Query 029529
Match_columns 192
No_of_seqs 116 out of 346
Neff 5.2
Searched_HMMs 46136
Date Fri Mar 29 14:22:38 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029529.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029529hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3106 ER lumen protein retai 100.0 5E-74 1.1E-78 477.4 12.7 178 1-180 1-181 (212)
2 COG5196 ERD2 ER lumen protein 100.0 1E-64 2.3E-69 416.4 14.9 179 1-181 1-184 (214)
3 PF00810 ER_lumen_recept: ER l 100.0 7.4E-56 1.6E-60 356.7 13.2 140 28-169 1-147 (147)
4 TIGR00951 2A43 Lysosomal Cysti 94.4 1.5 3.3E-05 37.5 13.1 49 116-164 137-188 (220)
5 PF04193 PQ-loop: PQ loop repe 91.1 1.1 2.4E-05 29.9 6.2 51 118-168 2-55 (61)
6 PF04193 PQ-loop: PQ loop repe 89.3 0.75 1.6E-05 30.8 4.1 37 12-48 13-49 (61)
7 smart00679 CTNS Repeated motif 85.8 0.56 1.2E-05 27.6 1.7 22 20-41 7-28 (32)
8 KOG3211 Predicted endoplasmic 79.8 25 0.00054 30.7 9.9 119 20-144 50-168 (230)
9 PTZ00154 40S ribosomal protein 63.1 5.3 0.00012 32.2 2.0 27 5-38 49-75 (134)
10 KOG2489 Transmembrane protein 37.3 8.6 0.00019 37.4 -0.7 52 98-149 441-500 (592)
11 PHA02246 hypothetical protein 36.3 1.6E+02 0.0034 24.9 6.5 119 21-160 25-153 (192)
12 TIGR00951 2A43 Lysosomal Cysti 35.8 1.1E+02 0.0023 26.2 5.7 31 130-160 16-48 (220)
13 PF02790 COX2_TM: Cytochrome C 31.1 1.1E+02 0.0025 21.1 4.4 22 93-114 60-81 (84)
14 PF03083 MtN3_slv: Sugar efflu 28.4 88 0.0019 22.1 3.5 34 5-38 4-40 (87)
15 COG4095 Uncharacterized conser 27.6 1.3E+02 0.0028 22.7 4.3 35 8-42 12-46 (89)
16 PF00833 Ribosomal_S17e: Ribos 26.8 48 0.001 26.3 2.0 27 5-38 49-75 (121)
17 PF10192 GpcrRhopsn4: Rhodopsi 24.5 4.3E+02 0.0092 22.6 7.7 17 97-113 218-235 (257)
No 1
>KOG3106 consensus ER lumen protein retaining receptor [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=5e-74 Score=477.35 Aligned_cols=178 Identities=53% Similarity=0.912 Sum_probs=175.3
Q ss_pred CchhhhhhhHHHHHHHHHHHHHHhhcccccccccchhHHHHHHHHhhcccccchhHHHHHHHHHHHHHHHHHHHHHHHhh
Q 029529 1 MNIFRLAGDMTHLASVLVLLLKIHTIKSCAGISLKTQELYALVFATRYLDIFTNYISFYNTIMKLIFLGSSFSIVWYIKR 80 (192)
Q Consensus 1 mn~fr~~gd~~Hl~s~~iLl~Ki~~~kS~~GiSlkTQ~ly~iVf~~Ryldl~~~~~s~Ynt~mki~~i~ss~~ivyl~~~ 80 (192)
||.||++||++|++|+++|++||+|+|||+|+|+|||++||+||++||+|+|+++.|.||++||+++++++.+++|+|+.
T Consensus 1 mn~fr~~gd~~H~~~i~vLi~Ki~ktrsCaGiSlKSQ~L~Alvf~~Ryldlf~~~~s~ynt~mki~fl~~t~~ivymi~~ 80 (212)
T KOG3106|consen 1 MNNFRFAGDLSHLAAIIVLILKIWKTKSCAGISLKSQELFALVFATRYLDLFTFYESLYNTIMKIAFLASTLWIVYMIRF 80 (212)
T ss_pred CcchhhHHHHHHHHHHHHHHHHHHhcCccccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred ccccccccccccccchhHHhHHHHHHHHHHhcCCcchhhhHHHHHHHHHHhhhhhHHHHHhhcCCcchhHHHHHHHHHHH
Q 029529 81 HKIVHRSYDKDQDTFRHWFIVLPCLVLALLINERFTFKEVMWTFSLYLEAVAILPQLVLLQRTRNIDNLTGQYVFLLGYI 160 (192)
Q Consensus 81 ~~~~~~TY~~~~D~f~~~~ll~p~~vLali~~~~~~~~eilWtFSiyLEsvAILPQL~mlqk~~~vE~lTshYv~aLG~y 160 (192)
++|+|||+|+|||+.+|+++||+++|+++||++++.|++|+||+|||||||||||+|+||+||+|++|+||+||||+|
T Consensus 81 --k~~~tYd~~~DtFri~~llvp~~vlsl~i~~~~t~~eilWtFsiyLEsVaILPQL~~lq~tg~~E~~TahYvfaLG~y 158 (212)
T KOG3106|consen 81 --KLRATYDKEKDTFRIEYLLVPSAVLSLLINHSFTILEILWTFSIYLESVAILPQLFMLQKTGEAETITAHYLFALGLY 158 (212)
T ss_pred --HHHHHHhcccCceeEEEEehhheeeeeeecCCccHHHHHHHHHHHHHHHHHhHHHHHHHhcCCccchHHHHHHHHHHH
Confidence 489999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ---HHHHHHHHHHhhcccCeeeh
Q 029529 161 ---VVLNFVIDEIVFCFFNNFVI 180 (192)
Q Consensus 161 ---yilnWi~r~~~~~~~~~~~~ 180 (192)
|++|||+|+..++++|.+++
T Consensus 159 R~ly~~~WI~r~~~e~~~~~iai 181 (212)
T KOG3106|consen 159 RALYIANWIYRYVTEDFWDPIAI 181 (212)
T ss_pred HHHHHHHHHHHHHhhccccchHH
Confidence 99999999999999999875
No 2
>COG5196 ERD2 ER lumen protein retaining receptor [Intracellular trafficking and secretion]
Probab=100.00 E-value=1e-64 Score=416.41 Aligned_cols=179 Identities=42% Similarity=0.729 Sum_probs=173.3
Q ss_pred CchhhhhhhHHHHHHHHHHHHHHhhcccccccccchhHHHHHHHHhhcccccc-hhHHHHHHHHHHHHHHHHHHHHHHHh
Q 029529 1 MNIFRLAGDMTHLASVLVLLLKIHTIKSCAGISLKTQELYALVFATRYLDIFT-NYISFYNTIMKLIFLGSSFSIVWYIK 79 (192)
Q Consensus 1 mn~fr~~gd~~Hl~s~~iLl~Ki~~~kS~~GiSlkTQ~ly~iVf~~Ryldl~~-~~~s~Ynt~mki~~i~ss~~ivyl~~ 79 (192)
||.||++||++|++|+.+|+.||+|+|+|+|+|+|||.+|++||++||+|+++ .+.|+||.+||++||+++.+++++|+
T Consensus 1 m~~Fr~lGD~~Hlasi~vLih~ik~tr~csGlSlKtq~Ly~lVfitRYldLf~f~~~slYn~lMki~FI~s~~yI~~lm~ 80 (214)
T COG5196 1 MDTFRFLGDFLHLASIAVLIHKIKRTRSCSGLSLKTQFLYSLVFITRYLDLFDFYARSLYNSLMKILFIGSQVYILFLMR 80 (214)
T ss_pred CcHHHHHhHHHHHHHHHHHHHHhhhcceecceehHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 89999999999999999999999999999999999999999999999999994 45799999999999999999999999
Q ss_pred hccccccccccccccchhHHhHHHHHHHHHHhcCCcchhhhHHHHHHHHHHhhhhhHHHHHhhcCCcchhHHHHHHHHHH
Q 029529 80 RHKIVHRSYDKDQDTFRHWFIVLPCLVLALLINERFTFKEVMWTFSLYLEAVAILPQLVLLQRTRNIDNLTGQYVFLLGY 159 (192)
Q Consensus 80 ~~~~~~~TY~~~~D~f~~~~ll~p~~vLali~~~~~~~~eilWtFSiyLEsvAILPQL~mlqk~~~vE~lTshYv~aLG~ 159 (192)
.+ +++|||+..|+|+..++++||+++|+++|++.++.+++|+||+|||||||||||+|+||.||-|++|+||++|+|+
T Consensus 81 ~~--~r~tYdk~lDtF~i~~ll~gsav~slff~~~~tisnvlwtfS~wLESVAILPQL~mLq~~GeteslT~hYvfamgL 158 (214)
T COG5196 81 FK--YRSTYDKKLDTFNILTLLVGSAVFSLFFTRGGTISNVLWTFSLWLESVAILPQLVMLQEAGETESLTSHYVFAMGL 158 (214)
T ss_pred hc--ccchHHHhhhhhhhhhhhhhhhhheeeecCCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcceeHHHHHHHHHH
Confidence 84 6899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred H---HHHHHHHHHHhh-cccCeeehh
Q 029529 160 I---VVLNFVIDEIVF-CFFNNFVIN 181 (192)
Q Consensus 160 y---yilnWi~r~~~~-~~~~~~~~~ 181 (192)
| |++|||+|+-.+ ++.|++-|-
T Consensus 159 YRalYip~wI~r~~~~~kk~~~iai~ 184 (214)
T COG5196 159 YRALYIPYWILRKVYDIKKTGNIAIA 184 (214)
T ss_pred HHHhhhhHHHHHhhhcccccccchhH
Confidence 9 999999999999 899988654
No 3
>PF00810 ER_lumen_recept: ER lumen protein retaining receptor; InterPro: IPR000133 Proteins resident in the lumen of the endoplasmic reticulum (ER) contain a C-terminal tetrapeptide, commonly known as Lys-Asp-Glu-Leu (KDEL) in mammals and His-Asp-Glu-Leu (HDEL) in yeast (Saccharomyces cerevisiae) that acts as a signal for their retrieval from subsequent compartments of the secretory pathway. The receptor for this signal is a ~26 kDa Golgi membrane protein, initially identified as the ERD2 gene product in S. cerevisiae. The receptor molecule, known variously as the ER lumen protein retaining receptor or the 'KDEL receptor', is believed to cycle between the cis side of the Golgi apparatus and the ER. It has also been characterised in a number of other species, including plants, Plasmodium, Drosophila and mammals. In mammals, 2 highly related forms of the receptor are known. The KDEL receptor is a highly hydrophobic protein of 220 residues; its sequence exhibits 7 hydrophobic regions, all of which have been suggested to traverse the membrane []. More recently, however, it has been suggested that only 6 of these regions are transmembrane (TM), resulting in both N- and C-termini on the cytoplasmic side of the membrane.; GO: 0046923 ER retention sequence binding, 0006621 protein retention in ER lumen, 0016021 integral to membrane
Probab=100.00 E-value=7.4e-56 Score=356.70 Aligned_cols=140 Identities=54% Similarity=0.961 Sum_probs=134.3
Q ss_pred cccccccchhHHHHHHHHhhcccc--cchhHHHHHHHHHHHHHHHHHHHHHHHhhccccccccccccccchhHHhHHHHH
Q 029529 28 SCAGISLKTQELYALVFATRYLDI--FTNYISFYNTIMKLIFLGSSFSIVWYIKRHKIVHRSYDKDQDTFRHWFIVLPCL 105 (192)
Q Consensus 28 S~~GiSlkTQ~ly~iVf~~Ryldl--~~~~~s~Ynt~mki~~i~ss~~ivyl~~~~~~~~~TY~~~~D~f~~~~ll~p~~ 105 (192)
||+|+|+|||+||++|+++||+|+ +.++.+.||++||+++++++++++|+|+. ++|+|||+++|+|+..++++||+
T Consensus 1 S~~GlSlktq~ly~~vf~~Ryldl~~f~~~~s~y~~~~k~~~i~~s~~iiyli~~--~~~~Ty~~~~D~f~~~~li~p~~ 78 (147)
T PF00810_consen 1 SCSGLSLKTQILYAIVFLTRYLDLFWFESYLSLYNTIMKVFFIVSSLYIIYLIFF--KYKSTYDKEIDTFRLEYLIVPCF 78 (147)
T ss_pred CcchhhHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHhhhe--eehhhhhccccchhhhHHHHHHH
Confidence 799999999999999999999999 66667999999999999999999999965 58999999999999999999999
Q ss_pred HHHHHhc--CCcchhhhHHHHHHHHHHhhhhhHHHHHhhcCCcchhHHHHHHHHHHH---HHHHHHHHH
Q 029529 106 VLALLIN--ERFTFKEVMWTFSLYLEAVAILPQLVLLQRTRNIDNLTGQYVFLLGYI---VVLNFVIDE 169 (192)
Q Consensus 106 vLali~~--~~~~~~eilWtFSiyLEsvAILPQL~mlqk~~~vE~lTshYv~aLG~y---yilnWi~r~ 169 (192)
+||+++| +++++.|++|+||+|||||||+|||+|+||+||+|++|+||+++||+| |++|||+|+
T Consensus 79 vLa~i~~p~~~~~~~ei~wtfSi~LEsvAIlPQL~m~~k~~~ve~ltshYv~~Lg~yR~ly~~~Wi~rY 147 (147)
T PF00810_consen 79 VLALIFHPLNSFFFLEILWTFSIYLESVAILPQLFMLQKTGEVENLTSHYVFALGLYRALYLLNWIYRY 147 (147)
T ss_pred HHHHHHhccccchHHHHHHHHHHHHHHHHHhHHHHHHHHhcCeeehHHHHHHHHHHHHHHHHHHHHHhC
Confidence 9999999 457899999999999999999999999999999999999999999999 999999996
No 4
>TIGR00951 2A43 Lysosomal Cystine Transporter.
Probab=94.43 E-value=1.5 Score=37.48 Aligned_cols=49 Identities=10% Similarity=0.236 Sum_probs=33.1
Q ss_pred chhhhHHHHHHHHHHhhhhhHHHHHhhcCCcch--hHHHHHHHHHHH-HHHH
Q 029529 116 TFKEVMWTFSLYLEAVAILPQLVLLQRTRNIDN--LTGQYVFLLGYI-VVLN 164 (192)
Q Consensus 116 ~~~eilWtFSiyLEsvAILPQL~mlqk~~~vE~--lTshYv~aLG~y-yiln 164 (192)
...+.++...+-+-.++-+||..+-.|.|..+. +.+-.+-..|.- +++.
T Consensus 137 ~~l~~l~~iki~is~ikyiPQi~~Ny~~ksT~glSi~~i~Ld~~G~lqri~t 188 (220)
T TIGR00951 137 AFVTMLSYIKVAVTLVKYFPQAATNYHNKSTGQLSIITVFLDFTGLLQRIFQ 188 (220)
T ss_pred HHHHHHHHHHHHHHHHHHhHHHHHHHhcCCCCcCCHHHHHHHHHHHHHHHHH
Confidence 355666667777777888999999988765554 444455566644 5543
No 5
>PF04193 PQ-loop: PQ loop repeat
Probab=91.12 E-value=1.1 Score=29.94 Aligned_cols=51 Identities=22% Similarity=0.397 Sum_probs=38.0
Q ss_pred hhhHHHHHHHHHHhhhhhHHHHHhhcCCcchhHHHHHH--HHHHH-HHHHHHHH
Q 029529 118 KEVMWTFSLYLEAVAILPQLVLLQRTRNIDNLTGQYVF--LLGYI-VVLNFVID 168 (192)
Q Consensus 118 ~eilWtFSiyLEsvAILPQL~mlqk~~~vE~lTshYv~--aLG~y-yilnWi~r 168 (192)
.+++...+.-+.+++-+||+....|+|++|.+.--++. ..|.. ++++.+..
T Consensus 2 ~~~~g~i~~~~~~~~~lPQi~~~~k~ks~~glS~~~~~l~~~g~~~~~~~~~~~ 55 (61)
T PF04193_consen 2 SNILGIISIVLWIISFLPQIIKNYKRKSTGGLSLWFLLLWLIGSILWVLYSILS 55 (61)
T ss_pred HHHHHHHHHHHHHHHHHhHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHh
Confidence 46778889999999999999999999999886554444 44444 66655443
No 6
>PF04193 PQ-loop: PQ loop repeat
Probab=89.29 E-value=0.75 Score=30.82 Aligned_cols=37 Identities=24% Similarity=0.140 Sum_probs=28.1
Q ss_pred HHHHHHHHHHHHhhcccccccccchhHHHHHHHHhhc
Q 029529 12 HLASVLVLLLKIHTIKSCAGISLKTQELYALVFATRY 48 (192)
Q Consensus 12 Hl~s~~iLl~Ki~~~kS~~GiSlkTQ~ly~iVf~~Ry 48 (192)
-+.+.+==++|.+|+||+.|+|.-+..+..+...++.
T Consensus 13 ~~~~~lPQi~~~~k~ks~~glS~~~~~l~~~g~~~~~ 49 (61)
T PF04193_consen 13 WIISFLPQIIKNYKRKSTGGLSLWFLLLWLIGSILWV 49 (61)
T ss_pred HHHHHHhHHHHHHHccccccccHHHHHHHHHHHHHHH
Confidence 3344444468999999999999998888877766655
No 7
>smart00679 CTNS Repeated motif present between transmembrane helices in cystinosin, yeast ERS1p, mannose-P-dolichol utilization defect 1, and other hypothetical proteins. Function unknown, but likely to be associated with the glycosylation machinery.
Probab=85.79 E-value=0.56 Score=27.62 Aligned_cols=22 Identities=27% Similarity=0.286 Sum_probs=18.2
Q ss_pred HHHHhhcccccccccchhHHHH
Q 029529 20 LLKIHTIKSCAGISLKTQELYA 41 (192)
Q Consensus 20 l~Ki~~~kS~~GiSlkTQ~ly~ 41 (192)
++|++|+||+.|+|.-...+-.
T Consensus 7 i~~~~~~ks~~glS~~~~~l~~ 28 (32)
T smart00679 7 IIKNYRRKSTEGLSILFVLLWL 28 (32)
T ss_pred HHHHHHcCCcCcCCHHHHHHHH
Confidence 5799999999999988766544
No 8
>KOG3211 consensus Predicted endoplasmic reticulum membrane protein Lec35/MPDU1 involved in monosaccharide-P-dolichol utilization [General function prediction only]
Probab=79.83 E-value=25 Score=30.69 Aligned_cols=119 Identities=15% Similarity=0.092 Sum_probs=62.4
Q ss_pred HHHHhhcccccccccchhHHHHHHHHhhcccccchhHHHHHHHHHHHHHHHHHHHHHHHhhccccccccccccccchhHH
Q 029529 20 LLKIHTIKSCAGISLKTQELYALVFATRYLDIFTNYISFYNTIMKLIFLGSSFSIVWYIKRHKIVHRSYDKDQDTFRHWF 99 (192)
Q Consensus 20 l~Ki~~~kS~~GiSlkTQ~ly~iVf~~Ryldl~~~~~s~Ynt~mki~~i~ss~~ivyl~~~~~~~~~TY~~~~D~f~~~~ 99 (192)
+.||...||+.|+|+.+|+|=++.+..-..--.++ ---..+.++..++..+..++-.+.++ |+ --.-..|.|-..+
T Consensus 50 I~kI~aakSa~GLSv~s~~LElvgytvtl~Y~~~~-g~pFss~gE~~fLl~Q~vili~~if~--f~-~~~~~~v~~l~~~ 125 (230)
T KOG3211|consen 50 IMKIRAAKSARGLSVVSLLLELVGYTVTLSYSYTS-GYPFSSYGEYPFLLLQAVILILCIFH--FS-GQTVTVVQFLGYI 125 (230)
T ss_pred HHHHHhhcccccccHHHHHHHHHHHHheeeehhhc-CCCchhHHHHHHHHHHHHHHHHHHHH--hc-cceeehhhHHHHH
Confidence 48999999999999999999887775322111110 00122446667777777666665553 33 1112234444444
Q ss_pred hHHHHHHHHHHhcCCcchhhhHHHHHHHHHHhhhhhHHHHHhhcC
Q 029529 100 IVLPCLVLALLINERFTFKEVMWTFSLYLEAVAILPQLVLLQRTR 144 (192)
Q Consensus 100 ll~p~~vLali~~~~~~~~eilWtFSiyLEsvAILPQL~mlqk~~ 144 (192)
.+++....+.. .|- .+.+..=+-.+-.-.++=+||+.-..|++
T Consensus 126 ~~v~~~~~sk~-~p~-~~~~L~~~~~l~i~v~sr~~Qi~~n~~~~ 168 (230)
T KOG3211|consen 126 ALVVSVLASKA-LPL-WIITLAQNLCLPIVVVSRLLQIQCNYHNR 168 (230)
T ss_pred HHHHHHHHHhh-hhH-HHHHHHHhcCchhhhHHHHHHHHHHhccc
Confidence 44443333211 111 11122222222223366688988887654
No 9
>PTZ00154 40S ribosomal protein S17; Provisional
Probab=63.10 E-value=5.3 Score=32.20 Aligned_cols=27 Identities=48% Similarity=0.582 Sum_probs=20.2
Q ss_pred hhhhhHHHHHHHHHHHHHHhhcccccccccchhH
Q 029529 5 RLAGDMTHLASVLVLLLKIHTIKSCAGISLKTQE 38 (192)
Q Consensus 5 r~~gd~~Hl~s~~iLl~Ki~~~kS~~GiSlkTQ~ 38 (192)
|++|...|+ .|-.+...+.|||+|.|+
T Consensus 49 rIAGYIThl-------mkri~~gpvrgis~klqe 75 (134)
T PTZ00154 49 KIAGFVTHL-------MKRIQKGPVRGISLKLQE 75 (134)
T ss_pred HHHHHHHHH-------HhhhccCCccccceehhH
Confidence 567777775 344556789999999997
No 10
>KOG2489 consensus Transmembrane protein [General function prediction only]
Probab=37.27 E-value=8.6 Score=37.42 Aligned_cols=52 Identities=21% Similarity=0.397 Sum_probs=28.0
Q ss_pred HHhHHHHHH----HHHHhcC--Ccc--hhhhHHHHHHHHHHhhhhhHHHHHhhcCCcchh
Q 029529 98 WFIVLPCLV----LALLINE--RFT--FKEVMWTFSLYLEAVAILPQLVLLQRTRNIDNL 149 (192)
Q Consensus 98 ~~ll~p~~v----Lali~~~--~~~--~~eilWtFSiyLEsvAILPQL~mlqk~~~vE~l 149 (192)
.|++.|-.+ -+++..| +|. ..+.+..+=.-.--+-++|||+.-+|-+.|-.+
T Consensus 441 s~~L~PL~vg~aVYSLlY~~hKsWYSWvLn~l~~~vy~FGFi~M~PQLFINYKLKSVAHL 500 (592)
T KOG2489|consen 441 SYLLFPLLVGGAVYSLLYVEHKSWYSWVLNSLYNGVYAFGFIFMLPQLFINYKLKSVAHL 500 (592)
T ss_pred HHHHHHHHHHHHHHhhhhcccccHHHHHHHHHHhHHHHHHHHHhChHHHhhhhhhhhhcC
Confidence 356656443 3444433 332 333333332222334579999999997766543
No 11
>PHA02246 hypothetical protein
Probab=36.29 E-value=1.6e+02 Score=24.86 Aligned_cols=119 Identities=25% Similarity=0.383 Sum_probs=59.8
Q ss_pred HHHhhcccccccccchhHHHHHHHHhhcccccchhHHHHHHHHH------HHH--HHHHHHHHHHHhhcccccccccccc
Q 029529 21 LKIHTIKSCAGISLKTQELYALVFATRYLDIFTNYISFYNTIMK------LIF--LGSSFSIVWYIKRHKIVHRSYDKDQ 92 (192)
Q Consensus 21 ~Ki~~~kS~~GiSlkTQ~ly~iVf~~Ryldl~~~~~s~Ynt~mk------i~~--i~ss~~ivyl~~~~~~~~~TY~~~~ 92 (192)
..+.+.||..|+|-- .-|++++... .|.||.... ++. +-....++-+. -.+| |.+
T Consensus 25 ~slvk~~nv~GvS~~--FWYLi~~tvg--------iSfyNlL~T~~~~fqi~svg~nl~lgivcLl------v~~~-rkk 87 (192)
T PHA02246 25 VALVKAESVKGVSNY--FWYLIVATVG--------ISFYNLLLTDASVFQIVSVGLNLTLGIVCLL------VASY-RKK 87 (192)
T ss_pred HHHhhhcccccHHHH--HHHHHHHHHH--------HHHHHHHhcCCceEEEeeeehhhhhhhhhee------eehh-hcc
Confidence 567899999999843 5566555332 355663311 110 00111111111 1122 234
Q ss_pred ccchhHHhHHHHHHHHHHhcCCcchhhhHHHHHHHHHHhhhhhHHHHHhhcCCcchhHHHH--HHHHHHH
Q 029529 93 DTFRHWFIVLPCLVLALLINERFTFKEVMWTFSLYLEAVAILPQLVLLQRTRNIDNLTGQY--VFLLGYI 160 (192)
Q Consensus 93 D~f~~~~ll~p~~vLali~~~~~~~~eilWtFSiyLEsvAILPQL~mlqk~~~vE~lTshY--v~aLG~y 160 (192)
|-|...++++-++.+-++ . +..|+.-+.+.----.|-.||...+.|++..|...... +++.|+.
T Consensus 88 d~f~~~fiiifSLllfll-~---~~~evtQtVat~tIiLaYi~QIIqfyKTK~SEg~n~~l~lii~~GL~ 153 (192)
T PHA02246 88 DYFSIPFIIVFSLLLFLL-S---DFTALTQTVATITIILAYVTQITTFYKTKSAEGTNRFLFLIIGLGLA 153 (192)
T ss_pred ccccchHHHHHHHHHHHH-h---hhHHHHHHHHHHHHHHHHHHHHHHHhhhcccCCCChhHHHHHHHHHH
Confidence 666555555444332221 1 12233333333333457889999999999888755433 3445555
No 12
>TIGR00951 2A43 Lysosomal Cystine Transporter.
Probab=35.83 E-value=1.1e+02 Score=26.18 Aligned_cols=31 Identities=23% Similarity=0.574 Sum_probs=22.9
Q ss_pred HhhhhhHHHHHhhcCCcchhHHHHHH--HHHHH
Q 029529 130 AVAILPQLVLLQRTRNIDNLTGQYVF--LLGYI 160 (192)
Q Consensus 130 svAILPQL~mlqk~~~vE~lTshYv~--aLG~y 160 (192)
+++-+||+..-.|++.+|.+.-.++. .+|..
T Consensus 16 ~~~~~PQi~~n~k~ks~~GlS~~~~~l~~~g~~ 48 (220)
T TIGR00951 16 SISFYPQIIKNWRRKSAEGLSFDFVMLNLVGFT 48 (220)
T ss_pred HHHHhhHHHHHHhccccCCcCHHHHHHHHHHHH
Confidence 56778999999999999986555544 44443
No 13
>PF02790 COX2_TM: Cytochrome C oxidase subunit II, transmembrane domain This family corresponds to chains b and o.; InterPro: IPR011759 Cytochrome c oxidase (1.9.3.1 from EC) [, ] is an oligomeric enzymatic complex which is a component of the respiratory chain and is involved in the transfer of electrons from cytochrome c to oxygen. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. The enzyme complex consists of 3-4 subunits (prokaryotes) to up to 13 polypeptides (mammals). Subunit 2 (CO II) transfers the electrons from cytochrome c to the catalytic subunit 1. It contains two adjacent transmembrane regions in its N terminus and the major part of the protein is exposed to the periplasmic or to the mitochondrial intermembrane space, respectively. CO II provides the substrate-binding site and contains a copper centre called Cu(A) (see IPR001505 from INTERPRO), probably the primary acceptor in cytochrome c oxidase. An exception is the corresponding subunit of the cbb3-type oxidase which lacks the copper A redox-centre. Several bacterial CO II have a C-terminal extension that contains a covalently bound haem c. The N-terminal domain of cytochrome C oxidase contains two transmembrane alpha-helices. ; GO: 0004129 cytochrome-c oxidase activity, 0005507 copper ion binding, 0009055 electron carrier activity, 0022900 electron transport chain, 0016021 integral to membrane; PDB: 3VRJ_C 2EIN_B 3AG3_B 2DYR_O 3AG1_B 2EIK_O 3ASN_B 1OCR_B 2EIJ_B 1OCC_O ....
Probab=31.05 E-value=1.1e+02 Score=21.14 Aligned_cols=22 Identities=14% Similarity=0.422 Sum_probs=14.8
Q ss_pred ccchhHHhHHHHHHHHHHhcCC
Q 029529 93 DTFRHWFIVLPCLVLALLINER 114 (192)
Q Consensus 93 D~f~~~~ll~p~~vLali~~~~ 114 (192)
.+.-...-++|++++..+.-|+
T Consensus 60 ~~lE~~WTiiP~iiLl~l~~pS 81 (84)
T PF02790_consen 60 NKLEIIWTIIPAIILLFLAFPS 81 (84)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHH
T ss_pred hhhhhhhhHHHHHHHHHHHhhh
Confidence 3344557788998887766554
No 14
>PF03083 MtN3_slv: Sugar efflux transporter for intercellular exchange; InterPro: IPR004316 This family includes proteins such as Drosophila saliva [], MtN3 involved in root nodule development [] and proteins involved in activation and expression of recombination activation genes (RAGs) []. Although the molecular function of these proteins is unknown, they are almost certainly transmembrane proteins. This signature maps to transmembrane helices which are found in two copies in most members of the family.; GO: 0016021 integral to membrane
Probab=28.35 E-value=88 Score=22.08 Aligned_cols=34 Identities=12% Similarity=0.154 Sum_probs=24.0
Q ss_pred hhhhhHHHHHHH---HHHHHHHhhcccccccccchhH
Q 029529 5 RLAGDMTHLASV---LVLLLKIHTIKSCAGISLKTQE 38 (192)
Q Consensus 5 r~~gd~~Hl~s~---~iLl~Ki~~~kS~~GiSlkTQ~ 38 (192)
..+|..+.++.+ +--+.|++|+||..++|.-...
T Consensus 4 g~~~~~~~i~~~~spl~~i~~v~k~ks~~~~~~~~~~ 40 (87)
T PF03083_consen 4 GILASVSSIIMFLSPLPQIRQVIKTKSTGSVSFPPFL 40 (87)
T ss_pred eHHHHHHHHHHHHHHHHHHHHHHhCCCCCccceehhH
Confidence 445555555433 4667999999999999987543
No 15
>COG4095 Uncharacterized conserved protein [Function unknown]
Probab=27.63 E-value=1.3e+02 Score=22.70 Aligned_cols=35 Identities=26% Similarity=0.253 Sum_probs=25.4
Q ss_pred hhHHHHHHHHHHHHHHhhcccccccccchhHHHHH
Q 029529 8 GDMTHLASVLVLLLKIHTIKSCAGISLKTQELYAL 42 (192)
Q Consensus 8 gd~~Hl~s~~iLl~Ki~~~kS~~GiSlkTQ~ly~i 42 (192)
|...-.++++-=..|+.|+||.+++|+-+-+...+
T Consensus 12 a~ilttf~flPQ~iki~ktK~t~~Isl~~fii~~i 46 (89)
T COG4095 12 AGILTTFAFLPQLIKIIKTKNTASISLPMFIILNI 46 (89)
T ss_pred HHHHHHHHHHHHHHHHHhccccccccHHHHHHHHH
Confidence 34445566777779999999999999875544443
No 16
>PF00833 Ribosomal_S17e: Ribosomal S17; InterPro: IPR001210 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaebacterial ribosomal proteins can be grouped in this family of ribosomal proteins, S17e. They include, vertebrate, Drosophila and Neurospora crassa (crp-3) S17's as well as yeast S17a (RP51A) and S17b (RP51B) and archaebacterial S17e [, , ].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1RQ6_A 2XZM_V 2XZN_V 3IZ6_Q 3IZB_Q 3O30_K 3O2Z_K 3U5G_R 3U5C_R.
Probab=26.83 E-value=48 Score=26.35 Aligned_cols=27 Identities=44% Similarity=0.585 Sum_probs=19.5
Q ss_pred hhhhhHHHHHHHHHHHHHHhhcccccccccchhH
Q 029529 5 RLAGDMTHLASVLVLLLKIHTIKSCAGISLKTQE 38 (192)
Q Consensus 5 r~~gd~~Hl~s~~iLl~Ki~~~kS~~GiSlkTQ~ 38 (192)
|++|...|+ .|-.+.....|+|+|.|+
T Consensus 49 kIAGYvThl-------mKriq~g~vrgis~klqE 75 (121)
T PF00833_consen 49 KIAGYVTHL-------MKRIQRGPVRGISIKLQE 75 (121)
T ss_dssp HHHHHHHHH-------HHHHTSSSSTTCSSCCCC
T ss_pred HHHHHHHHH-------HHHHHhccccccchhhhH
Confidence 466666664 455566778999999986
No 17
>PF10192 GpcrRhopsn4: Rhodopsin-like GPCR transmembrane domain; InterPro: IPR019336 G-protein-coupled receptors, GPCRs, constitute a vast protein family that encompasses a wide range of functions (including various autocrine, paracrine and endocrine processes). They show considerable diversity at the sequence level, on the basis of which they can be separated into distinct groups. We use the term clan to describe the GPCRs, as they embrace a group of families for which there are indications of evolutionary relationship, but between which there is no statistically significant similarity in sequence []. The currently known clan members include the rhodopsin-like GPCRs, the secretin-like GPCRs, the cAMP receptors, the fungal mating pheromone receptors, and the metabotropic glutamate receptor family. There is a specialised database for GPCRs (http://www.gpcr.org/7tm/). This region of 270 amino acids is the seven transmembrane alpha-helical domains included within five GPCRRHODOPSN4 motifs of a G-protein-coupled-receptor (GPCR) protein, conserved from nematodes to humans [].
Probab=24.53 E-value=4.3e+02 Score=22.62 Aligned_cols=17 Identities=35% Similarity=0.960 Sum_probs=8.6
Q ss_pred hHHhHHHHHHH-HHHhcC
Q 029529 97 HWFIVLPCLVL-ALLINE 113 (192)
Q Consensus 97 ~~~ll~p~~vL-ali~~~ 113 (192)
.+++..|..++ |..+.|
T Consensus 218 lWFl~~Pv~~~ia~~v~~ 235 (257)
T PF10192_consen 218 LWFLSLPVIVIIAHFVDP 235 (257)
T ss_pred HHHHHHHHHHHHHHhccH
Confidence 34666776544 444333
Done!