Query gi|254780204|ref|YP_003064617.1| hypothetical protein CLIBASIA_00445 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 180
No_of_seqs 2 out of 4
Neff 1.1
Searched_HMMs 39220
Date Mon May 23 11:23:29 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780204.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG4970 FimT Tfp pilus assembl 56.3 14 0.00035 18.0 3.3 25 89-113 14-38 (181)
2 COG4968 PilE Tfp pilus assembl 54.7 8.6 0.00022 19.3 2.0 46 90-139 13-58 (139)
3 TIGR02596 TIGR02596 Verrucomic 51.3 18 0.00046 17.3 3.2 58 90-147 6-71 (210)
4 PRK10574 putative major pilin 50.4 11 0.00027 18.7 2.0 21 89-109 11-31 (146)
5 pfam11359 gpUL132 Glycoprotein 45.3 20 0.00052 17.0 2.7 22 15-36 59-80 (235)
6 COG5075 Uncharacterized conser 41.5 10 0.00026 18.9 0.7 29 32-61 112-146 (305)
7 COG4915 XpaC 5-bromo-4-chloroi 41.4 29 0.00074 16.0 7.9 18 108-125 61-78 (204)
8 PRK00413 thrS threonyl-tRNA sy 38.2 20 0.0005 17.0 1.8 47 16-62 267-313 (639)
9 TIGR03470 HpnH hopanoid biosyn 37.6 6.8 0.00017 19.9 -0.7 48 24-72 194-249 (318)
10 PRK12305 thrS threonyl-tRNA sy 34.7 30 0.00076 15.9 2.2 48 16-63 207-254 (576)
11 COG5617 Predicted integral mem 33.7 27 0.0007 16.2 1.9 50 49-99 45-100 (801)
12 pfam08092 Toxin_22 Magi peptid 32.0 11 0.00028 18.7 -0.4 12 50-62 21-32 (38)
13 COG2165 PulG Type II secretory 31.8 41 0.001 15.1 3.0 27 89-115 14-40 (149)
14 COG4969 PilA Tfp pilus assembl 31.1 40 0.001 15.2 2.4 22 90-111 12-33 (125)
15 PRK12304 thrS threonyl-tRNA sy 30.9 31 0.00078 15.9 1.8 48 16-63 238-285 (604)
16 PRK03772 threonyl-tRNA synthet 30.1 41 0.0011 15.1 2.3 46 17-62 271-316 (642)
17 PRK04483 threonyl-tRNA synthet 29.2 35 0.00089 15.5 1.8 47 16-62 270-316 (634)
18 COG0381 WecB UDP-N-acetylgluco 29.1 27 0.00069 16.2 1.2 42 80-122 95-136 (383)
19 pfam06755 DUF1219 Protein of u 29.1 27 0.00069 16.2 1.2 24 108-131 32-55 (109)
20 TIGR01844 type_I_sec_TolC type 29.0 11 0.00027 18.7 -0.9 35 136-170 276-310 (437)
21 TIGR03603 cyclo_dehy_ocin bact 28.5 40 0.001 15.2 2.0 38 96-133 266-316 (318)
22 TIGR02484 CitB CitB domain pro 28.4 47 0.0012 14.7 2.8 24 14-37 228-251 (392)
23 COG4721 ABC-type cobalt transp 26.8 50 0.0013 14.5 4.5 44 60-106 131-174 (192)
24 PRK12444 threonyl-tRNA synthet 26.7 40 0.001 15.1 1.8 27 37-63 294-320 (639)
25 PRK10506 hypothetical protein; 24.1 51 0.0013 14.5 1.9 20 90-109 12-31 (155)
26 KOG2653 consensus 23.9 57 0.0015 14.2 3.0 55 5-59 204-272 (487)
27 TIGR02010 IscR iron-sulfur clu 23.2 27 0.00069 16.2 0.3 35 90-130 8-42 (140)
28 PRK00425 rpoZ DNA-directed RNA 23.1 47 0.0012 14.7 1.5 30 102-131 1-30 (69)
29 COG1758 RpoZ DNA-directed RNA 22.9 59 0.0015 14.1 2.1 31 103-133 1-31 (74)
30 TIGR00709 dat 2,4-diaminobutyr 22.9 15 0.00038 17.8 -1.1 50 20-77 4-53 (445)
31 TIGR02099 TIGR02099 conserved 22.3 61 0.0016 14.0 3.6 31 81-111 5-35 (1362)
32 TIGR02349 DnaJ_bact chaperone 20.9 45 0.0011 14.8 1.1 40 121-160 22-72 (386)
33 pfam04529 Herpes_U59 Herpesvir 20.8 20 0.00051 17.0 -0.8 38 79-118 259-302 (365)
34 cd00771 ThrRS_core Threonyl-tR 20.4 52 0.0013 14.4 1.3 47 16-62 29-75 (298)
No 1
>COG4970 FimT Tfp pilus assembly protein FimT [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=56.34 E-value=14 Score=18.02 Aligned_cols=25 Identities=44% Similarity=0.550 Sum_probs=20.0
Q ss_pred HHHHHHHHHHHHHHHCCHHHHHCCC
Q ss_conf 7999999999999723321761530
Q gi|254780204|r 89 ACLVVTAILAILLSIAIPTIEEGMT 113 (180)
Q Consensus 89 aclvvtailaillsiaiptiEE~l~ 113 (180)
.-|+|-||+|||..+|.|..-..++
T Consensus 14 ELliviAIlAIla~~A~P~fs~~i~ 38 (181)
T COG4970 14 ELLIVLAILAILAVIAAPNFSQWIR 38 (181)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 9999999999999985100888877
No 2
>COG4968 PilE Tfp pilus assembly protein PilE [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=54.65 E-value=8.6 Score=19.28 Aligned_cols=46 Identities=24% Similarity=0.353 Sum_probs=26.0
Q ss_pred HHHHHHHHHHHHHHCCHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999999999972332176153000001669999998853555889999
Q gi|254780204|r 90 CLVVTAILAILLSIAIPTIEEGMTMNDIKYERKQVISRKAKEKDLEESLY 139 (180)
Q Consensus 90 clvvtailaillsiaiptiEE~l~lNDIKYE~~Q~I~~K~KE~~~~E~L~ 139 (180)
-++|-+|++||.+||.|.-..- -.|-+|.|+-.--.+--..-||-|
T Consensus 13 LmIvVaIv~ILa~IAyPSY~~y----v~rs~R~~a~A~L~~~a~~~Er~y 58 (139)
T COG4968 13 LMIVVAIVGILALIAYPSYQNY----VLRSRRSAAKAALLENAQFMERYY 58 (139)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 9999999999999870768999----999899999999999999999999
No 3
>TIGR02596 TIGR02596 Verrucomicrobium spinosum paralogous family TIGR02596.
Probab=51.33 E-value=18 Score=17.29 Aligned_cols=58 Identities=21% Similarity=0.297 Sum_probs=46.6
Q ss_pred HHHHHHHHHHHHHHCCHHHHHCCCC-------CCCHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHH
Q ss_conf 9999999999997233217615300-------000166999999885355-588999999989898
Q gi|254780204|r 90 CLVVTAILAILLSIAIPTIEEGMTM-------NDIKYERKQVISRKAKEK-DLEESLYQISEFAAC 147 (180)
Q Consensus 90 clvvtailaillsiaiptiEE~l~l-------NDIKYE~~Q~I~~K~KE~-~~~E~L~q~sE~~AC 147 (180)
-|||-||.++|++++++.+..-|+- |.+--|-.+|+++-+||. ..|=|+||..+..+-
T Consensus 6 llvV~a~~~lLmals~~~~~~~l~aq~L~~~a~~la~e~~~A~llA~r~N~~VEVRFy~~~~d~g~ 71 (210)
T TIGR02596 6 LLVVIAIIALLMALSTLVVNQVLAAQQLGSSATRLANELAAAALLAVRENRPVEVRFYRRADDAGP 71 (210)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCC
T ss_conf 889999999999998633888999877889999999999999999986294144430003200278
No 4
>PRK10574 putative major pilin subunit; Provisional
Probab=50.45 E-value=11 Score=18.68 Aligned_cols=21 Identities=43% Similarity=0.665 Sum_probs=17.9
Q ss_pred HHHHHHHHHHHHHHHCCHHHH
Q ss_conf 799999999999972332176
Q gi|254780204|r 89 ACLVVTAILAILLSIAIPTIE 109 (180)
Q Consensus 89 aclvvtailaillsiaiptiE 109 (180)
..++|-||++||..||+|.-.
T Consensus 11 Elmivvaii~il~~ia~p~y~ 31 (146)
T PRK10574 11 ELMVVIGIIAILSAIGIPAYQ 31 (146)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
T ss_conf 999999999999999999999
No 5
>pfam11359 gpUL132 Glycoprotein UL132. Glycoprotein UL132 is a low-abundance structural component of Human cytomegalovirus (HCMV). The function of this protein is not fully understood.
Probab=45.26 E-value=20 Score=16.95 Aligned_cols=22 Identities=45% Similarity=0.557 Sum_probs=18.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 3359999999999889999886
Q gi|254780204|r 15 YGGLILSFLSVIVSPVYSYFRH 36 (180)
Q Consensus 15 ygglilsflsvivspvysyfrh 36 (180)
-|-.|||||-|.+.++|+-++.
T Consensus 59 ~g~sils~llVl~a~ly~sc~~ 80 (235)
T pfam11359 59 SGVSILSFLLVLVAVLYSSCHT 80 (235)
T ss_pred CCHHHHHHHHHHHHHHHHHHHC
T ss_conf 0269999999999877776641
No 6
>COG5075 Uncharacterized conserved protein [Function unknown]
Probab=41.49 E-value=10 Score=18.85 Aligned_cols=29 Identities=41% Similarity=0.780 Sum_probs=20.0
Q ss_pred HHHHHHHHHCHHHHHHHHHH------CCCCCHHHHH
Q ss_conf 99886552067899999760------5773055565
Q gi|254780204|r 32 SYFRHTVAETPKIMWKAFKK------SSGRWQWYKK 61 (180)
Q Consensus 32 syfrhtvaetpkimwkafkk------ssgrwqwykk 61 (180)
|--||-|.|||. |++.+-| .++||+|-..
T Consensus 112 sqk~~~V~ETpe-mYl~ivkpfiq~~~~~~~~wv~n 146 (305)
T COG5075 112 SQKRHYVRETPE-MYLDIVKPFIQEMRGSRWKWVNN 146 (305)
T ss_pred HHCEEEEECCHH-HHHHHHHHHHHHHCCCCHHHHHH
T ss_conf 432453223889-99998777998624642302666
No 7
>COG4915 XpaC 5-bromo-4-chloroindolyl phosphate hydrolysis protein [General function prediction only]
Probab=41.45 E-value=29 Score=16.02 Aligned_cols=18 Identities=39% Similarity=0.540 Sum_probs=8.4
Q ss_pred HHHCCCCCCCHHHHHHHH
Q ss_conf 761530000016699999
Q gi|254780204|r 108 IEEGMTMNDIKYERKQVI 125 (180)
Q Consensus 108 iEE~l~lNDIKYE~~Q~I 125 (180)
.|-|+|-.|+||-|+|.-
T Consensus 61 ~e~gLT~kdykyiR~nLe 78 (204)
T COG4915 61 HEAGLTDKDYKYIRENLE 78 (204)
T ss_pred HHCCCCCCHHHHHHHHHH
T ss_conf 980676004999997699
No 8
>PRK00413 thrS threonyl-tRNA synthetase; Reviewed
Probab=38.23 E-value=20 Score=17.04 Aligned_cols=47 Identities=21% Similarity=0.314 Sum_probs=29.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHCCCCCHHHHHH
Q ss_conf 35999999999988999988655206789999976057730555655
Q gi|254780204|r 16 GGLILSFLSVIVSPVYSYFRHTVAETPKIMWKAFKKSSGRWQWYKKS 62 (180)
Q Consensus 16 gglilsflsvivspvysyfrhtvaetpkimwkafkkssgrwqwykks 62 (180)
|..|..-|.-.+.-.+.-.--.-..||-|+-+..-+.||.|+.|+..
T Consensus 267 G~~i~~~le~~~r~~~~~~Gy~eV~TP~i~~~~Lw~~SGHw~~Y~e~ 313 (639)
T PRK00413 267 GWIIRNELEDYMRRRHLKAGYQEVNTPHILDRSLWETSGHWDHYREN 313 (639)
T ss_pred HHHHHHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHCCCHHHHCCC
T ss_conf 89999999999999999869859836413468899654742232254
No 9
>TIGR03470 HpnH hopanoid biosynthesis associated radical SAM protein HpnH. The sequences represented by this model are members of the radical SAM superfamily of enzymes (pfam04055). These enzymes utilize an iron-sulfur redox cluster and S-adenosylmethionine to carry out diverse radical mediated reactions. The members of this clade are frequently found in the same locus as squalene-hopene cyclase (SHC, TIGR01507) and other genes associated with the biosynthesis of hopanoid natural products. The linkage between SHC and this radical SAM enzyme is strong; one is nearly always observed in the same genome where the other is found. A hopanoid biosynthesis locus was described in Zymomonas mobilis consisting of the genes HpnA-E and SHC (HpnF). Continuing past SHC are found a phosphorylase enzyme (ZMO0873, i.e. HpnG, TIGR03468) and this radical SAM enzyme (ZMO0874) which we name here HpnH. Granted, in Z. mobilis, HpnH is in a convergent orientation with respect to HpnA-G, but one gene beyond HpnH
Probab=37.61 E-value=6.8 Score=19.91 Aligned_cols=48 Identities=27% Similarity=0.599 Sum_probs=31.1
Q ss_pred HHHHHHHHHHHHH-------HHHHCHHHHHHHHHHCCC-CCHHHHHHHHHHHHHHHH
Q ss_conf 9999889999886-------552067899999760577-305556557899977557
Q gi|254780204|r 24 SVIVSPVYSYFRH-------TVAETPKIMWKAFKKSSG-RWQWYKKSFQYLLFFSGL 72 (180)
Q Consensus 24 svivspvysyfrh-------tvaetpkimwkafkkssg-rwqwykksfqyllffsgl 72 (180)
.+++||.|+|.+. ...+|.+..-+.|+.+.+ +|. ...|.-||-|..|-
T Consensus 194 gi~isp~y~Ye~ap~q~~fl~r~~~~~lfr~il~~~~~k~w~-~n~s~~~ldfl~G~ 249 (318)
T TIGR03470 194 GMTISPGYAYEKAPDQDHFLGRRQTKKLFREVLSNGNGKRWR-FNHSPLFLDFLAGN 249 (318)
T ss_pred EEEECCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCC-CCCCHHHHHHHCCC
T ss_conf 389766531023763111158999999999999864565841-12699999986699
No 10
>PRK12305 thrS threonyl-tRNA synthetase; Reviewed
Probab=34.71 E-value=30 Score=15.92 Aligned_cols=48 Identities=21% Similarity=0.270 Sum_probs=30.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHCCCCCHHHHHHH
Q ss_conf 359999999999889999886552067899999760577305556557
Q gi|254780204|r 16 GGLILSFLSVIVSPVYSYFRHTVAETPKIMWKAFKKSSGRWQWYKKSF 63 (180)
Q Consensus 16 gglilsflsvivspvysyfrhtvaetpkimwkafkkssgrwqwykksf 63 (180)
|..|..-|.-.+.-.+.-.--.-..||.|+-+..-+.||+|+.|+...
T Consensus 207 G~~i~~~le~~~r~~~~~~Gy~eV~TP~i~~~~Lw~~SGH~~~Y~e~M 254 (576)
T PRK12305 207 GMIIKNAIRKFILELDRKYGFDEVLTPHFGEKKLYKTSGHLDHYKDDM 254 (576)
T ss_pred HHHHHHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHCCCHHHHHHHC
T ss_conf 789999999999999998699898464214288997666465566425
No 11
>COG5617 Predicted integral membrane protein [Function unknown]
Probab=33.72 E-value=27 Score=16.16 Aligned_cols=50 Identities=28% Similarity=0.639 Sum_probs=32.9
Q ss_pred HHHCCCCC------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 76057730------5556557899977557999986465899876679999999999
Q gi|254780204|r 49 FKKSSGRW------QWYKKSFQYLLFFSGLSYLLFHSASFVLSLTSACLVVTAILAI 99 (180)
Q Consensus 49 fkkssgrw------qwykksfqyllffsglsyllfhsasfvlsltsaclvvtailai 99 (180)
-.-+.|+| -||. .||++.|..-++|++.---.+++.-.+....+.-+||-
T Consensus 45 ~~l~~G~wy~~w~~~WY~-G~pflrYypPl~Yli~aal~~l~~d~~~t~~v~~~la~ 100 (801)
T COG5617 45 HSLKDGNWYPPWCEYWYN-GYPFLRYYPPLSYLIGAALNFLLGDVVTTYAVFLMLAF 100 (801)
T ss_pred HHHHCCCCCCCCCHHHHC-CCCCCEECCCHHHHHHHHHHHHHCCHHHHHHHHHHHHH
T ss_conf 998618988875433305-88752245868999999987762585699999999999
No 12
>pfam08092 Toxin_22 Magi peptide toxin family. This family consists of Magi peptide toxins (Magi 1, 2 and 5) isolated from the venom of Hexathelidae spider. These insecticidal peptide toxins bind to sodium channels and induce flaccid paralysis when injected into lepidopteran larvae. However, these peptides are not toxic to mice when injected intracranially at 20 pmol/g.
Probab=32.05 E-value=11 Score=18.65 Aligned_cols=12 Identities=50% Similarity=1.306 Sum_probs=7.4
Q ss_pred HHCCCCCHHHHHH
Q ss_conf 6057730555655
Q gi|254780204|r 50 KKSSGRWQWYKKS 62 (180)
Q Consensus 50 kkssgrwqwykks 62 (180)
-+.||+| |||+-
T Consensus 21 v~tSGyW-Wyk~~ 32 (38)
T pfam08092 21 VRTSGYW-WYKTY 32 (38)
T ss_pred ECCCCEE-EEEEE
T ss_conf 6344638-84238
No 13
>COG2165 PulG Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=31.81 E-value=41 Score=15.07 Aligned_cols=27 Identities=33% Similarity=0.588 Sum_probs=20.8
Q ss_pred HHHHHHHHHHHHHHHCCHHHHHCCCCC
Q ss_conf 799999999999972332176153000
Q gi|254780204|r 89 ACLVVTAILAILLSIAIPTIEEGMTMN 115 (180)
Q Consensus 89 aclvvtailaillsiaiptiEE~l~lN 115 (180)
.-|||-+|++|+.+++.|..-.-.+-.
T Consensus 14 ElLVvl~Iigil~~~~~p~~~~~~~~~ 40 (149)
T COG2165 14 ELLVVLAIIGILAALALPSLQGSIDKA 40 (149)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 999999999999999999999988999
No 14
>COG4969 PilA Tfp pilus assembly protein, major pilin PilA [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=31.10 E-value=40 Score=15.17 Aligned_cols=22 Identities=45% Similarity=0.615 Sum_probs=18.5
Q ss_pred HHHHHHHHHHHHHHCCHHHHHC
Q ss_conf 9999999999997233217615
Q gi|254780204|r 90 CLVVTAILAILLSIAIPTIEEG 111 (180)
Q Consensus 90 clvvtailaillsiaiptiEE~ 111 (180)
-++|-+|.+||-.|+||-.++-
T Consensus 12 lmivi~Ii~iLaaIaiP~YQ~y 33 (125)
T COG4969 12 LMIVLAIIAILAAIAIPLYQNY 33 (125)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
T ss_conf 9899999999998520578999
No 15
>PRK12304 thrS threonyl-tRNA synthetase; Reviewed
Probab=30.88 E-value=31 Score=15.85 Aligned_cols=48 Identities=21% Similarity=0.223 Sum_probs=30.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHCCCCCHHHHHHH
Q ss_conf 359999999999889999886552067899999760577305556557
Q gi|254780204|r 16 GGLILSFLSVIVSPVYSYFRHTVAETPKIMWKAFKKSSGRWQWYKKSF 63 (180)
Q Consensus 16 gglilsflsvivspvysyfrhtvaetpkimwkafkkssgrwqwykksf 63 (180)
|..|..-|.-.+.-.|.-.--.-..||.|+-+..=+.||.|+.|+...
T Consensus 238 G~~i~~~le~~~r~~~~~~Gy~eV~TP~i~~~~Lw~~SGH~~~Y~e~M 285 (604)
T PRK12304 238 GARLRSKLEHLLYKAHRLRGYEPVRGPEILKSDVWKISGHYANYKENM 285 (604)
T ss_pred HHHHHHHHHHHHHHHHHHCCCEEECCCCCCCHHHHHCCCHHHHHCCCC
T ss_conf 549999999999999998299680386545588873055153210576
No 16
>PRK03772 threonyl-tRNA synthetase; Validated
Probab=30.06 E-value=41 Score=15.06 Aligned_cols=46 Identities=20% Similarity=0.327 Sum_probs=27.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHCCCCCHHHHHH
Q ss_conf 5999999999988999988655206789999976057730555655
Q gi|254780204|r 17 GLILSFLSVIVSPVYSYFRHTVAETPKIMWKAFKKSSGRWQWYKKS 62 (180)
Q Consensus 17 glilsflsvivspvysyfrhtvaetpkimwkafkkssgrwqwykks 62 (180)
..|..-|--.+.-.|.-.--.-..||.|+-+..=+.||.|+.|+..
T Consensus 271 ~~i~~~le~~~r~~~~~~Gy~eV~TP~i~~~~Lw~~SGH~~~Y~e~ 316 (642)
T PRK03772 271 WTIFRELEVFVRSKLKEYQYQEVKGPFMMDRVLWEKTGHWDNYADA 316 (642)
T ss_pred HHHHHHHHHHHHHHHHHCCCEEEECCHHCCHHHHHHCCHHHHHHCC
T ss_conf 8999999999999999869859855432137788734447664103
No 17
>PRK04483 threonyl-tRNA synthetase; Validated
Probab=29.22 E-value=35 Score=15.51 Aligned_cols=47 Identities=19% Similarity=0.319 Sum_probs=29.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHCCCCCHHHHHH
Q ss_conf 35999999999988999988655206789999976057730555655
Q gi|254780204|r 16 GGLILSFLSVIVSPVYSYFRHTVAETPKIMWKAFKKSSGRWQWYKKS 62 (180)
Q Consensus 16 gglilsflsvivspvysyfrhtvaetpkimwkafkkssgrwqwykks 62 (180)
|..|..-|.-.+.-.+.-.--.-..||.|.-+..=+.||.|+.|+..
T Consensus 270 G~~i~~~le~~~r~~~~~~Gy~eV~tP~i~~~~Lw~~SGH~~~Y~e~ 316 (634)
T PRK04483 270 GWSLWQVVEQYMRKVYRDSGYGEVRCPQILDVSLWQKSGHWDNYQDA 316 (634)
T ss_pred HHHHHHHHHHHHHHHHHHCCCEEEECCEECCHHHHHHCCCHHHHHHC
T ss_conf 89999999999999999829959988625137787625616455303
No 18
>COG0381 WecB UDP-N-acetylglucosamine 2-epimerase [Cell envelope biogenesis, outer membrane]
Probab=29.14 E-value=27 Score=16.20 Aligned_cols=42 Identities=24% Similarity=0.369 Sum_probs=34.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHCCCCCCCHHHHH
Q ss_conf 6589987667999999999999723321761530000016699
Q gi|254780204|r 80 ASFVLSLTSACLVVTAILAILLSIAIPTIEEGMTMNDIKYERK 122 (180)
Q Consensus 80 asfvlsltsaclvvtailaillsiaiptiEE~l~lNDIKYE~~ 122 (180)
+..|..=|..||.. |+-|-.+.|.+-.||-|+|-.|.-+.||
T Consensus 95 ~VlVhGDT~t~lA~-alaa~~~~IpV~HvEAGlRt~~~~~PEE 136 (383)
T COG0381 95 LVLVHGDTNTTLAG-ALAAFYLKIPVGHVEAGLRTGDLYFPEE 136 (383)
T ss_pred EEEEECCCCHHHHH-HHHHHHHCCCEEEEECCCCCCCCCCCHH
T ss_conf 89991785368899-9999986893688742544478778379
No 19
>pfam06755 DUF1219 Protein of unknown function (DUF1219). This family consists of several hypothetical proteins which seem to be specific to the Enterobacteria Escherichia coli and Shigella flexneri. Family members are often known as YeeV proteins and are around 125 residues in length. The function of this family is unknown.
Probab=29.08 E-value=27 Score=16.19 Aligned_cols=24 Identities=25% Similarity=0.459 Sum_probs=20.4
Q ss_pred HHHCCCCCCCHHHHHHHHHHHHHH
Q ss_conf 761530000016699999988535
Q gi|254780204|r 108 IEEGMTMNDIKYERKQVISRKAKE 131 (180)
Q Consensus 108 iEE~l~lNDIKYE~~Q~I~~K~KE 131 (180)
-.-|+++||--+.++.+|+..|..
T Consensus 32 ~HYGLtLnDTpf~de~vI~ehIea 55 (109)
T pfam06755 32 QHYGLTLNDTPFSDETVIQEHIEA 55 (109)
T ss_pred HHCCCEECCCCCCCHHHHHHHHHC
T ss_conf 863970078877408999999992
No 20
>TIGR01844 type_I_sec_TolC type I secretion outer membrane protein, TolC family; InterPro: IPR010130 Members of group of are outer membrane proteins from the TolC family within the RND (Resistance-Nodulation-cell Division) efflux systems. These proteins, unlike the NodT family, appear not to be lipoproteins. All are believed to participate in type I protein secretion, an ABC transporter system for protein secretion without cleavage of a signal sequence, although they may, like TolC, participate also in the efflux of smaller molecules as well. This family includes the well-documented examples TolC (Escherichia coli), PrtF (Erwinia), and AprF (Pseudomonas aeruginosa).; GO: 0015031 protein transport, 0019867 outer membrane.
Probab=28.95 E-value=11 Score=18.67 Aligned_cols=35 Identities=26% Similarity=0.257 Sum_probs=27.2
Q ss_pred HHHHHHHHHHHHHHCCCHHCCCCCCCCCHHHHHHH
Q ss_conf 99999998989860520000155553201210461
Q gi|254780204|r 136 ESLYQISEFAACLEHPNRYWHTDSASIGFRVPIYL 170 (180)
Q Consensus 136 E~L~q~sE~~ACL~~~~RYwhtdsasigfrvpiyl 170 (180)
.+....+..++.+-|+|.|-.|+|..|.+++|||-
T Consensus 276 ~~~~~~~~g~~~~~~~D~~~~~~s~~l~~~~PlY~ 310 (437)
T TIGR01844 276 ASGGSGNSGAATTQQYDDYSDTDSIGLNVSIPLYQ 310 (437)
T ss_pred CCCCCCCCCCCCCCCCCCCCEEEEEEEEEEEEEEC
T ss_conf 43433121234433356401000356777520223
No 21
>TIGR03603 cyclo_dehy_ocin bacteriocin biosynthesis cyclodehydratase, SagC family. Members of this protein family include enzymes related to SagC, a cyclodehydratase involved in the biosynthesis of streptolysin S in Streptococcus pyogenes from the protoxin polypeptide (product of the sagA gene). This protein family serves as a marker for widely distributed prokaryotic systems for making a general class of heterocycle-containing bacteriocins. Note that this model does not find all possible examples of bacteriocin biosynthesis cyclodehydratases, an in particular misses the E. coli plasmid protein McbB of microcin B17 biosynthesis.
Probab=28.51 E-value=40 Score=15.16 Aligned_cols=38 Identities=34% Similarity=0.483 Sum_probs=29.5
Q ss_pred HHHHHHHHCCHHHH-------------HCCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf 99999972332176-------------153000001669999998853555
Q gi|254780204|r 96 ILAILLSIAIPTIE-------------EGMTMNDIKYERKQVISRKAKEKD 133 (180)
Q Consensus 96 ilaillsiaiptiE-------------E~l~lNDIKYE~~Q~I~~K~KE~~ 133 (180)
....+|+|-.||.| -|-+.|.+|||+.+.-+|++-++-
T Consensus 266 l~GrvL~iylPtlEiq~qdilr~s~C~aCg~isk~k~~eqnistr~Iv~~l 316 (318)
T TIGR03603 266 FEGRLLSINLPTLEIQFQDILKQSCCSTCGTFNKIKFEEQNISTRNIVKEL 316 (318)
T ss_pred EEEEEEEEECCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 331258997152788702000167870566888867777421599999996
No 22
>TIGR02484 CitB CitB domain protein; InterPro: IPR012830 This entry identifies proteins that are decribed as citrate utilization protein B, restricted to the proteobacteria. CitB has been identified in Salmonella and Escherichia coli as the signal transduction component of a two-component system for citrate in which CitA acts as a citrate transporter. This domain is also a C-terminal domain in the Rhodobacter capsulatus CobZ gene, which in most other species exists as the separate CitB gene adjacent to CobZ. CobZ is essential for cobalamin biosynthesis (by knockout of the R. capsulatus gene ) and is complemented by the characterised precorrin 3B synthase CobG. The enzyme has been shown to contain flavin, heme and Fe-S cluster cofactors and is believed to require dioxygen as a substrate..
Probab=28.44 E-value=47 Score=14.72 Aligned_cols=24 Identities=33% Similarity=0.604 Sum_probs=20.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 233599999999998899998865
Q gi|254780204|r 14 DYGGLILSFLSVIVSPVYSYFRHT 37 (180)
Q Consensus 14 dygglilsflsvivspvysyfrht 37 (180)
-.||..|+|+|.++.-||-|.=-.
T Consensus 228 ~agGF~Lc~~ST~~g~~YH~~LG~ 251 (392)
T TIGR02484 228 TAGGFMLCFLSTVAGTVYHHLLGR 251 (392)
T ss_pred HHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf 987999999999999999987274
No 23
>COG4721 ABC-type cobalt transport system, predicted permease component [Inorganic ion transport and metabolism]
Probab=26.76 E-value=50 Score=14.53 Aligned_cols=44 Identities=43% Similarity=0.435 Sum_probs=35.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCH
Q ss_conf 65578999775579999864658998766799999999999972332
Q gi|254780204|r 60 KKSFQYLLFFSGLSYLLFHSASFVLSLTSACLVVTAILAILLSIAIP 106 (180)
Q Consensus 60 kksfqyllffsglsyllfhsasfvlsltsaclvvtailaillsiaip 106 (180)
--||-|-.|++| |+ -.|.+|+|++----|.--|++|-+||-++-
T Consensus 131 ~~sf~~eyf~~G--yl-a~s~~fnli~lv~rlISga~laglLs~~lv 174 (192)
T COG4721 131 LASFVYEYFKLG--YL-AFSLGFNLILLVVRLISGAFLAGLLSRALV 174 (192)
T ss_pred HHHHHHHHHHHH--HH-HHCCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 899999999970--77-643155678999999999999999999999
No 24
>PRK12444 threonyl-tRNA synthetase; Reviewed
Probab=26.73 E-value=40 Score=15.13 Aligned_cols=27 Identities=30% Similarity=0.561 Sum_probs=21.0
Q ss_pred HHHHCHHHHHHHHHHCCCCCHHHHHHH
Q ss_conf 552067899999760577305556557
Q gi|254780204|r 37 TVAETPKIMWKAFKKSSGRWQWYKKSF 63 (180)
Q Consensus 37 tvaetpkimwkafkkssgrwqwykksf 63 (180)
.-..||.|+-+..-+.||.|+.|+.+.
T Consensus 294 ~eV~TP~i~~~~Lw~~SGH~~~Y~e~M 320 (639)
T PRK12444 294 QEVRTPFMMNQELWERSGHWGHYKDNM 320 (639)
T ss_pred EEECCCEEEHHHHHHHCCHHHHHHHCC
T ss_conf 782286662156876166043333027
No 25
>PRK10506 hypothetical protein; Provisional
Probab=24.10 E-value=51 Score=14.48 Aligned_cols=20 Identities=20% Similarity=0.267 Sum_probs=16.7
Q ss_pred HHHHHHHHHHHHHHCCHHHH
Q ss_conf 99999999999972332176
Q gi|254780204|r 90 CLVVTAILAILLSIAIPTIE 109 (180)
Q Consensus 90 clvvtailaillsiaiptiE 109 (180)
-|||-+|++||+.+|+|.--
T Consensus 12 llvvi~ii~il~~~a~p~~~ 31 (155)
T PRK10506 12 TLVAMTLVVILSAWGLYGWQ 31 (155)
T ss_pred HHHHHHHHHHHHHHHHHHHH
T ss_conf 99999999999988777799
No 26
>KOG2653 consensus
Probab=23.91 E-value=57 Score=14.21 Aligned_cols=55 Identities=29% Similarity=0.438 Sum_probs=36.8
Q ss_pred CHHHHHHHHH-------------HHHHHHHHHHHHHHHHHHHHHHHH-HHCHHHHHHHHHHCCCCCHHH
Q ss_conf 0113334532-------------335999999999988999988655-206789999976057730555
Q gi|254780204|r 5 GYDILKATVD-------------YGGLILSFLSVIVSPVYSYFRHTV-AETPKIMWKAFKKSSGRWQWY 59 (180)
Q Consensus 5 gydilkatvd-------------ygglilsflsvivspvysyfrhtv-aetpkimwkafkkssgrwqwy 59 (180)
.||++|.... -+|-.-|||--|...+..|-...- .-.+||+=++=.|..|.|.-.
T Consensus 204 aY~vlk~~~gls~~eia~vF~~WN~geleSfLieIT~dIlk~~d~~G~~lv~kI~D~aGqKGTGkwt~~ 272 (487)
T KOG2653 204 AYDVLKSVLGLSNDEIAEVFDDWNKGELESFLIEITADILKFKDEDGKPLVDKILDKAGQKGTGKWTVI 272 (487)
T ss_pred HHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHCEECCCCCCHHHHHHHHHCCCCCCHHHHH
T ss_conf 999999845866788999997643331668999986887600056787168999864168776289999
No 27
>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR; InterPro: IPR010242 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] . FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins , . It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly . The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA . SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA , acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins . Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen . This entry describes IscR, an iron-sulphur binding transcription factor of the ISC iron-sulphur cluster assembly system.; GO: 0003690 double-stranded DNA binding, 0003700 transcription factor activity, 0006355 regulation of transcription DNA-dependent.
Probab=23.21 E-value=27 Score=16.19 Aligned_cols=35 Identities=31% Similarity=0.322 Sum_probs=25.6
Q ss_pred HHHHHHHHHHHHHHCCHHHHHCCCCCCCHHHHHHHHHHHHH
Q ss_conf 99999999999972332176153000001669999998853
Q gi|254780204|r 90 CLVVTAILAILLSIAIPTIEEGMTMNDIKYERKQVISRKAK 130 (180)
Q Consensus 90 clvvtailaillsiaiptiEE~l~lNDIKYE~~Q~I~~K~K 130 (180)
-.-|||+|. +|+-.-.+-.+|+||- ++|-||+--=
T Consensus 8 RYAVTAmLD----lA~~~~~GPV~La~IS--~RQ~ISLSYL 42 (140)
T TIGR02010 8 RYAVTAMLD----LALNAETGPVTLADIS--ERQNISLSYL 42 (140)
T ss_pred HHHHHHHHH----HHHHCCCCCCCHHHHH--HHCCCCHHHH
T ss_conf 689999999----9973058991667654--4216135679
No 28
>PRK00425 rpoZ DNA-directed RNA polymerase subunit omega; Reviewed
Probab=23.08 E-value=47 Score=14.74 Aligned_cols=30 Identities=20% Similarity=0.335 Sum_probs=22.1
Q ss_pred HHCCHHHHHCCCCCCCHHHHHHHHHHHHHH
Q ss_conf 723321761530000016699999988535
Q gi|254780204|r 102 SIAIPTIEEGMTMNDIKYERKQVISRKAKE 131 (180)
Q Consensus 102 siaiptiEE~l~lNDIKYE~~Q~I~~K~KE 131 (180)
|+.-|+|++||..-|-+|.---+-+..+.+
T Consensus 1 ~M~~Psid~ll~kvdsrY~LV~~aAKRARq 30 (69)
T PRK00425 1 SMINPSIVDLLEKVDDRYSLVILTAKRARQ 30 (69)
T ss_pred CCCCCCHHHHHHHCCCHHHHHHHHHHHHHH
T ss_conf 987787999998457842468999999999
No 29
>COG1758 RpoZ DNA-directed RNA polymerase, subunit K/omega [Transcription]
Probab=22.94 E-value=59 Score=14.09 Aligned_cols=31 Identities=29% Similarity=0.401 Sum_probs=24.9
Q ss_pred HCCHHHHHCCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf 2332176153000001669999998853555
Q gi|254780204|r 103 IAIPTIEEGMTMNDIKYERKQVISRKAKEKD 133 (180)
Q Consensus 103 iaiptiEE~l~lNDIKYE~~Q~I~~K~KE~~ 133 (180)
.+.|++++|+..-+-|||.--++...|++=.
T Consensus 1 m~~~~~~~l~~~~~~ryelv~~aa~RA~Ql~ 31 (74)
T COG1758 1 MARPTIEDLLDKVGNRYELVVVAAKRARQLA 31 (74)
T ss_pred CCCCCHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 9856799986203578899999999999998
No 30
>TIGR00709 dat 2,4-diaminobutyrate 4-transaminase; InterPro: IPR004637 This is a very small family, with two known examples at the time of model creation. This enzyme is a pyridoxal phosphate-containing class III aminotransferase and is quite similar to 4-aminobutyrate aminotransferase (2.6.1.19 from EC). Diaminobutyrate-2-oxoglutarate transaminase (2.6.1.76 from EC) is a homotetramer which catalyses the conversion of L-2,4-diaminobutyrate and 2-oxoglutarate to L-glutamate and L-aspartic 4-semialdehyde during 1,3-diaminopropane biosynthesis.; GO: 0008483 transaminase activity, 0009058 biosynthetic process.
Probab=22.87 E-value=15 Score=17.81 Aligned_cols=50 Identities=34% Similarity=0.376 Sum_probs=40.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999988999988655206789999976057730555655789997755799998
Q gi|254780204|r 20 LSFLSVIVSPVYSYFRHTVAETPKIMWKAFKKSSGRWQWYKKSFQYLLFFSGLSYLLF 77 (180)
Q Consensus 20 lsflsvivspvysyfrhtvaetpkimwkafkkssgrwqwykksfqyllffsglsyllf 77 (180)
|+-.+..-|.|-||-|.- =-+|.|..|-|-|--..-+|+=||+|-.-|-+
T Consensus 4 L~~~~~~ES~VRSY~R~l--------P~~~~~A~G~~~~D~~G~~Y~DflaGAG~L~~ 53 (445)
T TIGR00709 4 LSRQNEMESNVRSYPRKL--------PLAFAKAQGCWVTDVEGKEYLDFLAGAGTLAL 53 (445)
T ss_pred HHHHHHHCCCCCCCCCCC--------CHHHHHCCCCEEEECCCCCHHHHHHHHHHHCC
T ss_conf 002442101113122344--------12424017427984277502122210002104
No 31
>TIGR02099 TIGR02099 conserved hypothetical protein TIGR02099; InterPro: IPR011836 This entry describes a family of long proteins, over 1250 amino acids in length and present in the Proteobacteria. The degree of sequence similarity is low between sequences from different genera. Apparent membrane-spanning regions at the N-terminus and C-terminus suggest the protein is inserted into (or exported through) the membrane..
Probab=22.26 E-value=61 Score=14.01 Aligned_cols=31 Identities=39% Similarity=0.503 Sum_probs=27.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCHHHHHC
Q ss_conf 5899876679999999999997233217615
Q gi|254780204|r 81 SFVLSLTSACLVVTAILAILLSIAIPTIEEG 111 (180)
Q Consensus 81 sfvlsltsaclvvtailaillsiaiptiEE~ 111 (180)
-+.+++-.+|+||.|.+.-++.++.|-++|-
T Consensus 5 ~~~~~l~A~~lV~~AL~Vs~~r~lLP~~d~~ 35 (1362)
T TIGR02099 5 RIALSLLALILVVAALLVSLLRQLLPLVDEY 35 (1362)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 8999999999999999999999862345544
No 32
>TIGR02349 DnaJ_bact chaperone protein DnaJ; InterPro: IPR012724 Molecular chaperones are a diverse family of proteins that function to protect proteins in the intracellular milieu from irreversible aggregation during synthesis and in times of cellular stress. The bacterial molecular chaperone DnaK is an enzyme that couples cycles of ATP binding, hydrolysis, and ADP release by an N-terminal ATP-hydrolizing domain to cycles of sequestration and release of unfolded proteins by a C-terminal substrate binding domain. Dimeric GrpE is the co-chaperone for DnaK, and acts as a nucleotide exchange factor, stimulating the rate of ADP release 5000-fold . DnaK is itself a weak ATPase; ATP hydrolysis by DnaK is stimulated by its interaction with another co-chaperone, DnaJ. Thus the co-chaperones DnaJ and GrpE are capable of tightly regulating the nucleotide-bound and substrate-bound state of DnaK in ways that are necessary for the normal housekeeping functions and stress-related functions of the DnaK molecular chaperone cycle. Besides stimulating the ATPase activity of DnaK through its J-domain, DnaJ also associates with unfolded polypeptide chains and prevents their aggregation . Thus, DnaK and DnaJ may bind to one and the same polypeptide chain to form a ternary complex. The formation of a ternary complex may result in cis-interaction of the J-domain of DnaJ with the ATPase domain of DnaK. An unfolded polypeptide may enter the chaperone cycle by associating first either with ATP-liganded DnaK or with DnaJ. DnaK interacts with both the backbone and side chains of a peptide substrate; it thus shows binding polarity and admits only L-peptide segments. In contrast, DnaJ has been shown to bind both L- and D-peptides and is assumed to interact only with the side chains of the substrate. DnaJ comprises a 70-residue N-terminal domain (the J-domain); a 30-residue glycine-rich region (the G-domain); a central domain containing 4 repeats of a CxxCxGxG motif (the CRR-domain); and a 120-170 residue C-terminal region. The J- and CRR-domains are found in many prokaryotic and eukaryotic proteins , either together or separately. This entry mostly consists of bacterial forms of DnaJ. The three components of the DnaK-DnaJ-GrpE system are typically encoded by consecutive genes. DnaJ homologues occur in many genomes, typically not encoded near DnaK and GrpE-like genes. Most such proteins are not included in this family, though some chloroplast homologues are included; GO: 0005524 ATP binding, 0051082 unfolded protein binding, 0006457 protein folding, 0009408 response to heat.
Probab=20.86 E-value=45 Score=14.83 Aligned_cols=40 Identities=25% Similarity=0.328 Sum_probs=30.9
Q ss_pred HHHHHHH---HHH--HHHHHHHHHHHHHHHHHHH------CCCHHCCCCCC
Q ss_conf 9999998---853--5558899999998989860------52000015555
Q gi|254780204|r 121 RKQVISR---KAK--EKDLEESLYQISEFAACLE------HPNRYWHTDSA 160 (180)
Q Consensus 121 ~~Q~I~~---K~K--E~~~~E~L~q~sE~~ACL~------~~~RYwhtdsa 160 (180)
||.|.+- +-| +++|||+--.|+||-.-|. +||||=|..-.
T Consensus 22 RkLA~kYHPD~Nkgn~~~AEeKFKEi~EAYeVLSD~~KRa~YDqfGh~g~~ 72 (386)
T TIGR02349 22 RKLAKKYHPDRNKGNDKEAEEKFKEINEAYEVLSDPEKRAQYDQFGHAGFN 72 (386)
T ss_pred HHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCC
T ss_conf 988885178888888837567657888775306897899874134365516
No 33
>pfam04529 Herpes_U59 Herpesvirus U59 protein. The proteins in this family have no known function. Cytomegalovirus UL88 is also a member of this family.
Probab=20.80 E-value=20 Score=17.03 Aligned_cols=38 Identities=29% Similarity=0.439 Sum_probs=24.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH------HHCCHHHHHCCCCCCCH
Q ss_conf 46589987667999999999999------72332176153000001
Q gi|254780204|r 79 SASFVLSLTSACLVVTAILAILL------SIAIPTIEEGMTMNDIK 118 (180)
Q Consensus 79 sasfvlsltsaclvvtailaill------siaiptiEE~l~lNDIK 118 (180)
+++|.+ ...|+-..+-||.+| .-..|++|+-+.++|--
T Consensus 259 ~~~F~l--H~~~~~na~~lA~iLn~ly~~q~~Lp~ve~RlD~~d~~ 302 (365)
T pfam04529 259 SAAFLL--HRKTMKNAACLALILNSLYEHQERLPAVERRLDEHDPI 302 (365)
T ss_pred CCHHHH--HHHHHHHHHHHHHHHHHHHHHHHHCCCHHHCCCCCCHH
T ss_conf 602889--99999999999999999999875078544412668848
No 34
>cd00771 ThrRS_core Threonyl-tRNA synthetase (ThrRS) class II core catalytic domain. ThrRS is a homodimer. It is responsible for the attachment of threonine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs in the core domain.
Probab=20.37 E-value=52 Score=14.43 Aligned_cols=47 Identities=26% Similarity=0.386 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHCCCCCHHHHHH
Q ss_conf 35999999999988999988655206789999976057730555655
Q gi|254780204|r 16 GGLILSFLSVIVSPVYSYFRHTVAETPKIMWKAFKKSSGRWQWYKKS 62 (180)
Q Consensus 16 gglilsflsvivspvysyfrhtvaetpkimwkafkkssgrwqwykks 62 (180)
|..|..-|.-.+.-.+.-.-..-..||-|.=+..-+.||.|..|+..
T Consensus 29 G~~i~~~L~~~ir~~~~~~Gy~eV~tP~i~~~~Lw~~SGH~~~y~e~ 75 (298)
T cd00771 29 GAIIRNELEDFLRELQRKRGYQEVETPIIYNKELWETSGHWDHYREN 75 (298)
T ss_pred HHHHHHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHCCCCCCCCCC
T ss_conf 89999999999999999869989988612665567547763113685
Done!