~~~~ 123 (125)
T pfam00482 75 GNLAEVLERLADYLEERRELRRKILAALLYPLILLVVALLVLLILLAIL 123 (125)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEE
T ss_conf 8599999999999999999999999999989999999999999998300
No 6
>PRK10573 type IV pilin biogenesis protein; Provisional
Probab=99.20 E-value=4.7e-09 Score=78.00 Aligned_cols=110 Identities=21% Similarity=0.183 Sum_probs=86.9
Q ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCHHHHH-HHHHHHH
Q ss_conf 999999999999974996899999999840778778999999999999659998999999998639958999-9999999
Q gi|254780721|r 182 AWPDALDLLLICVESGISIDQALRRVAEDIGGQSVPLSEEMLLTIAELSFLPNRQVAFENFYNRTQMDCVRN-ATQALIQ 260 (329)
Q Consensus 182 ~lP~~ld~l~~~~~aG~~l~~Al~~va~e~~~~~~~l~~e~~~~~~~~~~G~~~~~Al~~~a~r~~~~~~~~-~~~~l~~ 260 (329)
.+-.|...+...+++|.|+.+|++.+++-. .++.+.+.+..+..+++.|.+..+|+++-. .+.. +...+..
T Consensus 262 ~~~rf~~~L~~ll~sGv~l~~AL~~~~~~~--~n~~~~~~l~~~~~~v~~G~sls~al~~~~------~fp~~~~~mi~v 333 (397)
T PRK10573 262 KLSQIFTILALTQSAGIPFLQGLESAAESI--RCPYWQQALTQIQHQISQGHPIWLALKNHG------EFSPLCLQLVRT 333 (397)
T ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHHHHH--CCHHHHHHHHHHHHHHHCCCCHHHHHHHCC------CCCHHHHHHHHH
T ss_conf 999999999999868997999999999875--899999999999999876932899987379------998999999999
Q ss_pred HHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 9971995899999999999999999999999843336999
Q gi|254780721|r 261 SDRYGTSIGDSLRVLVSETRSERLMEAEKKAASLGPKLTV 300 (329)
Q Consensus 261 ~~~~G~~l~~~L~~~a~~~r~~~~~~~e~~a~~~~~k~~~ 300 (329)
.+++ |++.+.|+..++...++-..+.+.-..-+++-+.+
T Consensus 334 GEes-G~L~~~L~~~a~~ye~~~~~~i~~l~~llEPili~ 372 (397)
T PRK10573 334 GEES-GSLDLMLENLAHHHRQQTLALADNLAALLEPLLLI 372 (397)
T ss_pred HHHH-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 8652-64999999999999999999999999999899999
No 7
>PRK10573 type IV pilin biogenesis protein; Provisional
Probab=99.20 E-value=2.4e-07 Score=66.70 Aligned_cols=46 Identities=13% Similarity=-0.059 Sum_probs=28.4
Q ss_pred HHCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHH
Q ss_conf 9659998999999998639958999999999999719958999999
Q gi|254780721|r 229 LSFLPNRQVAFENFYNRTQMDCVRNATQALIQSDRYGTSIGDSLRV 274 (329)
Q Consensus 229 ~~~G~~~~~Al~~~a~r~~~~~~~~~~~~l~~~~~~G~~l~~~L~~ 274 (329)
++.|.|..+|++-.++-++++.++.-...+.+..+.|.++++.|+.
T Consensus 274 l~sGv~l~~AL~~~~~~~~n~~~~~~l~~~~~~v~~G~sls~al~~ 319 (397)
T PRK10573 274 QSAGIPFLQGLESAAESIRCPYWQQALTQIQHQISQGHPIWLALKN 319 (397)
T ss_pred HHCCCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCCHHHHHHH
T ss_conf 8689979999999998758999999999999998769328999873
No 8
>COG1955 FlaJ Archaeal flagella assembly protein J [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=99.12 E-value=3.1e-07 Score=66.01 Aligned_cols=120 Identities=12% Similarity=0.125 Sum_probs=99.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH-CCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHC
Q ss_conf 9999999999999999999999999997-499689999999984077877899999999999965999899999999863
Q gi|254780721|r 168 ISNLVQKRQSSIKRAWPDALDLLLICVE-SGISIDQALRRVAEDIGGQSVPLSEEMLLTIAELSFLPNRQVAFENFYNRT 246 (329)
Q Consensus 168 l~~~~~~r~~~i~~~lP~~ld~l~~~~~-aG~~l~~Al~~va~e~~~~~~~l~~e~~~~~~~~~~G~~~~~Al~~~a~r~ 246 (329)
+.++..++-++.++.||.|++.+..... .|.++.+|++.+.++ ..+++++-.++..+.+..|.+...|++.|...+
T Consensus 288 v~~~~E~kI~~rDe~F~~FIRSLgss~sa~G~~l~~aLe~l~~~---nfG~L~~~I~~LYkRL~~gids~~aW~~F~aeT 364 (527)
T COG1955 288 VARKEERKINRRDEAFPSFIRSLGSSLSAVGNTLVEALEALDRH---NFGILTEDIRRLYKRLAMGIDSNKAWRLFSAET 364 (527)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHH---CCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCC
T ss_conf 75588777753776679999986123422024599999986342---240031779999999871689888998850474
Q ss_pred CCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 99589999999999997199589999999999999999999999
Q gi|254780721|r 247 QMDCVRNATQALIQSDRYGTSIGDSLRVLVSETRSERLMEAEKK 290 (329)
Q Consensus 247 ~~~~~~~~~~~l~~~~~~G~~l~~~L~~~a~~~r~~~~~~~e~~ 290 (329)
++.-++.+......+.+.|||-..+=+..|+...+--+.|.++.
T Consensus 365 GS~LI~~~S~if~d~i~lGGdp~~~GeiIS~n~~~iv~LR~kR~ 408 (527)
T COG1955 365 GSYLISKFSEIFTDAIDLGGDPDVVGEIISENFLEIVLLRKKRE 408 (527)
T ss_pred HHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 66999999999999997189878999998772799999999998
No 9
>COG1459 PulF Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=99.07 E-value=6e-08 Score=70.67 Aligned_cols=112 Identities=18% Similarity=0.121 Sum_probs=88.4
Q ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf 99999999999999749968999999998407787789999999999996599989999999986399589999999999
Q gi|254780721|r 181 RAWPDALDLLLICVESGISIDQALRRVAEDIGGQSVPLSEEMLLTIAELSFLPNRQVAFENFYNRTQMDCVRNATQALIQ 260 (329)
Q Consensus 181 ~~lP~~ld~l~~~~~aG~~l~~Al~~va~e~~~~~~~l~~e~~~~~~~~~~G~~~~~Al~~~a~r~~~~~~~~~~~~l~~ 260 (329)
.....|...++..+++|+|+.+|++.+++.. .+...+.+.+....+++.|.+...|+++ .+.+...+.-|+.
T Consensus 261 ~~~arf~rtl~~Ll~sGvpl~~aL~i~~~~~--~~~~~~~~~~~~~~~v~~G~sl~~al~~------~~~Fp~~~~~mi~ 332 (397)
T COG1459 261 YALARFARTLGTLLSSGVPLLEALDIAAETV--SNAFLRQALEEIIQEVREGGSLSQALEK------TGLFPPLLLQMIA 332 (397)
T ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHHHHC--CCHHHHHHHHHHHHHHHCCHHHHHHHHH------CCCCHHHHHHHHH
T ss_conf 9999999999999978983999999987623--7499999999999999857569999873------6898199999999
Q ss_pred HHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 9971995899999999999999999999999843336999
Q gi|254780721|r 261 SDRYGTSIGDSLRVLVSETRSERLMEAEKKAASLGPKLTV 300 (329)
Q Consensus 261 ~~~~G~~l~~~L~~~a~~~r~~~~~~~e~~a~~~~~k~~~ 300 (329)
.-+.-|++++.|...|+..++.-..+.+.-.+-.++-+.+
T Consensus 333 ~GEesG~L~~mL~~~A~~~~~~~~~~i~~l~~llEP~l~i 372 (397)
T COG1459 333 VGEESGKLDEMLEKVADFYEEEVERKIDKLTSLLEPLLII 372 (397)
T ss_pred HHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 8343166899999999999999999999999999899999
No 10
>COG1955 FlaJ Archaeal flagella assembly protein J [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=98.87 E-value=6e-06 Score=57.48 Aligned_cols=136 Identities=15% Similarity=0.058 Sum_probs=116.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHH-CCCCHHHHHHHH
Q ss_conf 9999999999999999999999999999999749968999999998407787789999999999996-599989999999
Q gi|254780721|r 164 PSVWISNLVQKRQSSIKRAWPDALDLLLICVESGISIDQALRRVAEDIGGQSVPLSEEMLLTIAELS-FLPNRQVAFENF 242 (329)
Q Consensus 164 P~~~l~~~~~~r~~~i~~~lP~~ld~l~~~~~aG~~l~~Al~~va~e~~~~~~~l~~e~~~~~~~~~-~G~~~~~Al~~~ 242 (329)
-..+.+....++++.+++++|.++..|+....++.+.++-+..+++ ++.++|.++||+++..=.+ +|.+..+|.+=.
T Consensus 35 ~~l~~~~~~d~k~~~in~~l~f~lt~m~~LsTs~i~r~~If~~ls~--~~eyg~~~~~f~kI~~L~~~Wgy~~a~Ac~~i 112 (527)
T COG1955 35 AVLYPIISRDSKKNRINSDLLFFLTYMASLSTSDIPRDDIFRILSR--KEEYGPLRKEFRKIYNLVDKWGYSLAEACRFI 112 (527)
T ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHCCCCCHHHHHHHHCC--HHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHH
T ss_conf 9999986526777521312699999999996069988999999654--15212489999999999998684568999999
Q ss_pred HHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 98639958999999999999719958999999999999999999999998433369999
Q gi|254780721|r 243 YNRTQMDCVRNATQALIQSDRYGTSIGDSLRVLVSETRSERLMEAEKKAASLGPKLTVP 301 (329)
Q Consensus 243 a~r~~~~~~~~~~~~l~~~~~~G~~l~~~L~~~a~~~r~~~~~~~e~~a~~~~~k~~~~ 301 (329)
|+|++++.+++|-+=+.++...|.++.|.|+.--+..-+.+...-|..-.++..-..++
T Consensus 113 A~k~~~~~l~dfL~Rla~ai~sGe~~~eFl~~E~~~~~~~y~~~Yer~LeSl~~~~diY 171 (527)
T COG1955 113 AKKTPSEILADFLDRLAYALDSGEDLKEFLEREQDTTMDEYETEYERALESLDVWKDIY 171 (527)
T ss_pred HHHCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 86096799999999998774258737999999999999999999999998899999999
No 11
>COG1459 PulF Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=98.85 E-value=1.1e-05 Score=55.73 Aligned_cols=55 Identities=20% Similarity=0.125 Sum_probs=43.6
Q ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHH
Q ss_conf 9999999999996599989999999986399589999999999997199589999999
Q gi|254780721|r 218 LSEEMLLTIAELSFLPNRQVAFENFYNRTQMDCVRNATQALIQSDRYGTSIGDSLRVL 275 (329)
Q Consensus 218 l~~e~~~~~~~~~~G~~~~~Al~~~a~r~~~~~~~~~~~~l~~~~~~G~~l~~~L~~~ 275 (329)
++.++..+ ++.|.|..++|+-.++..+.+..+.-..-+.+..+.|.+++.+|++.
T Consensus 266 f~rtl~~L---l~sGvpl~~aL~i~~~~~~~~~~~~~~~~~~~~v~~G~sl~~al~~~ 320 (397)
T COG1459 266 FARTLGTL---LSSGVPLLEALDIAAETVSNAFLRQALEEIIQEVREGGSLSQALEKT 320 (397)
T ss_pred HHHHHHHH---HHCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHHHHHHHC
T ss_conf 99999999---97898399999998762374999999999999998575699998736
No 12
>TIGR02120 GspF general secretion pathway protein F; InterPro: IPR011850 This membrane protein is a component of the terminal branch complex of the general secretion pathway (GSP), also known as the "Type II" secretion pathway. The GSP transports proteins (generally virulence-associated cell wall hydrolases) across the outer membrase of the bacterial cell. Transport across the inner membrane is often, but not exclusively handled by the Sec system. GspF nearly always clusters with other GSP subunits. However, some genes from Xylella and Xanthomonas strains are excluded from this entry due to excessive divergence.; GO: 0008565 protein transporter activity, 0015628 protein secretion by the type II secretion system, 0015627 type II protein secretion system complex.
Probab=98.82 E-value=3.5e-07 Score=65.62 Aligned_cols=134 Identities=16% Similarity=0.067 Sum_probs=103.1
Q ss_pred HHHHHHHHHHH-HHHHHHHHHHHHH------------HHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHH
Q ss_conf 99999999999-9999999999999------------9999999999749968999999998407787789999999999
Q gi|254780721|r 161 FCAPSVWISNL-VQKRQSSIKRAWP------------DALDLLLICVESGISIDQALRRVAEDIGGQSVPLSEEMLLTIA 227 (329)
Q Consensus 161 ~~~P~~~l~~~-~~~r~~~i~~~lP------------~~ld~l~~~~~aG~~l~~Al~~va~e~~~~~~~l~~e~~~~~~ 227 (329)
.++-.+++++- .|.|.+++---+| -|-..++....||+|+=+|++.+.+-+.+ ..++..+.....
T Consensus 246 ~~l~~~~Lr~p~~r~~~dr~LLr~PviG~L~r~l~~ARfArTL~iL~~SGVPlL~AL~~a~~~~~N--~~lr~~v~~a~~ 323 (414)
T TIGR02120 246 VVLFRRLLRDPAFRLRFDRRLLRLPVIGRLVRGLNTARFARTLSILLSSGVPLLRALQIARETLTN--RALRAAVEDAAA 323 (414)
T ss_pred HHHHHHHHCCCCCCHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHH
T ss_conf 999999843898750454878320245689999999999999999986018999999999999875--999999999999
Q ss_pred HHHCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 996599989999999986399589999999999997199589999999999999999999999984333699999
Q gi|254780721|r 228 ELSFLPNRQVAFENFYNRTQMDCVRNATQALIQSDRYGTSIGDSLRVLVSETRSERLMEAEKKAASLGPKLTVPM 302 (329)
Q Consensus 228 ~~~~G~~~~~Al~~~a~r~~~~~~~~~~~~l~~~~~~G~~l~~~L~~~a~~~r~~~~~~~e~~a~~~~~k~~~~~ 302 (329)
.++-|.+...||+ ..+.+=-+..-|+.+-|.+|++.+.|..-||.....-..+...--.-+|+-+++.|
T Consensus 324 ~VREG~sLs~AL~------~~~~FPP~l~hmiasGE~sG~L~~ML~RAAd~~ere~e~~~~~~~~LLEPlLIv~M 392 (414)
T TIGR02120 324 RVREGGSLSRALR------ASKLFPPLLVHMIASGEKSGQLETMLERAADNQEREFERRVATLLALLEPLLIVVM 392 (414)
T ss_pred HHHCCHHHHHHHH------CCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 7225547898862------15664379989987724789807789998638899999999999998879999999
No 13
>TIGR02120 GspF general secretion pathway protein F; InterPro: IPR011850 This membrane protein is a component of the terminal branch complex of the general secretion pathway (GSP), also known as the "Type II" secretion pathway. The GSP transports proteins (generally virulence-associated cell wall hydrolases) across the outer membrase of the bacterial cell. Transport across the inner membrane is often, but not exclusively handled by the Sec system. GspF nearly always clusters with other GSP subunits. However, some genes from Xylella and Xanthomonas strains are excluded from this entry due to excessive divergence.; GO: 0008565 protein transporter activity, 0015628 protein secretion by the type II secretion system, 0015627 type II protein secretion system complex.
Probab=98.47 E-value=0.00014 Score=48.45 Aligned_cols=148 Identities=12% Similarity=0.126 Sum_probs=115.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCHHHHH
Q ss_conf 99999999999999999999974996899999999840778778999999999999659998999999998639958999
Q gi|254780721|r 174 KRQSSIKRAWPDALDLLLICVESGISIDQALRRVAEDIGGQSVPLSEEMLLTIAELSFLPNRQVAFENFYNRTQMDCVRN 253 (329)
Q Consensus 174 ~r~~~i~~~lP~~ld~l~~~~~aG~~l~~Al~~va~e~~~~~~~l~~e~~~~~~~~~~G~~~~~Al~~~a~r~~~~~~~~ 253 (329)
.+++-=..++.-+-..++..+.||.|+++|+..+.+.. ..+.+++-+..+=.++.-|.+..+||.+..+-++ .
T Consensus 69 ~~~~ls~~~la~~TRQLATLl~AglPLeeaL~~l~~Q~--e~~~~~~~l~~iR~~v~eG~~La~AL~~~P~~F~-----~ 141 (414)
T TIGR02120 69 LRRRLSRAELALFTRQLATLLGAGLPLEEALAALLEQA--EKPRLKSVLAAIRSRVLEGKSLADALAQEPRLFP-----P 141 (414)
T ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHHHCCCCHHHHHHCCCCCCC-----H
T ss_conf 16898999999999999999985340999999999625--9578999999999998618116899850889988-----7
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 9999999997199589999999999999999999999984333699999999999999999977999999997349
Q gi|254780721|r 254 ATQALIQSDRYGTSIGDSLRVLVSETRSERLMEAEKKAASLGPKLTVPMIIFFLPVLILVIIGPAILSIIDTMKDH 329 (329)
Q Consensus 254 ~~~~l~~~~~~G~~l~~~L~~~a~~~r~~~~~~~e~~a~~~~~k~~~~~il~~~p~~~~~~~~P~~~~~~~~~~~~ 329 (329)
+=.+|..|-|.+|.+..+|+.+||.++++++.+.|....-.=+=+.. .+-|..-.+.+.+..|-++++++.+++.
T Consensus 142 lYralV~AGE~SG~L~~VL~RLADylE~rq~lr~Ki~~AliYPa~l~-vVa~~vv~~Ll~~VVPkvV~~F~~~~q~ 216 (414)
T TIGR02120 142 LYRALVAAGEASGALDAVLERLADYLEERQALRSKITTALIYPAVLT-VVAIGVVIFLLAYVVPKVVEQFAHMKQT 216 (414)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHCCCEECHHHCCCCC
T ss_conf 88999996124788246899998899999999999999876589999-9999999999942044403102319978
No 14
>pfam09548 Spore_III_AB Stage III sporulation protein AB (spore_III_AB). SpoIIIAB represents the stage III sporulation protein AB, which is encoded in a spore formation operon: spoIIIAABCDEFGH that is under sigma G regulation. A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species.
Probab=96.70 E-value=0.046 Score=31.78 Aligned_cols=106 Identities=23% Similarity=0.250 Sum_probs=65.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHH
Q ss_conf 99999999999999999999999999999999999999999999-74996899999999840778778999999999999
Q gi|254780721|r 151 GAVILIGYVGFCAPSVWISNLVQKRQSSIKRAWPDALDLLLICV-ESGISIDQALRRVAEDIGGQSVPLSEEMLLTIAEL 229 (329)
Q Consensus 151 ~~~~~~~~~g~~~P~~~l~~~~~~r~~~i~~~lP~~ld~l~~~~-~aG~~l~~Al~~va~e~~~~~~~l~~e~~~~~~~~ 229 (329)
++...+..+||. ...+.++|.++++ ++-.++..+..-+ -+..|+++|+..+++..+ +|++.-|..+...+
T Consensus 7 LIi~s~~~~G~~-----~a~~~~~R~~~L~-~l~~~l~~L~~EI~Y~~tpL~eal~~i~~~~~---~~~~~~f~~~a~~L 77 (170)
T pfam09548 7 LIILSSTLIGFL-----YAKRYKERPKQLR-ELINALQSLEAEISYGATPLPEALERIASKSE---KPVSELFERAAERL 77 (170)
T ss_pred HHHHHHHHHHHH-----HHHHHHHHHHHHH-HHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCC---CHHHHHHHHHHHHH
T ss_conf 999987799999-----9999999999999-99999999999998818989999999987557---43999999999988
Q ss_pred H--CCCCHHHHHHHHHHH----C-----CCHHHHHHHHHHHHHHHCC
Q ss_conf 6--599989999999986----3-----9958999999999999719
Q gi|254780721|r 230 S--FLPNRQVAFENFYNR----T-----QMDCVRNATQALIQSDRYG 265 (329)
Q Consensus 230 ~--~G~~~~~Al~~~a~r----~-----~~~~~~~~~~~l~~~~~~G 265 (329)
. .|.+..+++++-.+. + +...+..|...|-.+++.+
T Consensus 78 ~~~~g~s~~e~w~~~~~~~~~~~~L~~~d~eiL~~lg~~LG~~D~~~ 124 (170)
T pfam09548 78 EKNEGITAYEAWEEALEELWKETALKKEDIEILLNLGKSLGQSDREG 124 (170)
T ss_pred HCCCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCHHH
T ss_conf 61789989999999999876537999999999999999877567899
No 15
>PRK08307 stage III sporulation protein SpoAB; Provisional
Probab=95.67 E-value=0.15 Score=28.31 Aligned_cols=106 Identities=21% Similarity=0.215 Sum_probs=64.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHH
Q ss_conf 99999999999999999999999999999999999999999999-74996899999999840778778999999999999
Q gi|254780721|r 151 GAVILIGYVGFCAPSVWISNLVQKRQSSIKRAWPDALDLLLICV-ESGISIDQALRRVAEDIGGQSVPLSEEMLLTIAEL 229 (329)
Q Consensus 151 ~~~~~~~~~g~~~P~~~l~~~~~~r~~~i~~~lP~~ld~l~~~~-~aG~~l~~Al~~va~e~~~~~~~l~~e~~~~~~~~ 229 (329)
++...+..+||. ...+.++|.+++ +++-.++..+..-+ -+..|+++|+..+++..+ +|++.-|..+...+
T Consensus 9 LIi~s~~~~G~~-----~a~~~~~R~~qL-~~l~~~l~~L~~EI~Y~~tpL~eal~~i~~~~~---~~~~~~f~~~a~~L 79 (172)
T PRK08307 9 LIVAASTWIGFL-----YAERYKERPRQL-RELKAALQSLEAEIMYGHTPLPEALENIAKKSP---KPISTLFQRFAERL 79 (172)
T ss_pred HHHHHHHHHHHH-----HHHHHHHHHHHH-HHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCC---CHHHHHHHHHHHHH
T ss_conf 999998899999-----999999999999-999999999999998808989999999987557---33999999999998
Q ss_pred HC--CCCHHHHHHHHHHHC----C-----CHHHHHHHHHHHHHHHCC
Q ss_conf 65--999899999999863----9-----958999999999999719
Q gi|254780721|r 230 SF--LPNRQVAFENFYNRT----Q-----MDCVRNATQALIQSDRYG 265 (329)
Q Consensus 230 ~~--G~~~~~Al~~~a~r~----~-----~~~~~~~~~~l~~~~~~G 265 (329)
.. |.+..+++++-.+.. . ...+..|...|-.+++.+
T Consensus 80 ~~~~g~s~~e~W~~~~~~~~~~~~L~~~d~eiL~~lG~~LG~~D~e~ 126 (172)
T PRK08307 80 EKGEVETVYEAWEKSLKENWKNTALKKEDYEILLQFGKTLGQSDREG 126 (172)
T ss_pred HHCCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCHHH
T ss_conf 73789989999999999875447999999999999999877578999
No 16
>TIGR02833 spore_III_AB stage III sporulation protein AB; InterPro: IPR014198 This entry represents the stage III sporulation protein AB, which is encoded in a spore formation operon: spoIIIAABCDEFGH that is under sigma G regulation . A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species..
Probab=93.83 E-value=0.45 Score=25.24 Aligned_cols=147 Identities=22% Similarity=0.256 Sum_probs=87.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHCCCCCHHHHHHHHHHHHH
Q ss_conf 9999999999999999999999999999999999999999999997499-689999999984077877899999999999
Q gi|254780721|r 150 VGAVILIGYVGFCAPSVWISNLVQKRQSSIKRAWPDALDLLLICVESGI-SIDQALRRVAEDIGGQSVPLSEEMLLTIAE 228 (329)
Q Consensus 150 ~~~~~~~~~~g~~~P~~~l~~~~~~r~~~i~~~lP~~ld~l~~~~~aG~-~l~~Al~~va~e~~~~~~~l~~e~~~~~~~ 228 (329)
++.+.....+||.+ ..+-++|.+++ +++-.++..+..-+.-|+ |+++|+..+|+.. .+|++.-|..+...
T Consensus 6 ~Liv~~~T~iGF~~-----a~r~~~R~~~L-r~l~~AL~~L~~EI~Y~~TPL~ea~~~iA~~~---~~pv~~lF~~~s~~ 76 (170)
T TIGR02833 6 ILIVLSSTWIGFEY-----ANRFKERPRQL-RQLKNALQSLEAEIVYGHTPLPEAFKKIAKKS---PKPVNKLFESASER 76 (170)
T ss_pred HHHHHHHHHHHHHH-----HHHHHHHHHHH-HHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHC---CCHHHHHHHHHHHH
T ss_conf 99999767999999-----98898879999-99999999999730178764689999999741---52489999999987
Q ss_pred HHCC--CCHHHHHHHHHHH---------CCCHHHHHHHHHHHHHHHCCC--CHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 9659--9989999999986---------399589999999999997199--58999999999999999999999998433
Q gi|254780721|r 229 LSFL--PNRQVAFENFYNR---------TQMDCVRNATQALIQSDRYGT--SIGDSLRVLVSETRSERLMEAEKKAASLG 295 (329)
Q Consensus 229 ~~~G--~~~~~Al~~~a~r---------~~~~~~~~~~~~l~~~~~~G~--~l~~~L~~~a~~~r~~~~~~~e~~a~~~~ 295 (329)
++.+ .+..+||+.-=+. -+-+-+..|+..|-++++.|- .+.=+++.+ ++....+|.. .+--
T Consensus 77 L~~~~~~~v~~Aw~~~l~e~~~~~~L~~~e~EILl~fg~~LG~~D~~~Q~K~~~Lt~~~L-----~~~l~eA~~~-~~kn 150 (170)
T TIGR02833 77 LKEGEGETVYEAWKKALNEVWKQTALKKSEKEILLQFGKTLGESDREGQQKHINLTLEHL-----ERQLAEAEDE-QKKN 150 (170)
T ss_pred HCCCCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHH-----HHHHHHHHHH-HHHC
T ss_conf 226899998889999998768852337236899999878725225788999999999999-----9989999999-9855
Q ss_pred HHHHHHHHHHHHHHHHHH
Q ss_conf 369999999999999999
Q gi|254780721|r 296 PKLTVPMIIFFLPVLILV 313 (329)
Q Consensus 296 ~k~~~~~il~~~p~~~~~ 313 (329)
.||.=+ ++++.-++++
T Consensus 151 ~Km~~~--LGvl~Gl~iv 166 (170)
T TIGR02833 151 EKMYRY--LGVLVGLLIV 166 (170)
T ss_pred HHHHHH--HHHHHHHHHH
T ss_conf 468887--9999999999
No 17
>PRK03072 heat shock protein HtpX; Provisional
Probab=82.41 E-value=3.1 Score=19.70 Aligned_cols=12 Identities=25% Similarity=0.661 Sum_probs=6.3
Q ss_pred CCHHHHHHHHHH
Q ss_conf 968999999998
Q gi|254780721|r 198 ISIDQALRRVAE 209 (329)
Q Consensus 198 ~~l~~Al~~va~ 209 (329)
..+.+|++++..
T Consensus 220 ~~LasAL~Kl~~ 231 (289)
T PRK03072 220 LALASALRKISG 231 (289)
T ss_pred HHHHHHHHHHHH
T ss_conf 999999999985
No 18
>PRK02391 heat shock protein HtpX; Provisional
Probab=77.51 E-value=4.4 Score=18.67 Aligned_cols=11 Identities=18% Similarity=0.459 Sum_probs=5.1
Q ss_pred CCHHHHHHHHH
Q ss_conf 96899999999
Q gi|254780721|r 198 ISIDQALRRVA 208 (329)
Q Consensus 198 ~~l~~Al~~va 208 (329)
..+.+|++++.
T Consensus 229 ~~LasAL~Ki~ 239 (297)
T PRK02391 229 SALASALTKIS 239 (297)
T ss_pred HHHHHHHHHHH
T ss_conf 99999999985
No 19
>PRK05457 heat shock protein HtpX; Provisional
Probab=72.57 E-value=5.8 Score=17.86 Aligned_cols=12 Identities=33% Similarity=0.138 Sum_probs=5.0
Q ss_pred HHCCCCCHHHHH
Q ss_conf 960766089999
Q gi|254780721|r 34 PSLGSGELEKRM 45 (329)
Q Consensus 34 ~~~~~~~~~~R~ 45 (329)
.+|.++++..+.
T Consensus 51 sy~~Sd~i~l~~ 62 (289)
T PRK05457 51 SLLMSKWMAKRS 62 (289)
T ss_pred HHHHHHHHHHHH
T ss_conf 999239999997
No 20
>PRK01345 heat shock protein HtpX; Provisional
Probab=71.65 E-value=6.1 Score=17.72 Aligned_cols=11 Identities=18% Similarity=0.335 Sum_probs=4.9
Q ss_pred CHHHHHHHHHH
Q ss_conf 68999999998
Q gi|254780721|r 199 SIDQALRRVAE 209 (329)
Q Consensus 199 ~l~~Al~~va~ 209 (329)
.+.+|++++..
T Consensus 218 aLasAL~KIe~ 228 (314)
T PRK01345 218 WLASALGKIER 228 (314)
T ss_pred HHHHHHHHHHH
T ss_conf 99999999986
No 21
>PRK03001 heat shock protein HtpX; Provisional
Probab=69.86 E-value=6.7 Score=17.46 Aligned_cols=13 Identities=15% Similarity=0.273 Sum_probs=7.7
Q ss_pred CCHHHHHHHHHHH
Q ss_conf 9689999999984
Q gi|254780721|r 198 ISIDQALRRVAED 210 (329)
Q Consensus 198 ~~l~~Al~~va~e 210 (329)
..+.+|+++..+.
T Consensus 216 ~~LasAL~Kl~~~ 228 (284)
T PRK03001 216 QALASALDKIHRY 228 (284)
T ss_pred HHHHHHHHHHHHH
T ss_conf 9999999999987
No 22
>PRK03982 heat shock protein HtpX; Provisional
Probab=67.82 E-value=7.4 Score=17.19 Aligned_cols=13 Identities=23% Similarity=0.521 Sum_probs=6.9
Q ss_pred CCHHHHHHHHHHH
Q ss_conf 9689999999984
Q gi|254780721|r 198 ISIDQALRRVAED 210 (329)
Q Consensus 198 ~~l~~Al~~va~e 210 (329)
..+.+|+.+..+.
T Consensus 221 ~~LasAL~KL~~~ 233 (288)
T PRK03982 221 IALANALTKLEKG 233 (288)
T ss_pred HHHHHHHHHHHHH
T ss_conf 9999999999841
No 23
>pfam12169 DNA_pol3_gamma3 DNA polymerase III subunits gamma and tau domain III. This domain family is found in bacteria, and is approximately 110 amino acids in length. The family is found in association with pfam00004. Domains I-III are shared between the tau and the gamma subunits, while most of the DnaB-binding Domain IV and all of the alpha-interacting Domain V are unique to tau.
Probab=65.90 E-value=8 Score=16.95 Aligned_cols=83 Identities=12% Similarity=0.012 Sum_probs=52.1
Q ss_pred HHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCHHHHHHHHHH
Q ss_conf 99999999999999997499689999999984077877899999999999965999899999999863995899999999
Q gi|254780721|r 179 IKRAWPDALDLLLICVESGISIDQALRRVAEDIGGQSVPLSEEMLLTIAELSFLPNRQVAFENFYNRTQMDCVRNATQAL 258 (329)
Q Consensus 179 i~~~lP~~ld~l~~~~~aG~~l~~Al~~va~e~~~~~~~l~~e~~~~~~~~~~G~~~~~Al~~~a~r~~~~~~~~~~~~l 258 (329)
++.+.+.+++.+....+.|..+.+-+....+.+... -+.............+.+-.+.+++++++++.+.+..+...+
T Consensus 26 ~~~d~~~~l~~l~~l~~~G~d~~~~l~~L~~~~r~l--~~~k~~~~~~~~~~~~~~~~~~l~~~a~~~~~~~L~~~~qil 103 (143)
T pfam12169 26 LEGDAAAALAEFRDQYAAGADPVVVLRDLLELLHLL--TRLKIAPDAADDLSLPEEERERIAALAKKLSPEVLSRLWQML 103 (143)
T ss_pred HCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHH--HHHHHCCCCCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 828999999999999987989999999999999999--999867630001225778899999998606799999999999
Q ss_pred HHHHH
Q ss_conf 99997
Q gi|254780721|r 259 IQSDR 263 (329)
Q Consensus 259 ~~~~~ 263 (329)
.++.+
T Consensus 104 ~~~~~ 108 (143)
T pfam12169 104 LKGIE 108 (143)
T ss_pred HHHHH
T ss_conf 99999
No 24
>PRK08475 F0F1 ATP synthase subunit B; Validated
Probab=62.34 E-value=9.3 Score=16.52 Aligned_cols=52 Identities=13% Similarity=-0.024 Sum_probs=33.3
Q ss_pred HHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 7320012158999999999999999999999999999999999999999999
Q gi|254780721|r 138 YDKLLEYPFQLRVGAVILIGYVGFCAPSVWISNLVQKRQSSIKRAWPDALDL 189 (329)
Q Consensus 138 ~~~~~~~~~~~~~~~~~~~~~~g~~~P~~~l~~~~~~r~~~i~~~lP~~ld~ 189 (329)
.+......+.+..+-.++..++.||+-.-.+...-+.|++.|...+-++=..
T Consensus 19 ~~~~~~~Dii~r~iNf~I~~gIL~yf~~kpi~~~l~~R~~~I~~~L~eae~~ 70 (170)
T PRK08475 19 DIGSGETDIIERTINFLIFVGILWYFAAKPIKNFYKSRINSISKRLEEIQAK 70 (170)
T ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 5788864059999999999999999928789999998999999999999999
No 25
>TIGR02606 antidote_CC2985 putative addiction module antidote protein, CC2985 family; InterPro: IPR005360 Proteins in this entry are almost always found adjacent to a plasmid stabilisation protein (IPR007712 from INTERPRO), which is the killing partner of an addiction module for plasmid stabilisation. Proteins in this entry, therefore, are putative addiction module antidote proteins. Some are encoded on plasmids or in prophage regions, but others appear to be chromosomal. A genome may contain several identical copies, for example four are found in Magnetococcus sp. MC-1. This entry is named after one member, CC2985 of Caulobacter crescentus CB15..
Probab=62.11 E-value=9.4 Score=16.49 Aligned_cols=46 Identities=17% Similarity=0.218 Sum_probs=34.1
Q ss_pred CHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH-HHHHHHHHH
Q ss_conf 95899999999999971995899999999999999999-999999843
Q gi|254780721|r 248 MDCVRNATQALIQSDRYGTSIGDSLRVLVSETRSERLM-EAEKKAASL 294 (329)
Q Consensus 248 ~~~~~~~~~~l~~~~~~G~~l~~~L~~~a~~~r~~~~~-~~e~~a~~~ 294 (329)
.|.++.|+...+++-|+| |.++++|.--+-++++... +.+..|.+.
T Consensus 7 g~~l~~Fi~~qv~sGRYg-saSEVvR~aLRlLee~E~r~~~k~~aLr~ 53 (77)
T TIGR02606 7 GEHLESFIDSQVQSGRYG-SASEVVRAALRLLEERETRARLKLEALRA 53 (77)
T ss_pred CHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 878899999987607999-86369999998619999899999999999
No 26
>KOG3533 consensus
Probab=56.82 E-value=12 Score=15.91 Aligned_cols=72 Identities=26% Similarity=0.346 Sum_probs=44.9
Q ss_pred HHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 98639958999999999999719958999999999999999999999998433369999999999999999997799999
Q gi|254780721|r 243 YNRTQMDCVRNATQALIQSDRYGTSIGDSLRVLVSETRSERLMEAEKKAASLGPKLTVPMIIFFLPVLILVIIGPAILSI 322 (329)
Q Consensus 243 a~r~~~~~~~~~~~~l~~~~~~G~~l~~~L~~~a~~~r~~~~~~~e~~a~~~~~k~~~~~il~~~p~~~~~~~~P~~~~~ 322 (329)
.+|.-..-+--.++.+.|..|.||.+.++|+.-|.+-- . -..| .++=.+|++ .+++++++-.|=-|
T Consensus 2500 kersCdtLlMCIvt~lnqGLRnGGGiGDvLR~Psk~E~---l---------F~aR-V~YDllFff-ivIiIVLNLIFGVI 2565 (2706)
T KOG3533 2500 KERSCETLLMCIVTTLNQGLRNGGGIGDVLRNPSKWED---L---------FIAR-VAYDLLFFF-IVIIIVLNLIFGVI 2565 (2706)
T ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCHHHHHCCCCCCCC---H---------HHHH-HHHHHHHHH-HHHHHHHHHHHHHH
T ss_conf 23013589999999876533168870466508986431---2---------5999-999999999-99999998878855
Q ss_pred HHHHHC
Q ss_conf 999734
Q gi|254780721|r 323 IDTMKD 328 (329)
Q Consensus 323 ~~~~~~ 328 (329)
.++|.|
T Consensus 2566 IDTFaD 2571 (2706)
T KOG3533 2566 IDTFAD 2571 (2706)
T ss_pred HHHHHH
T ss_conf 564777
No 27
>pfam04799 Fzo_mitofusin fzo-like conserved region. Family of putative transmembrane GTPase. The fzo protein is a mediator of mitochondrial fusion. This conserved region is also found in the human mitofusin protein.
Probab=48.38 E-value=16 Score=15.04 Aligned_cols=72 Identities=13% Similarity=0.206 Sum_probs=36.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHC-CCCH
Q ss_conf 9999999999999999999999999----9999999997499689999999984077877899999999999965-9998
Q gi|254780721|r 161 FCAPSVWISNLVQKRQSSIKRAWPD----ALDLLLICVESGISIDQALRRVAEDIGGQSVPLSEEMLLTIAELSF-LPNR 235 (329)
Q Consensus 161 ~~~P~~~l~~~~~~r~~~i~~~lP~----~ld~l~~~~~aG~~l~~Al~~va~e~~~~~~~l~~e~~~~~~~~~~-G~~~ 235 (329)
|.+-++-...++|. +.+.+||-+ =+.+++....++-+ +.|-+| ++..|.+...+.+. -.++
T Consensus 60 YlyERltWT~~AKE--r~fK~QfV~~At~KL~liVs~TS~ncs-----hQVqqE-------Ls~tfarLc~qVd~~~~~l 125 (171)
T pfam04799 60 YLYERLTWTTKAKE--RAFKRQFVDYATEKLQLIVSLTSSNCS-----HQVQQE-------LASTFARLCQQVDVTSKDL 125 (171)
T ss_pred HHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHCCCHH-----HHHHHH-------HHHHHHHHHHHHHHHHHHH
T ss_conf 99999752107788--899999999999988888877605806-----899999-------9999999999986899999
Q ss_pred HHHHHHHHHHC
Q ss_conf 99999999863
Q gi|254780721|r 236 QVAFENFYNRT 246 (329)
Q Consensus 236 ~~Al~~~a~r~ 246 (329)
++-++++..++
T Consensus 126 e~ei~~L~~ei 136 (171)
T pfam04799 126 EEEIAELTKEI 136 (171)
T ss_pred HHHHHHHHHHH
T ss_conf 99999999999
No 28
>pfam12046 DUF3529 Protein of unknown function (DUF3529). This family of proteins is functionally uncharacterized. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 176 to 190 amino acids in length.
Probab=47.38 E-value=12 Score=15.77 Aligned_cols=63 Identities=16% Similarity=0.097 Sum_probs=25.2
Q ss_pred CCCHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 6758999999--999999999999999999732001215899999999999999999999999999999999999
Q gi|254780721|r 110 EYSLNILLVV--RLVVPIIFLILGIIWIFGYDKLLEYPFQLRVGAVILIGYVGFCAPSVWISNLVQKRQSSIKRA 182 (329)
Q Consensus 110 ~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~P~~~l~~~~~~r~~~i~~~ 182 (329)
.-.+..+.+. .+..+++.+-+++++.......+ ...+.+.+++.+.|.+ +.+...|.++++-.
T Consensus 75 ~V~~S~~lAifLt~l~~~Gl~clgLVl~~l~P~~g----~~~~~L~lLsPlAG~~------Yw~kA~R~E~v~lk 139 (173)
T pfam12046 75 IVAPSRFLAVFLTLLAAVGLACLGLVLSQLVPQLG----WWPLLLVLLSPLAGLY------YWQRASRPEQVELK 139 (173)
T ss_pred EECCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC----HHHHHHHHHHHHHHHH------HHHCCCCCCEEEEE
T ss_conf 85475859999999999999999999999768855----0999999973224442------33327875018999
No 29
>pfam00745 GlutR_dimer Glutamyl-tRNAGlu reductase, dimerization domain.
Probab=44.10 E-value=18 Score=14.61 Aligned_cols=91 Identities=21% Similarity=0.219 Sum_probs=63.9
Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCHHHHHHHH
Q ss_conf 99999999999999999974996899999999840778778999999999999659998999999998639958999999
Q gi|254780721|r 177 SSIKRAWPDALDLLLICVESGISIDQALRRVAEDIGGQSVPLSEEMLLTIAELSFLPNRQVAFENFYNRTQMDCVRNATQ 256 (329)
Q Consensus 177 ~~i~~~lP~~ld~l~~~~~aG~~l~~Al~~va~e~~~~~~~l~~e~~~~~~~~~~G~~~~~Al~~~a~r~~~~~~~~~~~ 256 (329)
.-++.+.-.|..-+.. ..-.|+-.+++.-++++ -..|+.+..+.+..|.+.+++++.+..++-..-++.-+.
T Consensus 5 ~II~ee~~~f~~w~~~--~~~~p~I~~lr~~~e~i------~~~El~ka~~~l~~~~~~~~~i~~~~~~l~nKllh~P~~ 76 (101)
T pfam00745 5 AIIEEEVEEFLEWLKS--LAVVPTIRALREKAEEI------REEELERALKKLDLGEDPEEVLEKLARSLTNKLLHAPTV 76 (101)
T ss_pred HHHHHHHHHHHHHHHH--CCCHHHHHHHHHHHHHH------HHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 9999999999999987--64538999999999999------999999998743798528999999999999998788999
Q ss_pred HHHHHHHCCCCHHHHHHHHH
Q ss_conf 99999971995899999999
Q gi|254780721|r 257 ALIQSDRYGTSIGDSLRVLV 276 (329)
Q Consensus 257 ~l~~~~~~G~~l~~~L~~~a 276 (329)
.+..+...|.+ .+.++.+.
T Consensus 77 ~Lk~~a~~~~~-~~~i~~~~ 95 (101)
T pfam00745 77 ALREAAEEGDG-DELLDALR 95 (101)
T ss_pred HHHHHHHCCCH-HHHHHHHH
T ss_conf 99998868879-99999999
No 30
>pfam06697 DUF1191 Protein of unknown function (DUF1191). This family contains hypothetical plant proteins of unknown function.
Probab=42.25 E-value=19 Score=14.43 Aligned_cols=17 Identities=18% Similarity=0.278 Sum_probs=10.6
Q ss_pred HHHHHHHHHHHHHHHHH
Q ss_conf 99999999999999999
Q gi|254780721|r 166 VWISNLVQKRQSSIKRA 182 (329)
Q Consensus 166 ~~l~~~~~~r~~~i~~~ 182 (329)
...+.++++|++++|++
T Consensus 232 ~~~k~~rkkk~~eMEr~ 248 (275)
T pfam06697 232 RLVKYKRRKRREEMERR 248 (275)
T ss_pred HHHHHHHHHHHHHHHHH
T ss_conf 66657789899999987
No 31
>TIGR00814 stp serine transporter; InterPro: IPR004694 The Hydroxy/Aromatic Amino Acid Permease (HAAAP) family includes well characterised aromatic amino acid:H+ symport permeases and hydroxy amino acid permeases. This group is specific for hydroxy amino acid transporters and includes the serine permease, SdaC and threonine permease, TdcC, of Escherichia coli.; GO: 0005215 transporter activity, 0006810 transport, 0016021 integral to membrane.
Probab=41.25 E-value=20 Score=14.33 Aligned_cols=87 Identities=20% Similarity=0.276 Sum_probs=37.5
Q ss_pred HHHHHHHHHCC---------CHHHHHHHHHHHHHHH----CCC--CHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHH
Q ss_conf 99999998639---------9589999999999997----199--5899999999999999999999999-843336999
Q gi|254780721|r 237 VAFENFYNRTQ---------MDCVRNATQALIQSDR----YGT--SIGDSLRVLVSETRSERLMEAEKKA-ASLGPKLTV 300 (329)
Q Consensus 237 ~Al~~~a~r~~---------~~~~~~~~~~l~~~~~----~G~--~l~~~L~~~a~~~r~~~~~~~e~~a-~~~~~k~~~ 300 (329)
.+|.-+|...+ .+-++.....+..-.= .|. -..|.++.+--..-. ++++.|++. ++++ + +
T Consensus 276 siLS~LAn~~~g~~Gtktt~~~~i~~~~~i~A~~Ai~~SFfG~YlG~~EG~~G~v~~~l~-lk~~~~k~~~~~L~-~--~ 351 (419)
T TIGR00814 276 SILSYLANHFNGDGGTKTTAAAWISYAGPIVAIVAISKSFFGHYLGAREGLNGIVLKSLR-LKMKGKKINIRKLN-R--A 351 (419)
T ss_pred HHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HCCCCCCCCHHHHH-H--H
T ss_conf 689999706788887410366799999999999999987676778899878889998731-10353002146788-9--9
Q ss_pred HHHHHH-HHHHHHHHHHHHHHHHHHHHH
Q ss_conf 999999-999999999779999999973
Q gi|254780721|r 301 PMIIFF-LPVLILVIIGPAILSIIDTMK 327 (329)
Q Consensus 301 ~~il~~-~p~~~~~~~~P~~~~~~~~~~ 327 (329)
.+++.+ +-...+..++|.++++.++++
T Consensus 352 ~~iF~~sl~~w~v~~~Np~iL~~i~~lG 379 (419)
T TIGR00814 352 IAIFLVSLTTWIVAYINPSILSFIEALG 379 (419)
T ss_pred HHHHHHHHHHHHHHHHCCCHHHHHHHHH
T ss_conf 9999999987733441378789987530
No 32
>pfam04228 Zn_peptidase Putative neutral zinc metallopeptidase. Members of this family have a predicted zinc binding motif characteristic of neutral zinc metallopeptidases (Prosite:PDOC00129).
Probab=41.24 E-value=20 Score=14.33 Aligned_cols=14 Identities=7% Similarity=0.031 Sum_probs=6.5
Q ss_pred HHHHHHHHCCCCCC
Q ss_conf 99999996799986
Q gi|254780721|r 97 NIVNKLRAAGFRSE 110 (329)
Q Consensus 97 ~l~~~L~~AG~~~~ 110 (329)
.....+.+.|..-+
T Consensus 102 vW~~~F~~~g~~Y~ 115 (292)
T pfam04228 102 TWTQIFADQGRTYQ 115 (292)
T ss_pred HHHHHHHHCCCCCC
T ss_conf 99999997499889
No 33
>TIGR02203 MsbA_lipidA lipid A export permease/ATP-binding protein MsbA; InterPro: IPR011917 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain . The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , . The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , . Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). This family consists of a single polypeptide chain transporter in the ATP-binding cassette (ABC) transporter family, MsbA, which exports lipid A. It may also act in multidrug resistance. Lipid A, a part of lipopolysaccharide, is found in the outer leaflet of the outer membrane of most Gram-negative bacteria. Members of this family are restricted to the Proteobacteria (although lipid A is more broadly distributed) and often are clustered with lipid A biosynthesis genes .; GO: 0005524 ATP binding, 0006869 lipid transport, 0009276 1-2nm peptidoglycan-based cell wall, 0016021 integral to membrane.
Probab=40.45 E-value=21 Score=14.25 Aligned_cols=47 Identities=21% Similarity=0.328 Sum_probs=30.5
Q ss_pred HCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 00121589999999999999999999999999999999999999999999999
Q gi|254780721|r 141 LLEYPFQLRVGAVILIGYVGFCAPSVWISNLVQKRQSSIKRAWPDALDLLLIC 193 (329)
Q Consensus 141 ~~~~~~~~~~~~~~~~~~~g~~~P~~~l~~~~~~r~~~i~~~lP~~ld~l~~~ 193 (329)
.++.+|...+++.++.+++++ +-+..+||.+++.++.-....-+...
T Consensus 178 LLy~sW~LtLi~~v~lPv~~~------~~~~~~kRlR~~~~~~Q~~~g~~~~v 224 (603)
T TIGR02203 178 LLYMSWQLTLIVVVILPVIAL------LMRRVSKRLRRISKEIQNSMGELTQV 224 (603)
T ss_pred HHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 998709999999999989999------99999998886428999989999999
No 34
>pfam12072 DUF3552 Domain of unknown function (DUF3552). This presumed domain is functionally uncharacterized. This domain is found in bacteria, archaea and eukaryotes. This domain is about 200 amino acids in length. This domain is found associated with pfam00013, pfam01966. This domain has a single completely conserved residue A that may be functionally important.
Probab=36.61 E-value=23 Score=13.86 Aligned_cols=16 Identities=13% Similarity=-0.135 Sum_probs=7.1
Q ss_pred CCCCHHHHHHHHHHHC
Q ss_conf 5999899999999863
Q gi|254780721|r 231 FLPNRQVAFENFYNRT 246 (329)
Q Consensus 231 ~G~~~~~Al~~~a~r~ 246 (329)
.|.+.++|=+.+-+.+
T Consensus 144 aglt~eEAk~~Ll~~~ 159 (201)
T pfam12072 144 SGLTAEEAKEILLEEV 159 (201)
T ss_pred HCCCHHHHHHHHHHHH
T ss_conf 6999999999999999
No 35
>PRK04897 heat shock protein HtpX; Provisional
Probab=36.25 E-value=24 Score=13.82 Aligned_cols=13 Identities=15% Similarity=0.276 Sum_probs=7.7
Q ss_pred CCCHHHHHHHHHH
Q ss_conf 9968999999998
Q gi|254780721|r 197 GISIDQALRRVAE 209 (329)
Q Consensus 197 G~~l~~Al~~va~ 209 (329)
-.++.+|++++..
T Consensus 240 p~~L~sAL~KL~~ 252 (298)
T PRK04897 240 PQGLISALEKISN 252 (298)
T ss_pred HHHHHHHHHHHHC
T ss_conf 8999999999866
No 36
>TIGR01477 RIFIN variant surface antigen, rifin family; InterPro: IPR006373 Malaria is still a major cause of mortality in many areas of the world. Plasmodium falciparum causes the most severe human form of the disease and is responsible for most fatalities. Severe cases of malaria can occur when the parasite invades and then proliferates within red blood cell erythrocytes. The parasite produces many variant antigenic proteins, encoded by multigene families, which are present on the surface of the infected erythrocyte and play important roles in virulence. A crucial survival mechanism for the malaria parasite is its ability to evade the immune response by switching these variant surface antigens. The high virulence of P. falciparum relative to other malarial parasites is in large part due to the fact that in this organism many of these surface antigens mediate the binding of infected erythrocytes to the vascular endothelium (cytoadherence) and non-infected erythrocytes (rosetting). This can lead to the accumulation of infected cells in the vasculature of a variety of organs, blocking the blood flow and reducing the oxygen supply. Clinical symptoms of severe infection can include fever, progressive anaemia, multi-organ dysfunction and coma. For more information see . This entry represents the rifin family of variant surface antigens, encoded by the rif (short for "repetetive interspersed family") genes. This is the largest variant surface antigen family in P. falciparum, with roughly 150 genes present in the genome of this parasite . The function of these proteins is not yet known, but rifins are strongly immunogenic and high levels of anti-rifin antibodies are correlated with rapid parasite clearance and asymptomatic infections . .
Probab=32.71 E-value=27 Score=13.45 Aligned_cols=20 Identities=5% Similarity=0.094 Sum_probs=8.0
Q ss_pred HHHHHHHHHHHHHCCCCHHH
Q ss_conf 99999999999971995899
Q gi|254780721|r 251 VRNATQALIQSDRYGTSIGD 270 (329)
Q Consensus 251 ~~~~~~~l~~~~~~G~~l~~ 270 (329)
...++.....+...++..++
T Consensus 309 v~~~~~~~~~~a~~a~k~a~ 328 (395)
T TIGR01477 309 VKEIVANAEKAAKAAAKAAT 328 (395)
T ss_pred HHHHHHHHHHHHHHHHHHHH
T ss_conf 98998888999999999999
No 37
>PRK12482 flagellar motor protein MotA; Provisional
Probab=30.69 E-value=29 Score=13.23 Aligned_cols=108 Identities=14% Similarity=0.078 Sum_probs=59.9
Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHCCCCH
Q ss_conf 99999999999999973200121589999999999999999999999999999999--9999999999999999749968
Q gi|254780721|r 123 VPIIFLILGIIWIFGYDKLLEYPFQLRVGAVILIGYVGFCAPSVWISNLVQKRQSS--IKRAWPDALDLLLICVESGISI 200 (329)
Q Consensus 123 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~P~~~l~~~~~~r~~~--i~~~lP~~ld~l~~~~~aG~~l 200 (329)
.++++.+++++-...............+..++++...|-++-+.++.=.++|=+.. -+..+-..+.-...+...|.++
T Consensus 175 ~GIvgaVlGlI~~M~~l~~~pa~LG~~IA~ALVgTfyGi~lAy~~~~PiA~kLk~~~~~e~~~~~~ik~~l~A~~~G~~P 254 (287)
T PRK12482 175 FGICAAVLGIIITMQSIDGSIAEIGLKVAAALVGTFLGVFICYCLMDPLSNAMEQEIKKELSLLECVRTVLVAHVAGKPT 254 (287)
T ss_pred HHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf 36999999999999834899999999999999999999999999898899999999999989999999999997279993
Q ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHHHHHH
Q ss_conf 999999998407787789999999999996
Q gi|254780721|r 201 DQALRRVAEDIGGQSVPLSEEMLLTIAELS 230 (329)
Q Consensus 201 ~~Al~~va~e~~~~~~~l~~e~~~~~~~~~ 230 (329)
.-|.+.-=+.++....|--.|++...+++.
T Consensus 255 ~~avE~gRk~i~~~~rPsf~ele~~~~~~~ 284 (287)
T PRK12482 255 LLAVDAGRKLLPLDNKPTFATLDSWINKMI 284 (287)
T ss_pred HHHHHHHHCCCCCCCCCCHHHHHHHHHHHH
T ss_conf 999999871189777989899999999864
No 38
>PRK01844 hypothetical protein; Provisional
Probab=30.62 E-value=29 Score=13.23 Aligned_cols=20 Identities=20% Similarity=0.228 Sum_probs=9.7
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999999999999999999
Q gi|254780721|r 150 VGAVILIGYVGFCAPSVWIS 169 (329)
Q Consensus 150 ~~~~~~~~~~g~~~P~~~l~ 169 (329)
++..++++++|||+-+.+..
T Consensus 11 i~~li~G~~~GffiaRk~m~ 30 (72)
T PRK01844 11 VVALVAGVALGFFIARKYMM 30 (72)
T ss_pred HHHHHHHHHHHHHHHHHHHH
T ss_conf 99999999999999999999
No 39
>PRK05289 UDP-N-acetylglucosamine acyltransferase; Provisional
Probab=29.76 E-value=30 Score=13.13 Aligned_cols=30 Identities=10% Similarity=-0.044 Sum_probs=15.6
Q ss_pred CCCCHHHHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf 599989999999986399589999999999
Q gi|254780721|r 231 FLPNRQVAFENFYNRTQMDCVRNATQALIQ 260 (329)
Q Consensus 231 ~G~~~~~Al~~~a~r~~~~~~~~~~~~l~~ 260 (329)
.+.+++++++++.+..+.|+++.|++-+..
T Consensus 222 ~~~~~~~~~~~~~~~~~~~~v~~~~~Fi~~ 251 (261)
T PRK05289 222 SGLTLEEALEELAELADSPEVKEILDFIEA 251 (261)
T ss_pred CCCCHHHHHHHHHHCCCCHHHHHHHHHHHC
T ss_conf 799899999999853799899999999961
No 40
>TIGR02029 AcsF magnesium-protoporphyrin IX monomethyl ester aerobic oxidative cyclase; InterPro: IPR008434 This family represents the oxidative cyclase responsible for forming the distinctive E-ring of the chlorin ring system under aerobic conditions . This enzyme is believed to utilise a binuclear iron centre and molecular oxygen. There are two isoforms of this enzyme in some plants and cyanobacteria, which are differentially regulated based on the levels of copper and oxygen , . This step is essential in the biosynthesis of both bacteriochlorophyll and chlorophyll under aerobic conditions (a separate enzyme, BchE, acts under anaerobic conditions). This enzyme is found in plants, cyanobacteria and other photosynthetic bacteria. CRD1 (AcsF) is required for the maintenance of photosystem I and its associated light-harvesting complexes in copper-deficient (-Cu) and oxygen-deficient (-O(2)) Chlamydomonas reinhardtii cells and is localised to the thylakoid membrane. The family also contains the Rhodocyclus gelatinosus (Rhodopseudomonas gelatinosa) AcsF protein .; GO: 0016491 oxidoreductase activity, 0046872 metal ion binding, 0015979 photosynthesis, 0015995 chlorophyll biosynthetic process.
Probab=29.18 E-value=31 Score=13.07 Aligned_cols=70 Identities=11% Similarity=0.107 Sum_probs=40.2
Q ss_pred HHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHCCCHH
Q ss_conf 99999999999999999749968999999998407787789999999999996599-98999999998639958
Q gi|254780721|r 178 SIKRAWPDALDLLLICVESGISIDQALRRVAEDIGGQSVPLSEEMLLTIAELSFLP-NRQVAFENFYNRTQMDC 250 (329)
Q Consensus 178 ~i~~~lP~~ld~l~~~~~aG~~l~~Al~~va~e~~~~~~~l~~e~~~~~~~~~~G~-~~~~Al~~~a~r~~~~~ 250 (329)
.++++|-|||..--.+==||-=+- ++..+.++...|.+++-|+.+.+|=.... =+.+||.++.-++++.-
T Consensus 75 ~lk~~FieFL~~SctaEFSGflLY---kEl~r~~~n~~PVva~lf~lMARDEARHAGFlN~AL~~~~l~ldL~~ 145 (344)
T TIGR02029 75 ELKQEFIEFLERSCTAEFSGFLLY---KELERRLKNEDPVVAELFQLMARDEARHAGFLNKALKDFGLALDLGF 145 (344)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH---HHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCEEHHHHH
T ss_conf 899999999999989887777999---99730578987178999765212555667789888887150110222
No 41
>pfam03918 CcmH Cytochrome C biogenesis protein. Members of this family include NrfF, CcmH, CycL, Ccl2.
Probab=27.45 E-value=33 Score=12.87 Aligned_cols=16 Identities=25% Similarity=0.273 Sum_probs=5.8
Q ss_pred HCCCCCCCCHHHHHHHH
Q ss_conf 67999867589999999
Q gi|254780721|r 104 AAGFRSEYSLNILLVVR 120 (329)
Q Consensus 104 ~AG~~~~~~~~~~~~~~ 120 (329)
.+|. ++.....|+..+
T Consensus 68 ~~G~-sd~eI~~~~~~r 83 (145)
T pfam03918 68 VEGK-SDEEIIDYMVAR 83 (145)
T ss_pred HCCC-CHHHHHHHHHHH
T ss_conf 8599-999999999986
No 42
>PRK10862 SoxR reducing system protein RseC; Provisional
Probab=26.85 E-value=34 Score=12.80 Aligned_cols=43 Identities=19% Similarity=0.135 Sum_probs=20.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999999999999999732001215899999999999999999999
Q gi|254780721|r 121 LVVPIIFLILGIIWIFGYDKLLEYPFQLRVGAVILIGYVGFCAPSVW 167 (329)
Q Consensus 121 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~P~~~ 167 (329)
+..++++++++......+. ..-...++++++++++||++-+++
T Consensus 82 YllPLl~l~~ga~l~~~l~----~sel~~il~a~~G~~~gf~~~R~~ 124 (158)
T PRK10862 82 YMSPLVGLFLGAALFQLLF----GSDLAALCGAVLGGVGGFLLARGY 124 (158)
T ss_pred HHHHHHHHHHHHHHHHHHC----CCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf 9999999999999999970----153999999999999999999999
No 43
>pfam04246 RseC_MucC Positive regulator of sigma(E), RseC/MucC. This bacterial family of integral membrane proteins represents a positive regulator of the sigma(E) transcription factor, namely RseC/MucC. The sigma(E) transcription factor is up-regulated by cell envelope protein misfolding, and regulates the expression of genes that are collectively termed ECF (devoted to Extra-Cellular Functions). In Pseudomonas aeruginosa, de-repression of sigma(E) is associated with the alginate-overproducing phenotype characteristic of chronic respiratory tract colonisation in cystic fibrosis patients. The mechanism by which RseC/MucC positively regulates the sigma(E) transcription factor is unknown. RseC is also thought to have a role in thiamine biosynthesis in Salmonella typhimurium. In addition, this family also includes an N-terminal part of RnfF, a Rhodobacter capsulatus protein, of unknown function, that is essential for nitrogen fixation. This protein also contains an ApbE domain pfam02424, w
Probab=26.59 E-value=34 Score=12.77 Aligned_cols=44 Identities=18% Similarity=0.181 Sum_probs=20.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 999999999999999997320012158999999999999999999999
Q gi|254780721|r 121 LVVPIIFLILGIIWIFGYDKLLEYPFQLRVGAVILIGYVGFCAPSVWI 168 (329)
Q Consensus 121 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~P~~~l 168 (329)
+..+++.++++.+....+ ...-...++.++.+.+++|++.+++-
T Consensus 75 Y~lPLl~ll~g~~~~~~l----~~~e~~~~l~~~~gl~~~~~~~r~~~ 118 (135)
T pfam04246 75 YLLPLLGLLLGALLGQAL----GLSELLAILGGLLGLALGFLILRLLA 118 (135)
T ss_pred HHHHHHHHHHHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 999999999999999996----31289999999999999999999998
No 44
>KOG3385 consensus
Probab=25.78 E-value=35 Score=12.68 Aligned_cols=31 Identities=19% Similarity=0.202 Sum_probs=20.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999984333699999999999999999
Q gi|254780721|r 284 LMEAEKKAASLGPKLTVPMIIFFLPVLILVI 314 (329)
Q Consensus 284 ~~~~e~~a~~~~~k~~~~~il~~~p~~~~~~ 314 (329)
.-+.+.-+.....++..+|++|++.++|++.
T Consensus 84 m~r~~~~ar~sg~~l~~~m~~f~lV~~fi~~ 114 (118)
T KOG3385 84 MGRLKTMARRSGISLLCWMAVFSLVAFFILW 114 (118)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHHHHHHHHHH
T ss_conf 8999999962781138999999999999862
No 45
>PRK08374 homoserine dehydrogenase; Provisional
Probab=25.21 E-value=26 Score=13.54 Aligned_cols=54 Identities=17% Similarity=0.103 Sum_probs=35.1
Q ss_pred HHHHHCCCCHHHHHHHH--HHHCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf 99997499689999999--9840778778999999999999659998999999998
Q gi|254780721|r 191 LICVESGISIDQALRRV--AEDIGGQSVPLSEEMLLTIAELSFLPNRQVAFENFYN 244 (329)
Q Consensus 191 ~~~~~aG~~l~~Al~~v--a~e~~~~~~~l~~e~~~~~~~~~~G~~~~~Al~~~a~ 244 (329)
-.++-+|.|+-+.++.. +.++....+-+......+..+++.|.++++|+++--+
T Consensus 140 EasVggGiPiI~~lr~~l~gd~I~~i~GIlNGT~NyILt~me~g~~f~eal~eAq~ 195 (316)
T PRK08374 140 EATVMAGTPIIGLLRENLLGETIERIEAVVNASTTFILTRMEKGKTFEEALEEAQS 195 (316)
T ss_pred EEEECCCCCCHHHHHHHHCCCCCCEEEEEEECCHHHHHHHHHCCCCHHHHHHHHHH
T ss_conf 53400020316999875146886389999947089999999759989999999997
No 46
>pfam03564 DUF1759 Protein of unknown function (DUF1759). This is a family of proteins of unknown function.
Probab=25.10 E-value=36 Score=12.59 Aligned_cols=121 Identities=16% Similarity=0.159 Sum_probs=72.0
Q ss_pred HHHHHHHHHHHHHHHCC--CCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHH-CCCCHHHHHHHHHHHCCCHHHH--HHH
Q ss_conf 99999999999999749--968999999998407787789999999999996-5999899999999863995899--999
Q gi|254780721|r 181 RAWPDALDLLLICVESG--ISIDQALRRVAEDIGGQSVPLSEEMLLTIAELS-FLPNRQVAFENFYNRTQMDCVR--NAT 255 (329)
Q Consensus 181 ~~lP~~ld~l~~~~~aG--~~l~~Al~~va~e~~~~~~~l~~e~~~~~~~~~-~G~~~~~Al~~~a~r~~~~~~~--~~~ 255 (329)
.++|.|.|.+...+... +|-.+-+...-.-+.+ +- ..+++.+. .+.+.+.|++.+.+|++.+.+- .+.
T Consensus 6 ~~w~~F~~~F~~~i~~~~~l~~~~Kl~yL~~~L~G---~A----~~~V~~l~~t~~nY~~A~~~L~~Ry~n~rli~~s~~ 78 (146)
T pfam03564 6 KEWQAFWELFESLIHSKTDLPEIQKFNYLKSALEG---EA----ATLVTHLPITAANYDVAWEALKERYDNPRVIIRSLL 78 (146)
T ss_pred HHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCC---HH----HHHHHCCCCCCCCHHHHHHHHHHHHCCHHHHHHHHH
T ss_conf 88899999999999727999878999999998586---19----999871667877999999999987128889999999
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 999999971995899999999999999999999999843336999999999999
Q gi|254780721|r 256 QALIQSDRYGTSIGDSLRVLVSETRSERLMEAEKKAASLGPKLTVPMIIFFLPV 309 (329)
Q Consensus 256 ~~l~~~~~~G~~l~~~L~~~a~~~r~~~~~~~e~~a~~~~~k~~~~~il~~~p~ 309 (329)
..+..-.....+-+..|+.+++.++.-.+. .+......+.-+.+.++..-+|.
T Consensus 79 ~~l~~lp~~~~~s~~~Lr~l~d~~~~~i~a-L~~Lg~~~~d~~li~ii~~KLp~ 131 (146)
T pfam03564 79 NKLMKLPSTNNDSVSQLRRLYDEANEIIRQ-LEQLGENADDTILAHLLLQKLDE 131 (146)
T ss_pred HHHHCCCCCCCCCHHHHHHHHHHHHHHHHH-HHHCCCCCCCCHHHHHHHHHCCH
T ss_conf 999828678888899999999999999999-99859988750999999984999
No 47
>COG0398 Uncharacterized conserved protein [Function unknown]
Probab=25.08 E-value=36 Score=12.59 Aligned_cols=76 Identities=14% Similarity=0.082 Sum_probs=34.4
Q ss_pred HHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 699999996799986758999999999999999999999999732--001215899999999999999999999999999
Q gi|254780721|r 96 ENIVNKLRAAGFRSEYSLNILLVVRLVVPIIFLILGIIWIFGYDK--LLEYPFQLRVGAVILIGYVGFCAPSVWISNLVQ 173 (329)
Q Consensus 96 ~~l~~~L~~AG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~g~~~P~~~l~~~~~ 173 (329)
+.+++.+.+.|. +.+..|+............-+.+....... .....+.....++..++.+.|++-+.+.+...+
T Consensus 36 ~~l~~~i~~~g~---~~pl~~fil~~l~~~~~~iP~~il~l~~g~ifG~~~G~~~s~~G~~~gs~~~Fll~R~~gr~~~~ 112 (223)
T COG0398 36 ETLREWIQAYGA---LGPLVFFILLYLVATLPIIPGSILTLAGGLLFGPFLGFLYSLIGATAGSTLAFLLARYLGRDWVL 112 (223)
T ss_pred HHHHHHHHHCCC---HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 999999998374---38999999999999984385999999888999859999999999999999999999997498999
Q ss_pred H
Q ss_conf 9
Q gi|254780721|r 174 K 174 (329)
Q Consensus 174 ~ 174 (329)
+
T Consensus 113 ~ 113 (223)
T COG0398 113 K 113 (223)
T ss_pred H
T ss_conf 9
No 48
>COG4980 GvpP Gas vesicle protein [General function prediction only]
Probab=24.84 E-value=37 Score=12.56 Aligned_cols=28 Identities=18% Similarity=0.134 Sum_probs=11.8
Q ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHHHHCC
Q ss_conf 999999999999659998999999998639
Q gi|254780721|r 218 LSEEMLLTIAELSFLPNRQVAFENFYNRTQ 247 (329)
Q Consensus 218 l~~e~~~~~~~~~~G~~~~~Al~~~a~r~~ 247 (329)
++.+...++.++ |....+++.++-++..
T Consensus 62 ~s~~~a~~~~~~--~~~ik~~v~~~~e~~q 89 (115)
T COG4980 62 LSKESAETLKDQ--GGEIKESVKKWKEDIQ 89 (115)
T ss_pred HHHHHHHHHHHH--HHHHHHHHHHHHHHCC
T ss_conf 868899999984--4999999998576316
No 49
>pfam03649 UPF0014 Uncharacterized protein family (UPF0014).
Probab=24.60 E-value=37 Score=12.53 Aligned_cols=28 Identities=14% Similarity=0.063 Sum_probs=14.9
Q ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf 8999999999999659998999999998
Q gi|254780721|r 217 PLSEEMLLTIAELSFLPNRQVAFENFYN 244 (329)
Q Consensus 217 ~l~~e~~~~~~~~~~G~~~~~Al~~~a~ 244 (329)
+++++-+.+...+..|.+.+||.+.+.+
T Consensus 151 ~l~~~~~~iE~~LaLGAt~~~A~~~~~r 178 (250)
T pfam03649 151 MVKSERDIIWGYLALGATPIQALAPFIR 178 (250)
T ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHHH
T ss_conf 9998799999999879998999999999
No 50
>PRK13455 F0F1 ATP synthase subunit B; Provisional
Probab=24.34 E-value=38 Score=12.50 Aligned_cols=44 Identities=23% Similarity=0.477 Sum_probs=22.3
Q ss_pred CHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 158999999999999999-999999999999999999999999999
Q gi|254780721|r 145 PFQLRVGAVILIGYVGFC-APSVWISNLVQKRQSSIKRAWPDALDL 189 (329)
Q Consensus 145 ~~~~~~~~~~~~~~~g~~-~P~~~l~~~~~~r~~~i~~~lP~~ld~ 189 (329)
.|.+.+...++.+++.|+ +|. .+...-.+|.++|..++-++-.+
T Consensus 29 ~FWv~IsFvif~~iL~~~~vp~-~I~~~LD~R~~~I~~dLdeAe~l 73 (184)
T PRK13455 29 DFIVTLAFLLFIGILVYFKVPG-MIGGMLDKRAEGIRSELEEARAL 73 (184)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 4999999999999999995589-99999999999999999999999
No 51
>PRK03427 cell division protein ZipA; Provisional
Probab=23.38 E-value=39 Score=12.38 Aligned_cols=21 Identities=24% Similarity=0.488 Sum_probs=14.3
Q ss_pred HHCCHHHHHHHHHHHHHHHHH
Q ss_conf 605089999999999999999
Q gi|254780721|r 8 LFDATELAVAITTAVSIFSLI 28 (329)
Q Consensus 8 ~m~~~~lli~il~~i~v~~~i 28 (329)
||.+..++++++.++++.+++
T Consensus 1 mMqdLRliLIIvGaIAIiALL 21 (331)
T PRK03427 1 MMQDLRLILIIVGAIAIIALL 21 (331)
T ss_pred CCHHHHHHHHHHHHHHHHHHH
T ss_conf 935889999999999999999
No 52
>TIGR02857 CydD ABC transporter, CydDC cysteine exporter (CydDC-E) family, permease/ATP-binding protein CydD; InterPro: IPR014216 The gene pair cydCD encodes an ABC-family transporter in which each gene contains an N-terminal membrane-spanning domain and a C-terminal ATP-binding domain. In Escherichia coli these genes were discovered as mutants which caused the terminal heme-copper oxidase complex cytochrome bd to fail to assemble. Recent work has shown that the transporter is involved in the export of redox-active thiol compounds such as cysteine and glutathione , . The linkage to assembly of the cytochrome bd complex is further supported by the conserved operon structure found outside the gammaproteobacteria (cydABCD) containing both the transporter and oxidase genes components. The genes used as the seed members for this entry are all either found in the gammaproteobacterial context, or the CydABCD context. All members of this entry scoring above the trusted cut off at the time of its creation were from genomes which encode a cytochrome bd complex. Unfortunately, the gene symbol nomenclature, based on this operon in Bacillus subtilis, assigns cydC to the third gene in the operon, where this gene is actually homologous to the E. coli cydD gene. We have chosen to name all homologues in this family in accordance with the precedence of publication of the E. coli name, CydD..
Probab=22.78 E-value=40 Score=12.31 Aligned_cols=106 Identities=14% Similarity=0.054 Sum_probs=52.5
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 589999999999999999999999997320012158999----9999999999999999999999999999999999999
Q gi|254780721|r 112 SLNILLVVRLVVPIIFLILGIIWIFGYDKLLEYPFQLRV----GAVILIGYVGFCAPSVWISNLVQKRQSSIKRAWPDAL 187 (329)
Q Consensus 112 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~g~~~P~~~l~~~~~~r~~~i~~~lP~~l 187 (329)
+...|+.-.+.-.+.+.+++.+........-+.+....+ ++.++..++|+ .-..+.+|+.+.+.+-=-.|+
T Consensus 118 aLd~Y~arYLPql~~A~~~P~~~l~av~~~Dw~sg~ill~T~PLIP~FMiLiG~-----~a~~~~~~q~~~l~rLSg~FL 192 (570)
T TIGR02857 118 ALDGYFARYLPQLVLAVIVPLAILAAVLPADWISGLILLLTAPLIPIFMILIGW-----AAQAAARKQWAALSRLSGHFL 192 (570)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHH
T ss_conf 889999999999999889999999999995499999999997245799999989-----999999999999987528999
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHH
Q ss_conf 99999997499689999999984077877899999999999
Q gi|254780721|r 188 DLLLICVESGISIDQALRRVAEDIGGQSVPLSEEMLLTIAE 228 (329)
Q Consensus 188 d~l~~~~~aG~~l~~Al~~va~e~~~~~~~l~~e~~~~~~~ 228 (329)
|.+. |++--++|.+.-++.. .-...+++|+.-+.+
T Consensus 193 D~~~-----GL~tLk~F~r~~~~~~-~i~~~s~~~R~~TM~ 227 (570)
T TIGR02857 193 DRLR-----GLPTLKLFGRAKAQAA-AIRRSSEEYRERTMR 227 (570)
T ss_pred HHHH-----HHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHH
T ss_conf 9997-----7899999998699999-999999998887899
No 53
>pfam05659 RPW8 Arabidopsis broad-spectrum mildew resistance protein RPW8. This family consists of several broad-spectrum mildew resistance proteins from Arabidopsis thaliana. Plant disease resistance (R) genes control the recognition of specific pathogens and activate subsequent defence responses. The Arabidopsis thaliana locus Resistance To Powdery Mildew 8 (RPW8) contains two naturally polymorphic, dominant R genes, RPW8.1 and RPW8.2, which individually control resistance to a broad range of powdery mildew pathogens. They induce localized, salicylic acid-dependent defences similar to those induced by R genes that control specific resistance. Apparently, broad-spectrum resistance mediated by RPW8 uses the same mechanisms as specific resistance.
Probab=22.46 E-value=41 Score=12.27 Aligned_cols=63 Identities=11% Similarity=0.038 Sum_probs=48.2
Q ss_pred HHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHH
Q ss_conf 999999999999999749968999999998407787789999999999996599989999999986
Q gi|254780721|r 180 KRAWPDALDLLLICVESGISIDQALRRVAEDIGGQSVPLSEEMLLTIAELSFLPNRQVAFENFYNR 245 (329)
Q Consensus 180 ~~~lP~~ld~l~~~~~aG~~l~~Al~~va~e~~~~~~~l~~e~~~~~~~~~~G~~~~~Al~~~a~r 245 (329)
...|-..++.+...+++=.|+-.=+....++.+. |..+|.+.....++-|...-+...+...+
T Consensus 29 ~~~F~~iL~rL~~Tl~~I~P~v~~I~kl~~e~d~---~~~~e~e~L~~lLekg~~LV~kcsk~~~~ 91 (147)
T pfam05659 29 SLTTRCILQRLDATIESITPLFDQIDKLSKESDD---PFRKVIEDLKRLLEKAVSLVEKYAELRRR 91 (147)
T ss_pred HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCC---CHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 9878999999999999724299999989877556---50689999999999999999997897999
No 54
>pfam03323 GerA Bacillus/Clostridium GerA spore germination protein.
Probab=22.36 E-value=41 Score=12.25 Aligned_cols=50 Identities=10% Similarity=0.260 Sum_probs=26.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHH
Q ss_conf 9999999999999999999999999999999999999999974996899999999
Q gi|254780721|r 154 ILIGYVGFCAPSVWISNLVQKRQSSIKRAWPDALDLLLICVESGISIDQALRRVA 208 (329)
Q Consensus 154 ~~~~~~g~~~P~~~l~~~~~~r~~~i~~~lP~~ld~l~~~~~aG~~l~~Al~~va 208 (329)
.++..+..++|..|+.-..-+ .+.+|.-+-.-....+.|.|++.-++..-
T Consensus 279 ~~~~~isl~LP~lYvAl~sfh-----~e~iP~~L~~~i~~sR~~vPfP~~iE~ll 328 (468)
T pfam03323 279 FLAFFISLFLPPLYVALTTFH-----PELIPTELLFSIAASREGVPFPPIIEALI 328 (468)
T ss_pred HHHHHHHHHHHHHHHHHHHCC-----HHHCCHHHHHHHHHHCCCCCCCHHHHHHH
T ss_conf 999999999899999999709-----43275989998876535898888999999
No 55
>TIGR03224 benzo_boxA benzoyl-CoA oxygenase/reductase, BoxA protein. Members of this protein family are BoxA, the A component of the BoxAB benzoyl-CoA oxygenase/reductase. This oxygen-requiring enzyme acts in an aerobic pathway of benzoate catabolism via coenzyme A ligation. BoxA is a homodimeric iron-sulphur-flavoprotein and acts as an NADPH-dependent reductase for BoxB.
Probab=22.35 E-value=29 Score=13.23 Aligned_cols=56 Identities=18% Similarity=0.317 Sum_probs=19.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC--CHHHHHHHHHHHCCCCCHHHHHH
Q ss_conf 999999999999999999999999999997499--68999999998407787789999
Q gi|254780721|r 166 VWISNLVQKRQSSIKRAWPDALDLLLICVESGI--SIDQALRRVAEDIGGQSVPLSEE 221 (329)
Q Consensus 166 ~~l~~~~~~r~~~i~~~lP~~ld~l~~~~~aG~--~l~~Al~~va~e~~~~~~~l~~e 221 (329)
.|+..+...+.+++.+-+-|-=..+..|=-.|| .+++||..+|+.-.-.+..+...
T Consensus 342 ~YVQDri~E~Adev~~lLqd~gahiYvCGLKGMe~GV~eAl~~iA~~~G~~W~~~~~~ 399 (411)
T TIGR03224 342 RYVQDAIRERAADVAALLKDPNTYIYICGLKGMEEGVLDAFRDVCATNGLSWETLEPR 399 (411)
T ss_pred EEHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCHHHHHHH
T ss_conf 4278899998999999973899489996603146779999999999739998999999
No 56
>TIGR00701 TIGR00701 conserved hypothetical protein TIGR00701; InterPro: IPR014351 There is currently no experimental data for members of this entry or their homologues, nor do they exhibit features indicative of any function. However, they are predicted to be integral membrane proteins (with several transmembrane segments). There is an indirect indication of a link between this protein and the function or assembly of cytochromes: in Escherichia coli, strains producing related proteins not included in this entry turn pink, perhaps because of an excess of accumulated haems ..
Probab=22.26 E-value=41 Score=12.24 Aligned_cols=21 Identities=14% Similarity=0.270 Sum_probs=14.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q ss_conf 999999999999999999999
Q gi|254780721|r 174 KRQSSIKRAWPDALDLLLICV 194 (329)
Q Consensus 174 ~r~~~i~~~lP~~ld~l~~~~ 194 (329)
+|.=++-|+.|..+-.+...+
T Consensus 121 ~~fyR~~NEaPtIlmv~iVil 141 (151)
T TIGR00701 121 KKFYRVLNEAPTILMVVIVIL 141 (151)
T ss_pred CHHHHHHHHHHHHHHHHHHHH
T ss_conf 213012432669999999999
No 57
>PRK12461 UDP-N-acetylglucosamine acyltransferase; Provisional
Probab=21.61 E-value=42 Score=12.15 Aligned_cols=30 Identities=10% Similarity=-0.066 Sum_probs=14.5
Q ss_pred CCCCHHHHHHHHHHHC-CCHHHHHHHHHHHH
Q ss_conf 5999899999999863-99589999999999
Q gi|254780721|r 231 FLPNRQVAFENFYNRT-QMDCVRNATQALIQ 260 (329)
Q Consensus 231 ~G~~~~~Al~~~a~r~-~~~~~~~~~~~l~~ 260 (329)
.+.++++|++++.+.. ++|+++.|++-+..
T Consensus 219 ~~~~~~~~~~~~~~~~~~~~~v~~~~~Fi~~ 249 (256)
T PRK12461 219 SGLSLQDAVQELEDQFPMSPEIRELIDFVKA 249 (256)
T ss_pred CCCCHHHHHHHHHHHCCCCHHHHHHHHHHHH
T ss_conf 8998999999998765499999999999862
No 58
>PRK13721 conjugal transfer ATP-binding protein TraC; Provisional
Probab=21.36 E-value=43 Score=12.12 Aligned_cols=33 Identities=18% Similarity=0.154 Sum_probs=19.9
Q ss_pred HHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 999997199589999999999999999999999
Q gi|254780721|r 258 LIQSDRYGTSIGDSLRVLVSETRSERLMEAEKK 290 (329)
Q Consensus 258 l~~~~~~G~~l~~~L~~~a~~~r~~~~~~~e~~ 290 (329)
+..-.+.|-++.|+.+.++...--..+.+.|.-
T Consensus 827 ie~l~~~G~s~~eAI~~la~~~~~~e~~~~~~~ 859 (864)
T PRK13721 827 VQQKRKEGLSIHEAVWQLAWKKFGPEMASLEAW 859 (864)
T ss_pred HHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 999998699999999999987728999999999
No 59
>TIGR02362 dhaK1b probable dihydroxyacetone kinase DhaK1b subunit; InterPro: IPR012735 Two types of dihydroxyacetone kinase (glycerone kinase) are described. In yeast and a few bacteria, e.g. Citrobacter freundii, the enzyme is a single chain that uses ATP as phosphoryl donor and is designated 2.7.1.29 from EC. By contract, Escherichia coli and many other bacterial species have a multisubunit form with a phosphoprotein donor related to PTS transport proteins. This family represents a protein, unique to the firmicutes (low GC Gram-positives), that appears to be a divergent second copy of the K subunit of that complex; its gene is always found in operons with the other three proteins of the complex..
Probab=21.15 E-value=27 Score=13.49 Aligned_cols=19 Identities=16% Similarity=0.188 Sum_probs=8.5
Q ss_pred HHHHHHHHHHHHCCCCHHH
Q ss_conf 9999999999971995899
Q gi|254780721|r 252 RNATQALIQSDRYGTSIGD 270 (329)
Q Consensus 252 ~~~~~~l~~~~~~G~~l~~ 270 (329)
--+-.+|-+|.+.|.||.+
T Consensus 153 vLvHKIlGaAA~~GaSL~~ 171 (328)
T TIGR02362 153 VLVHKILGAAAKEGASLDE 171 (328)
T ss_pred HHHHHHHHHHHHCCCCHHH
T ss_conf 7998999998523766789
No 60
>PRK01265 heat shock protein HtpX; Provisional
Probab=20.60 E-value=45 Score=12.02 Aligned_cols=12 Identities=17% Similarity=0.302 Sum_probs=7.4
Q ss_pred CCHHHHHHHHHH
Q ss_conf 968999999998
Q gi|254780721|r 198 ISIDQALRRVAE 209 (329)
Q Consensus 198 ~~l~~Al~~va~ 209 (329)
..+..|+.++..
T Consensus 236 ~~La~AL~KI~~ 247 (326)
T PRK01265 236 ENLQTALAKIVL 247 (326)
T ss_pred HHHHHHHHHHHH
T ss_conf 999999999874
No 61
>TIGR02332 HpaX 4-hydroxyphenylacetate permease; InterPro: IPR012707 Among the different families of transporter only two occur ubiquitously in all classifications of organisms. These are the ATP-Binding Cassette (ABC) superfamily and the Major Facilitator Superfamily (MFS). The MFS transporters are single-polypeptide secondary carriers capable only of transporting small solutes in response to chemiosmotic ion gradients , . This entry represents a group of MFS proteins encoded in a number of proteobacterial genomes, but only in the context of having genes for 4-hydroxyphenylacetate (4-HPA) degradation. The protein is characterised as 4-HPA permease in Escherichia coli, where 3-HPA and 3,4-dihydroxyphenylacetate, but not other substrate analogues, were shown to competitively inhibit 4-HPA transport, indicating a narrow substrate specificity ..
Probab=20.37 E-value=45 Score=11.99 Aligned_cols=53 Identities=17% Similarity=0.156 Sum_probs=25.4
Q ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHCCCC---------HHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 999999863995899999999999971995---------89999999999999999999999
Q gi|254780721|r 238 AFENFYNRTQMDCVRNATQALIQSDRYGTS---------IGDSLRVLVSETRSERLMEAEKK 290 (329)
Q Consensus 238 Al~~~a~r~~~~~~~~~~~~l~~~~~~G~~---------l~~~L~~~a~~~r~~~~~~~e~~ 290 (329)
.|.-|.-......++...--+.|+-.+|++ +.+....+.-....|+..+.+|+
T Consensus 248 tlayfCltntlsai~iWtPqilqsfn~Gssni~iGllaa~Pq~Cti~Gm~~Wsr~sdr~~er 309 (412)
T TIGR02332 248 TLAYFCLTNTLSAISIWTPQILQSFNTGSSNITIGLLAAVPQICTILGMVYWSRRSDRLKER 309 (412)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHH
T ss_conf 99999987667666431247888740463267888997677899998778741003456654
No 62
>COG5249 RER1 Golgi protein involved in Golgi-to-ER retrieval [Intracellular trafficking and secretion]
Probab=20.36 E-value=45 Score=11.99 Aligned_cols=21 Identities=14% Similarity=0.048 Sum_probs=8.8
Q ss_pred HHHHHHHHHHCCCHHHHHHHHHH
Q ss_conf 99999999863995899999999
Q gi|254780721|r 236 QVAFENFYNRTQMDCVRNATQAL 258 (329)
Q Consensus 236 ~~Al~~~a~r~~~~~~~~~~~~l 258 (329)
++-++-|-+|. ||+++.-..+
T Consensus 99 d~EFrPFIRrL--PEFkFWy~s~ 119 (180)
T COG5249 99 DNEFRPFIRRL--PEFKFWYFST 119 (180)
T ss_pred CCHHHHHHHCC--CHHHHHHHHH
T ss_conf 32013898748--5148999999
No 63
>COG1826 TatA Sec-independent protein secretion pathway components [Intracellular trafficking and secretion]
Probab=20.21 E-value=39 Score=12.40 Aligned_cols=17 Identities=24% Similarity=0.446 Sum_probs=6.9
Q ss_pred HCCHHHHHHHHHHHHHH
Q ss_conf 05089999999999999
Q gi|254780721|r 9 FDATELAVAITTAVSIF 25 (329)
Q Consensus 9 m~~~~lli~il~~i~v~ 25 (329)
+..+.+++++.+++.+|
T Consensus 4 ig~~elliIlvV~lllf 20 (94)
T COG1826 4 IGWSELLIILVVALLVF 20 (94)
T ss_pred CCHHHHHHHHHHHHHHC
T ss_conf 88999999999999862
Done!