Query psy1882
Match_columns 233
No_of_seqs 173 out of 650
Neff 4.9
Searched_HMMs 46136
Date Fri Aug 16 18:41:15 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1882.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1882hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3274|consensus 100.0 1.5E-69 3.3E-74 463.6 15.4 196 36-231 9-204 (210)
2 PF01871 AMMECR1: AMMECR1; In 100.0 7.3E-57 1.6E-61 381.9 14.4 165 44-219 1-171 (171)
3 TIGR00296 uncharacterized prot 100.0 1.1E-54 2.4E-59 376.9 17.3 170 41-220 9-191 (200)
4 PRK00801 hypothetical protein; 100.0 8.1E-54 1.8E-58 371.8 17.7 168 41-219 9-186 (201)
5 COG2078 AMMECR1 Uncharacterize 100.0 9.3E-50 2E-54 345.2 18.1 174 41-221 10-192 (203)
6 PRK03881 hypothetical protein; 100.0 5.7E-44 1.2E-48 341.5 17.2 162 41-218 299-467 (467)
7 PRK04219 rpl5p 50S ribosomal p 48.2 37 0.00081 29.6 4.9 106 84-194 64-172 (177)
8 PF03544 TonB_C: Gram-negative 22.4 1E+02 0.0022 21.5 2.9 53 75-132 18-71 (79)
9 KOG1612|consensus 19.6 1E+02 0.0022 28.8 2.9 56 77-140 131-186 (288)
10 PF06102 DUF947: Domain of unk 19.4 50 0.0011 28.2 0.8 13 111-123 32-44 (168)
No 1
>KOG3274|consensus
Probab=100.00 E-value=1.5e-69 Score=463.60 Aligned_cols=196 Identities=61% Similarity=1.063 Sum_probs=188.2
Q ss_pred CCcccChhHHhHHHHHHHHhhcCCCCCCCCCCCCCCCCceEEEEEeCCCCcceeeeccCCCccHHHHHHHHHHHhhhcCC
Q psy1882 36 VDKIAQPEMCFFCFDVLYCHLHSLEPPNPPSGISNDAFPLFVTWKIGKDQRLRGCIGTFNAINLHGGLREYAVTSAFKDS 115 (233)
Q Consensus 36 ~~~~~~~~m~~~cfd~L~~~L~~~~~p~~p~~~~~~~~g~FVTl~~~~~g~LRGCIGt~~~~~L~~~i~~~Ai~AA~~Dp 115 (233)
...+++.+||+||||+|.++|++.+.|..|+.+.+..+|+||||+++.+.+||||||||+++||+.++.+||+.|||+|.
T Consensus 9 ~~~~~~~~ma~ycF~vl~~~ln~~k~p~~~~~~~~~~~PLFvtwk~g~dkrLRGCIGTFsam~L~~Gl~eYaltsAl~Ds 88 (210)
T KOG3274|consen 9 EMTSANSEMAVYCFDVLYAHLNNEKSPSLPPDFRNRLYPLFVTWKKGHDKRLRGCIGTFSAMPLHSGLREYALTSALKDS 88 (210)
T ss_pred cccccCcceEEEehhhhhhhhccccCCCcchhhhccCcceeEEeccCCCcccccceeehhhcchhhhHHHHHHHHHhhcc
Confidence 35678999999999999999998776665669999999999999998899999999999999999999999999999999
Q ss_pred CCCCCChhccccceEEEEeeecccCCCCcccccccccceEEEEEecCCCeeeeEEcCccCccCCCCHHHHHHHHHHhcCC
Q psy1882 116 RFNPITVDEFSKLHVSVSILRHFEDGNDYTDWKIGVHGIRIEFHNERGNKRTATYLPEVAPEQGWDQIQTIDSLLRKGGF 195 (233)
Q Consensus 116 RF~Pl~~~EL~~L~ieVSvL~~~e~~~~~~d~~~G~hGl~i~f~~~~G~~~~atfLP~Va~EqgW~~~~~l~~l~~KaG~ 195 (233)
||+||+++||++|.|+||||++||++.|++||++|+|||+|+|.+++|.+|+|||||+||.||||||+++|++|+|||||
T Consensus 89 RF~PIsr~ELp~L~CsvslL~nFE~i~d~lDWevG~HGIrieF~~e~g~krsATyLPeVa~EQgWd~~eTidsLirKaGY 168 (210)
T KOG3274|consen 89 RFPPISREELPSLQCSVSLLTNFEDIFDYLDWEVGVHGIRIEFTNETGTKRSATYLPEVAAEQGWDQIETIDSLIRKAGY 168 (210)
T ss_pred cCCCCChhhcCceEEEEEeeccchhcccccceeeccceEEEEEEcCCCcEeeeeecccchhhcCCcHHHHHHHHHHhcCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCcccCCceEEEEEEEEEEEeeHHHHHHHHhhC
Q psy1882 196 KGPITPDIRCNIKLTRYQSELVSVSYQDYLNHWKNG 231 (233)
Q Consensus 196 ~~~~~~~~~~~i~l~Ryqs~k~~~sy~ey~~~~~~~ 231 (233)
+|.|++++++.|+++||++++++++|+||++.++.+
T Consensus 169 ~g~It~~~r~~I~ltRY~S~k~~~~Y~EY~~~~q~~ 204 (210)
T KOG3274|consen 169 KGPITEELRKSIKLTRYRSEKISITYEEYLAYLQHH 204 (210)
T ss_pred CCccCHHHHhheeeeEeeceeeeeeHHHHHHHHHhh
Confidence 999999999999999999999999999999999874
No 2
>PF01871 AMMECR1: AMMECR1; InterPro: IPR002733 The contiguous gene deletion syndrome is characterised by Alport syndrome (A), mental retardation (M), midface hypoplasia (M), and elliptocytosis (E), as well as generalized hypoplasia and cardiac abnormalities. It is caused by a deletion in Xq22.3, comprising several genes including AMME chromosomal region gene 1 (AMMECR1), which encodes a protein with a nuclear location and presently unknown function. The C-terminal region of AMMECR1 (from residue 122 to 333) is well conserved, and homologues appear in species ranging from bacteria and archaea to eukaryotes. The high level of conservation of the AMMECR1 domain points to a basic cellular function, potentially in either the transcription, replication, repair or translation machinery [, ]. The AMMECR1 domain contains a 6-amino-acid motif (LRGCIG) that might be functionally important since it is strikingly conserved throughout evolution []. The AMMECR1 domain consists of two distinct subdomains of different sizes. The large subdomain, which contains both the N- and C-terminal regions, consists of five alpha-helices and five beta-strands. These five beta-strands form an antiparallel beta-sheet. The small subdomain consists of four alpha-helices and three beta-strands, and these beta-strands also form an antiparallel beta-sheet. The conserved 'LRGCIG' motif is located at beta(2) and its N-terminal loop, and most of the side chains of these residues point toward the interface of the two subdomains. The two subdomains are connected by only two loops, and the interaction between the two subdomains is not strong. Thus, these subdomains may move dynamically when the substrate enters the cleft. The size of the cleft suggests that the substrate is large, e.g., the substrate may be a nucleic acid or protein. However, the inner side of the cleft is not filled with positively charged residues, and therefore it is unlikely that negatively charged nucleic acids such as DNA or RNA interact at this site []. ; PDB: 1WSC_B 1VAJ_A 1ZQ7_D.
Probab=100.00 E-value=7.3e-57 Score=381.93 Aligned_cols=165 Identities=38% Similarity=0.598 Sum_probs=130.5
Q ss_pred HHhHHHHHHHHhhcCCCC----CCCCCCCCCCCCceEEEEEeCCCCcceeeeccCCC-ccHHHHHHHHHHHhhhcCCCCC
Q psy1882 44 MCFFCFDVLYCHLHSLEP----PNPPSGISNDAFPLFVTWKIGKDQRLRGCIGTFNA-INLHGGLREYAVTSAFKDSRFN 118 (233)
Q Consensus 44 m~~~cfd~L~~~L~~~~~----p~~p~~~~~~~~g~FVTl~~~~~g~LRGCIGt~~~-~~L~~~i~~~Ai~AA~~DpRF~ 118 (233)
||.+||++|.++|.+.+. ++.++.+ .+++|+||||++ +|+||||||||.| +||+++|++||++|||+||||+
T Consensus 1 Ll~~Ar~ai~~~l~~~~~~~~~~~~~~~l-~~~~g~FVTl~~--~g~LRGCIGt~~p~~~L~~~v~~~A~~AA~~DpRF~ 77 (171)
T PF01871_consen 1 LLRLAREAIESYLRGGPLPPPPPPLPPEL-SEPRGVFVTLKK--DGELRGCIGTFEPVRPLAEDVIENAIAAAFEDPRFP 77 (171)
T ss_dssp HHHHHHHHHHHHHHHSSSCCCCCT--GGG-GSBEEEEEEEEE--CCCEEEEEEESSSESBHHHHHHHHHHHHHHT-TTS-
T ss_pred CHHHHHHHHHHHHcCCCCCCCCCCCChhh-cCceeEEEEEEE--CCEEEEEeccCCcchhHHHHHHHHHHHHhhCCCCCC
Confidence 789999999999987552 2223344 669999999995 8999999999999 8999999999999999999999
Q ss_pred CCChhccccceEEEEeeecccCCCCcccccccccceEEEEEecCCCeeeeEEcCccCccCCCCHHHHHHHHHHhcCCCCC
Q psy1882 119 PITVDEFSKLHVSVSILRHFEDGNDYTDWKIGVHGIRIEFHNERGNKRTATYLPEVAPEQGWDQIQTIDSLLRKGGFKGP 198 (233)
Q Consensus 119 Pl~~~EL~~L~ieVSvL~~~e~~~~~~d~~~G~hGl~i~f~~~~G~~~~atfLP~Va~EqgW~~~~~l~~l~~KaG~~~~ 198 (233)
||+.+||++|.|+||||++|+++.++.+|++|+|||+|++ |. |+||||||||.||+||+++||+++|+|||++
T Consensus 78 Pl~~~El~~l~ieVSvL~~~~~i~~~~~~~~g~~Glil~~----~~-~~~~~LPqVa~E~~w~~~~fl~~l~~KAG~~-- 150 (171)
T PF01871_consen 78 PLTPSELPELSIEVSVLSPPEPISDPEDWEPGRHGLILEF----GG-YRGTFLPQVAWEQGWDPEEFLRHLCRKAGLP-- 150 (171)
T ss_dssp ---GGGGGGEEEEEEEE---EE--GGGG--TTT-EEEEEE----TT-EEEEE-THHHHHTT--HHHHHHHHHHHTTS---
T ss_pred CCCHHHHcccEEEEEeccCcEEcCCHHHcccCcceeEEEe----cC-cceEECCCchhhcCCCHHHHHHHHHHHCCCC--
Confidence 9999999999999999999999999999999999999996 54 6899999999999999999999999999996
Q ss_pred CCccc-CCceEEEEEEEEEEEe
Q psy1882 199 ITPDI-RCNIKLTRYQSELVSV 219 (233)
Q Consensus 199 ~~~~~-~~~i~l~Ryqs~k~~~ 219 (233)
.+.| ..+++++|||+++|+.
T Consensus 151 -~~~w~~~~~~~~rf~~~~f~E 171 (171)
T PF01871_consen 151 -PDAWKSPDIKLYRFQAEVFSE 171 (171)
T ss_dssp -TTCCCTTTSEEEEE-EEEEEE
T ss_pred -ccccccCCeEEEEEEEEEEeC
Confidence 2334 5689999999999973
No 3
>TIGR00296 uncharacterized protein, PH0010 family. Members of this functionally uncharacterized protein family have been crystallized from Pyrococcus Horikoshii, Methanosarcina Mazei, and Sulfolobus Tokodaii.
Probab=100.00 E-value=1.1e-54 Score=376.93 Aligned_cols=170 Identities=29% Similarity=0.455 Sum_probs=147.2
Q ss_pred ChhHHhHHHHHHHHhhcCCCCCCCCCCC---CCCCCceEEEEEeCCCCc--ceeeeccCCC-ccHHHHHHHHHHHhhhcC
Q psy1882 41 QPEMCFFCFDVLYCHLHSLEPPNPPSGI---SNDAFPLFVTWKIGKDQR--LRGCIGTFNA-INLHGGLREYAVTSAFKD 114 (233)
Q Consensus 41 ~~~m~~~cfd~L~~~L~~~~~p~~p~~~---~~~~~g~FVTl~~~~~g~--LRGCIGt~~~-~~L~~~i~~~Ai~AA~~D 114 (233)
...||.+||++|.++|.+..++++|+.+ ++++.||||||++ +|+ |||||||+.| .||+++|++||++|||+|
T Consensus 9 ~~~l~~lAr~ai~~~l~~~~~~~~~~~~p~~l~~~~g~FVTl~~--~~~~~LRGCIGs~~p~~pL~~~v~~~A~~AA~~D 86 (200)
T TIGR00296 9 GSSAVRYARYAIESHLNGGKSSRLYPDLPIVFNEKRGVFITLKK--KGNKHLRGCIGTPEPVMPLIEAIEEAAISAATED 86 (200)
T ss_pred HHHHHHHHHHHHHHHHccCCCCCCCccCChhhCCcccEEEEEEE--CCCcCCCcccccCCCcccHHHHHHHHHHHHHcCC
Confidence 4669999999999999865433222233 3789999999985 566 9999999999 799999999999999999
Q ss_pred CCCCCCChhccccceEEEEeeecccCC------CCcccccccccceEEEEEecCCCeeeeEEcCccCccCCCCHHHHHHH
Q psy1882 115 SRFNPITVDEFSKLHVSVSILRHFEDG------NDYTDWKIGVHGIRIEFHNERGNKRTATYLPEVAPEQGWDQIQTIDS 188 (233)
Q Consensus 115 pRF~Pl~~~EL~~L~ieVSvL~~~e~~------~~~~d~~~G~hGl~i~f~~~~G~~~~atfLP~Va~EqgW~~~~~l~~ 188 (233)
|||+||+.+||++|.|+||||++++++ ++..+|+||+|||+|++ |. |+||||||||.||+||+++||++
T Consensus 87 pRF~Pl~~~EL~~l~ieVSvL~~~e~i~~~~~~~~~~~~~~G~hGlii~~----g~-~~gt~LPqVa~E~~wd~~~fl~~ 161 (200)
T TIGR00296 87 PRFPPVQLEELDDIKVEVSILTPPETIFVGGPKDYPFDIEIGRHGLIVEF----GP-KRGLLLPQVAVEYGWDAEEFLAN 161 (200)
T ss_pred CCCCCCChHHhCCcEEEEEeCCCCEEcccCCccccHHHcccccceEEEEE----CC-ccEEECCccHhhcCCCHHHHHHH
Confidence 999999999999999999999999998 35568999999999995 54 68999999999999999999999
Q ss_pred HHHhcCCCCCCCcccCC-ceEEEEEEEEEEEee
Q psy1882 189 LLRKGGFKGPITPDIRC-NIKLTRYQSELVSVS 220 (233)
Q Consensus 189 l~~KaG~~~~~~~~~~~-~i~l~Ryqs~k~~~s 220 (233)
+|+|||+++ +.|++ +++++||++++|+..
T Consensus 162 l~~KAGl~~---d~w~~~~~~v~rf~~~~f~E~ 191 (200)
T TIGR00296 162 LCMKAGLPP---DCFLTYGIEVYRFEGQIFEEF 191 (200)
T ss_pred HHHhCCCCc---cccccCCcEEEEEEEEEEEec
Confidence 999999963 33443 699999999998753
No 4
>PRK00801 hypothetical protein; Provisional
Probab=100.00 E-value=8.1e-54 Score=371.84 Aligned_cols=168 Identities=23% Similarity=0.332 Sum_probs=148.2
Q ss_pred ChhHHhHHHHHHHHhhcCCCCCCC----CCCCCCCCCceEEEEEeCCCCcceeeeccCCC-ccHHHHHHHHHHHhhhcCC
Q psy1882 41 QPEMCFFCFDVLYCHLHSLEPPNP----PSGISNDAFPLFVTWKIGKDQRLRGCIGTFNA-INLHGGLREYAVTSAFKDS 115 (233)
Q Consensus 41 ~~~m~~~cfd~L~~~L~~~~~p~~----p~~~~~~~~g~FVTl~~~~~g~LRGCIGt~~~-~~L~~~i~~~Ai~AA~~Dp 115 (233)
-..++.+||++|.++|.+..++.+ |+.| +++.||||||++ +|+|||||||+.| +||+++|++||++|||+||
T Consensus 9 ~~~Ll~lAR~ai~~~l~~~~~~~~~~~~~~~l-~~~~g~FVTl~~--~g~LRGCIGs~~p~~pL~~~v~~~A~~AA~~Dp 85 (201)
T PRK00801 9 GEFAVRLARRAIEEYLRTGKVIEPPKDLPPVF-WEKRGVFVTLNK--HGVLRGCIGFPYPDSPLVEAIIDSAISAATRDP 85 (201)
T ss_pred HHHHHHHHHHHHHHHHccCCCCCCCccCCHhH-cccccEEEEEEE--CCeeccccCCCCCcccHHHHHHHHHHHHHcCCC
Confidence 456999999999999986543322 2233 678999999984 8999999999888 6999999999999999999
Q ss_pred CCCCCChhccccceEEEEeeecccCCCC-----cccccccccceEEEEEecCCCeeeeEEcCccCccCCCCHHHHHHHHH
Q psy1882 116 RFNPITVDEFSKLHVSVSILRHFEDGND-----YTDWKIGVHGIRIEFHNERGNKRTATYLPEVAPEQGWDQIQTIDSLL 190 (233)
Q Consensus 116 RF~Pl~~~EL~~L~ieVSvL~~~e~~~~-----~~d~~~G~hGl~i~f~~~~G~~~~atfLP~Va~EqgW~~~~~l~~l~ 190 (233)
||+||+.+||++|.|+||||++++++.+ +.+|+||+|||+|++ |. |+||||||||.|||||+++||.++|
T Consensus 86 RF~Pl~~~EL~~l~ieVSvLs~~e~i~~~~~~l~~~~~~G~~Glii~~----g~-~~g~~LPqV~~e~~wd~~efl~~l~ 160 (201)
T PRK00801 86 RFPPVKLEEMDEITVEVTVLTPPELIEGPPEELPEKIEVGRHGLIVKK----GI-YSGLLLPQVAPEWGFDSEEFLSHTC 160 (201)
T ss_pred CCCCCChHHhCCcEEEEEEcCCCEEccCcchhhHHhccccceEEEEEe----CC-ccEEECCcchhhcCCCHHHHHHHHH
Confidence 9999999999999999999999999865 567999999999995 54 6899999999999999999999999
Q ss_pred HhcCCCCCCCcccCCceEEEEEEEEEEEe
Q psy1882 191 RKGGFKGPITPDIRCNIKLTRYQSELVSV 219 (233)
Q Consensus 191 ~KaG~~~~~~~~~~~~i~l~Ryqs~k~~~ 219 (233)
+|||++ ++.|.++++++||++++|+.
T Consensus 161 ~KAGl~---~d~w~~~~~v~rf~~~~f~E 186 (201)
T PRK00801 161 LKAGLP---PDCWLDDAEVYRFEGQIFKE 186 (201)
T ss_pred HhcCCC---ccccccCcEEEEEEEEEEEc
Confidence 999996 34466689999999999975
No 5
>COG2078 AMMECR1 Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=9.3e-50 Score=345.24 Aligned_cols=174 Identities=25% Similarity=0.398 Sum_probs=153.0
Q ss_pred ChhHHhHHHHHHHHhhcCCCCCCCC--CCCCCCCCceEEEEEeC-CCCcceeeeccCCC-ccHHHHHHHHHHHhhhcCCC
Q psy1882 41 QPEMCFFCFDVLYCHLHSLEPPNPP--SGISNDAFPLFVTWKIG-KDQRLRGCIGTFNA-INLHGGLREYAVTSAFKDSR 116 (233)
Q Consensus 41 ~~~m~~~cfd~L~~~L~~~~~p~~p--~~~~~~~~g~FVTl~~~-~~g~LRGCIGt~~~-~~L~~~i~~~Ai~AA~~DpR 116 (233)
-..+|.|||.+|+++|++.+.++++ +...+++.|+||||++. .+++||||||++.| .+|+++|+++|+.||++|||
T Consensus 10 g~~~V~lAR~ai~~~L~~gk~~~~~~~~~~~~~k~gvFvTl~~~~~~~~LRGCIG~~~p~~~l~~ai~~~Ai~AA~~DPR 89 (203)
T COG2078 10 GHPLVRLAREAIENYLEGGKVIEPEPFPKLFQEKRGVFVTLEKYSPDGELRGCIGTPEPVKPLAEAIIKAAIEAALSDPR 89 (203)
T ss_pred ChHHHHHHHHHHHHHhccCCcCCCcccchhhhhccceEEEEEEeCCCCceeeecccCcccCcHHHHHHHHHHHHHhcCCC
Confidence 3789999999999999876544433 25558899999999986 46899999999999 58999999999999999999
Q ss_pred CCCCChhccccceEEEEeeecccCCCCc-----ccccccccceEEEEEecCCCeeeeEEcCccCccCCCCHHHHHHHHHH
Q psy1882 117 FNPITVDEFSKLHVSVSILRHFEDGNDY-----TDWKIGVHGIRIEFHNERGNKRTATYLPEVAPEQGWDQIQTIDSLLR 191 (233)
Q Consensus 117 F~Pl~~~EL~~L~ieVSvL~~~e~~~~~-----~d~~~G~hGl~i~f~~~~G~~~~atfLP~Va~EqgW~~~~~l~~l~~ 191 (233)
|+||+.+||+++.||||||++||++.+. .+|++|+|||+|. +|. ++|+||||||+|++||.++||+++|.
T Consensus 90 F~pv~~~EL~~i~veV~iLt~pe~i~~~p~~~p~~ie~G~~Gliv~----~g~-~sgllLPqV~vE~~w~~eefL~~~c~ 164 (203)
T COG2078 90 FPPVSLEELDDIVVEVTILTPPEEIDVPPEERPEDIEVGRHGLIVE----KGI-YSGLLLPQVPVEYRWDVEEFLEHTCE 164 (203)
T ss_pred CCCCChhHhcceEEEEEEcCCCeecCCCchhChhheeecceEEEEe----cCC-cceeecCccccccCCCHHHHHHHHHH
Confidence 9999999999999999999999987654 6799999999998 565 68999999999999999999999999
Q ss_pred hcCCCCCCCcccCCceEEEEEEEEEEEeeH
Q psy1882 192 KGGFKGPITPDIRCNIKLTRYQSELVSVSY 221 (233)
Q Consensus 192 KaG~~~~~~~~~~~~i~l~Ryqs~k~~~sy 221 (233)
|||++++++. .++++++||+++.|..+.
T Consensus 165 KAGlp~~~w~--~~~~~iy~F~~~If~E~~ 192 (203)
T COG2078 165 KAGLPGDCWL--DEDVKIYRFEAQIFKEKE 192 (203)
T ss_pred HcCCCccccc--ccCceEEEEEEEEEEecC
Confidence 9999655443 348999999999998653
No 6
>PRK03881 hypothetical protein; Provisional
Probab=100.00 E-value=5.7e-44 Score=341.52 Aligned_cols=162 Identities=26% Similarity=0.419 Sum_probs=142.6
Q ss_pred ChhHHhHHHHHHHHhhcCCCCCC----CCCCCCCCCCceEEEEEeCCCCcceeeeccCCCc--cHHHHHHHHHHHhhhcC
Q psy1882 41 QPEMCFFCFDVLYCHLHSLEPPN----PPSGISNDAFPLFVTWKIGKDQRLRGCIGTFNAI--NLHGGLREYAVTSAFKD 114 (233)
Q Consensus 41 ~~~m~~~cfd~L~~~L~~~~~p~----~p~~~~~~~~g~FVTl~~~~~g~LRGCIGt~~~~--~L~~~i~~~Ai~AA~~D 114 (233)
.+.++.+||++|+++|.+..+++ .|+.+++++.||||||++ +|+|||||||+.|. ||+++|++||++|||+|
T Consensus 299 ~~~l~~lAr~~i~~~l~~~~~~~~~~~~~~~~~~~~~g~FVTl~~--~g~LRGCIG~~~p~~~~L~~~v~~~a~~AA~~D 376 (467)
T PRK03881 299 EDPYVRLARESLESYVKTGKPLPVPDYLPEEMLNRRAGVFVSLKK--DGELRGCIGTIFPTRENIAEEIIRNAISAGTED 376 (467)
T ss_pred hhHHHHHHHHHHHHHhCcCCCCCCCccCChHHhCCcccEEEEEEE--CCeeeeeeeecCCCcchHHHHHHHHHHHHhcCC
Confidence 67799999999999998643222 223455889999999984 79999999999995 79999999999999999
Q ss_pred CCCCCCChhccccceEEEEeeecccCCCCcccccccccceEEEEEecCCCeeeeEEcCccCccCCCCH-HHHHHHHHHhc
Q psy1882 115 SRFNPITVDEFSKLHVSVSILRHFEDGNDYTDWKIGVHGIRIEFHNERGNKRTATYLPEVAPEQGWDQ-IQTIDSLLRKG 193 (233)
Q Consensus 115 pRF~Pl~~~EL~~L~ieVSvL~~~e~~~~~~d~~~G~hGl~i~f~~~~G~~~~atfLP~Va~EqgW~~-~~~l~~l~~Ka 193 (233)
|||+||+++||++|.||||||+++|++.++.+|+||+|||+|++ |. |+||||||| ++|+. ++||+++|+||
T Consensus 377 pRF~pl~~~El~~l~i~VsvL~~~~~~~~~~~~~~g~~Gli~~~----~~-~~g~~LP~v---~~~~~~~~fl~~~~~Ka 448 (467)
T PRK03881 377 PRFPPVEEDELDDLVYSVDVLTEPEPVSSLDELDPKRYGVIVRS----GR-RRGLLLPDL---EGVDTVEEQLSIALRKA 448 (467)
T ss_pred CCCCCCChHHhCCeEEEEEEcCCCeECCCHHHcCCccceEEEEE----CC-ccEEECCCC---CCCCCHHHHHHHHHHhc
Confidence 99999999999999999999999999998899999999999995 54 689999999 56888 89999999999
Q ss_pred CCCCCCCcccCCceEEEEEEEEEEE
Q psy1882 194 GFKGPITPDIRCNIKLTRYQSELVS 218 (233)
Q Consensus 194 G~~~~~~~~~~~~i~l~Ryqs~k~~ 218 (233)
|++ ++ ..++++||++++|+
T Consensus 449 Gl~----~~--~~~~~~~f~~~~~~ 467 (467)
T PRK03881 449 GID----PD--EDVEIERFEVVRHK 467 (467)
T ss_pred CCC----CC--CCeEEEEEEEEEeC
Confidence 995 33 24999999999874
No 7
>PRK04219 rpl5p 50S ribosomal protein L5P; Reviewed
Probab=48.17 E-value=37 Score=29.56 Aligned_cols=106 Identities=16% Similarity=0.176 Sum_probs=60.2
Q ss_pred CCcceeeeccCCCccHHHHHHHHHHHhhhcCCCCCCCChhccccceEEEEeeecccCCCCcccccccccceEEEEEecCC
Q psy1882 84 DQRLRGCIGTFNAINLHGGLREYAVTSAFKDSRFNPITVDEFSKLHVSVSILRHFEDGNDYTDWKIGVHGIRIEFHNERG 163 (233)
Q Consensus 84 ~g~LRGCIGt~~~~~L~~~i~~~Ai~AA~~DpRF~Pl~~~EL~~L~ieVSvL~~~e~~~~~~d~~~G~hGl~i~f~~~~G 163 (233)
.|+.-||.=|+.....+ +..+-.+..+ |||.++-+-+.--++.+-++-...|.++. .|-..|.+|+-|.+..++-
T Consensus 64 kG~pIG~kVTLRg~~m~-~FL~rli~iv--d~~l~~~sfD~~GN~sfGI~e~~~fpei~--yd~~~~i~GmdI~ivt~rp 138 (177)
T PRK04219 64 KGEPIGVKVTLRGEKAE-EFLKTALEAV--GNRLKASSFDETGNVSFGIEEHIDFPGVK--YDPEIGIFGMDVCVTLERP 138 (177)
T ss_pred CCCEEEEEEEEccHHHH-HHHHHHHHhh--cCCCCCcccCCCceEeeCchhhhccCccc--cCcccccccccEEEEEcCC
Confidence 34444444444443222 3444444444 88988877777777888777666665553 3555678888887766442
Q ss_pred Ceee---eEEcCccCccCCCCHHHHHHHHHHhcC
Q psy1882 164 NKRT---ATYLPEVAPEQGWDQIQTIDSLLRKGG 194 (233)
Q Consensus 164 ~~~~---atfLP~Va~EqgW~~~~~l~~l~~KaG 194 (233)
++|- --=--.|...|.-++++++..+..+-|
T Consensus 139 g~rv~~r~~~~~~i~~~~~~~~~e~~~~~~~~~~ 172 (177)
T PRK04219 139 GYRVARRRRKRRKIPSRHRVTKEEAIEFLEENFG 172 (177)
T ss_pred ccchhhhhhccccCCCCceeCHHHHHHHHHHhcC
Confidence 2210 001122444555677777777666554
No 8
>PF03544 TonB_C: Gram-negative bacterial TonB protein C-terminal; InterPro: IPR006260 The sequences in this set all contain a conserved C-terminal domain which is characteristic of TonB and is homologs. TonB is an energy-transducer for TonB-dependent receptors of Gram-negative bacteria []. Most members are designated as TonB or TonB-related proteins, but a few represent the paralogous TolA protein. Several bacteria have up to four TonB paralogs. In nearly every case, a proline-rich repetitive region is found N-terminal to this domain; these low-complexity regions are highly divergent and cannot readily be aligned. The region is suggested to span the periplasm. Iron is essential for growth in both bacteria and mammals. Controlling the amount of free iron in solution is often used as a tactic by hosts to limit invasion of pathogenic microbes; binding iron tightly within protein molecules can accomplish this. Some bacteria express surface receptors to capture eukaryotic iron-binding compounds, while others have evolved siderophores to scavenge iron from iron-binding host proteins []. The absence of free iron molecules in the surrounding environment triggers transcription of gene clusters that encode both siderophore-synthesis ezymes, and receptors that recognise iron-bound siderophores []. An example of the latter is Escherichia coli fepA, which resides in the outer envelope and captures iron-bound enterobactin []. To complete transport of bound iron across the inner membrane, a second receptor complex is needed. The major component of this is tonB, a 27kDa protein that facilitates energy transfer from the proton motive force to outer receptors. B-12 and colicin receptors also make use of the tonB system to drive active transport at the outer membrane.; GO: 0008565 protein transporter activity, 0015031 protein transport, 0016020 membrane, 0030288 outer membrane-bounded periplasmic space; PDB: 1U07_B 1IHR_A 2GRX_C 2GSK_B 1QXX_A 1XX3_A 2K9K_A.
Probab=22.42 E-value=1e+02 Score=21.51 Aligned_cols=53 Identities=25% Similarity=0.253 Sum_probs=26.1
Q ss_pred eEEEEEeCCCCcceeeeccCCC-ccHHHHHHHHHHHhhhcCCCCCCCChhccccceEEE
Q psy1882 75 LFVTWKIGKDQRLRGCIGTFNA-INLHGGLREYAVTSAFKDSRFNPITVDEFSKLHVSV 132 (233)
Q Consensus 75 ~FVTl~~~~~g~LRGCIGt~~~-~~L~~~i~~~Ai~AA~~DpRF~Pl~~~EL~~L~ieV 132 (233)
+-|.+....+|++..|-=.-.. .+ .+-+.|+ .|++.+||.|.... -....+.+
T Consensus 18 v~v~~~I~~~G~v~~~~v~~s~~~~---~l~~~a~-~~v~~~~~~p~~~~-g~~~~~~~ 71 (79)
T PF03544_consen 18 VVVEFTIDPDGRVSDVRVIQSSGPP---ILDEAAL-RAVKKWRFKPAPKN-GKPVKVTY 71 (79)
T ss_dssp EEEEEEEETTTEEEEEEEEEESSSS---CSHHHHH-HHHCC-EE-TT--C-CEECEEEE
T ss_pred EEEEEEEeCCCCEEEEEEEEccCHH---HHHHHHH-HHHHhCCCCCCCcC-CEEEEEEE
Confidence 4555555578999987422111 12 1333444 45555999998776 33344433
No 9
>KOG1612|consensus
Probab=19.61 E-value=1e+02 Score=28.80 Aligned_cols=56 Identities=27% Similarity=0.262 Sum_probs=36.8
Q ss_pred EEEEeCCCCcceeeeccCCCccHHHHHHHHHHHhhhcCCCCCCCChhccccceEEEEeeecccC
Q psy1882 77 VTWKIGKDQRLRGCIGTFNAINLHGGLREYAVTSAFKDSRFNPITVDEFSKLHVSVSILRHFED 140 (233)
Q Consensus 77 VTl~~~~~g~LRGCIGt~~~~~L~~~i~~~Ai~AA~~DpRF~Pl~~~EL~~L~ieVSvL~~~e~ 140 (233)
+.|++.-|.-+--|-| +|. +.+..|+.+|+++.|||-+...+-+...+ .++-+.++
T Consensus 131 ~~W~i~VDvlVi~s~g-----n~~-dAiS~Ai~~AL~~T~lPkv~v~~dd~~~~--~i~~s~~~ 186 (288)
T KOG1612|consen 131 YCWKIYVDVLVISSDG-----NLL-DAISIAIYAALNNTRLPKVIVAFDDDGEV--EILLSDEE 186 (288)
T ss_pred eeEEEEEeEEEEecCC-----CHH-HHHHHHHHHHHhcccCCccccccccCCce--eeccCccc
Confidence 6676644555555655 443 57789999999999999887665544444 44444443
No 10
>PF06102 DUF947: Domain of unknown function (DUF947); InterPro: IPR009292 This is a family of eukaryotic proteins with unknown function.
Probab=19.43 E-value=50 Score=28.20 Aligned_cols=13 Identities=23% Similarity=0.570 Sum_probs=9.7
Q ss_pred hhcCCCCCCCChh
Q psy1882 111 AFKDSRFNPITVD 123 (233)
Q Consensus 111 A~~DpRF~Pl~~~ 123 (233)
-..||||.|+.-.
T Consensus 32 ~~rDPRFd~~~G~ 44 (168)
T PF06102_consen 32 KRRDPRFDSLSGE 44 (168)
T ss_pred CCCCCCcCccccc
Confidence 3589999988533
Done!