Query 028001
Match_columns 215
No_of_seqs 107 out of 361
Neff 5.8
Searched_HMMs 46136
Date Fri Mar 29 04:45:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028001.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028001hhsearch_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 3.1E-90 6.8E-95 577.7 11.3 212 1-215 1-212 (212)
2 COG5196 ERD2 ER lumen protein 100.0 5.5E-78 1.2E-82 496.8 14.5 213 1-215 1-214 (214)
3 PF00810 ER_lumen_recept: ER l 100.0 1E-57 2.2E-62 372.0 12.1 143 28-172 1-147 (147)
4 PF04193 PQ-loop: PQ loop repe 94.1 0.23 5E-06 33.8 6.2 54 118-171 2-55 (61)
5 TIGR00951 2A43 Lysosomal Cysti 93.7 4.2 9.1E-05 35.2 14.6 50 116-165 137-189 (220)
6 PF04193 PQ-loop: PQ loop repe 90.4 0.44 9.6E-06 32.4 3.7 42 7-48 8-49 (61)
7 KOG3211 Predicted endoplasmic 85.8 16 0.00035 32.0 11.1 168 20-201 50-223 (230)
8 smart00679 CTNS Repeated motif 83.9 0.62 1.4E-05 27.7 1.3 23 19-41 6-28 (32)
9 PHA02246 hypothetical protein 79.3 16 0.00034 30.8 8.3 145 20-193 24-178 (192)
10 TIGR00951 2A43 Lysosomal Cysti 68.8 5.5 0.00012 34.5 3.3 44 128-171 14-64 (220)
11 smart00679 CTNS Repeated motif 66.8 4.7 0.0001 23.7 1.8 26 131-156 1-26 (32)
12 KOG1623 Multitransmembrane pro 58.8 97 0.0021 27.6 9.3 65 123-194 136-204 (243)
13 PTZ00154 40S ribosomal protein 54.8 8.6 0.00019 31.2 1.9 27 5-38 49-75 (134)
14 COG4095 Uncharacterized conser 50.2 1.1E+02 0.0024 23.2 8.0 49 123-171 10-58 (89)
15 COG4095 Uncharacterized conser 35.1 75 0.0016 24.1 4.1 45 7-54 11-55 (89)
16 PF02790 COX2_TM: Cytochrome C 33.2 73 0.0016 22.4 3.8 20 95-114 62-81 (84)
17 PF03083 MtN3_slv: Sugar efflu 25.3 1.1E+02 0.0023 22.0 3.5 34 4-37 3-39 (87)
18 PF10192 GpcrRhopsn4: Rhodopsi 23.6 3.3E+02 0.0071 23.7 6.9 16 98-113 219-235 (257)
19 PF00833 Ribosomal_S17e: Ribos 20.4 81 0.0017 25.2 2.1 27 5-38 49-75 (121)
No 1
>KOG3106 consensus ER lumen protein retaining receptor [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=3.1e-90 Score=577.67 Aligned_cols=212 Identities=59% Similarity=1.014 Sum_probs=208.6
Q ss_pred CchhhhhhhHHHHHHHHHHHHHHhhcccccccccchhHHHHHHHHhccccccchhhHHHHHHHHHHHHHHHHHHHHHHhh
Q 028001 1 MNIFRLAGDMTHLASVLVLLLKIHTIKSCAGISLKTQELYALVFATRYLDIFTNYISFYNTIMKLIFLGSSFSIVWYIKR 80 (215)
Q Consensus 1 mn~fr~~gd~~hl~s~~iLl~Ki~~~kS~~GlSlkTQ~ly~ivf~~Ryldl~~~~~s~Yn~~mk~~~i~ss~~ivyl~~~ 80 (215)
||.||++||++|++|+++|++||+|+|||+|+|+|||++|++||.+||+|+|+++.|.||++||++|++++.+++|+|+.
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 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccccccccccccchhHHhHHHHhhhhhhccCCcchhHHHHHHHHHHHHHHhhhHHHHHhhcCccchhHHHHHHHHHHH
Q 028001 81 HKIVHRSYDKDQDTFRHWFIVLPCLVLALLINERFTFKEVMWTFSLYLEAVAILPQLVLLQRTRNIDNLTGQYVFLLGAY 160 (215)
Q Consensus 81 ~~~~~~Tyd~~~D~f~~~~liip~~vla~l~~~~~~~~ei~WtFSiyLEsvAILPQL~mlqk~~~ve~~tshYv~~Lg~y 160 (215)
| +|+|||+|+|||+++++++||+++|+++||++++.|++||||+|||||||||||+|+||+||+|++|+||++|||+|
T Consensus 81 k--~~~tYd~~~DtFri~~llvp~~vlsl~i~~~~t~~eilWtFsiyLEsVaILPQL~~lq~tg~~E~~TahYvfaLG~y 158 (212)
T KOG3106|consen 81 K--LRATYDKEKDTFRIEYLLVPSAVLSLLINHSFTILEILWTFSIYLESVAILPQLFMLQKTGEAETITAHYLFALGLY 158 (212)
T ss_pred H--HHHHHhcccCceeEEEEehhheeeeeeecCCccHHHHHHHHHHHHHHHHHhHHHHHHHhcCCccchHHHHHHHHHHH
Confidence 4 89999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhhheeeeecCCcchhHHHHHHHHHHHHHhceeeeEEeeeecCccccCCC
Q 028001 161 RALYILNWIYRYFTEDHYIHWITWIAGLVQTLLYADFFYYYFQSWKNNAKLELPA 215 (215)
Q Consensus 161 R~ly~~~Wi~~y~~~~~~~~~~~~~~givQt~l~~DF~y~Y~~~~~~G~~~~Lp~ 215 (215)
|++|++|||+||..|+ +++++++++|++||++||||||+|++++++|+|++||+
T Consensus 159 R~ly~~~WI~r~~~e~-~~~~iai~agiVQT~ly~DFfy~Y~~~v~~g~~~~LP~ 212 (212)
T KOG3106|consen 159 RALYIANWIYRYVTED-FWDPIAIVAGIVQTVLYADFFYLYVTKVLQGKKLKLPA 212 (212)
T ss_pred HHHHHHHHHHHHHhhc-cccchHHHHHHHHHHHHHhHHHHHHHHHHcCCcCCCCC
Confidence 9999999999999998 56999999999999999999999999999999999996
No 2
>COG5196 ERD2 ER lumen protein retaining receptor [Intracellular trafficking and secretion]
Probab=100.00 E-value=5.5e-78 Score=496.84 Aligned_cols=213 Identities=46% Similarity=0.773 Sum_probs=206.6
Q ss_pred CchhhhhhhHHHHHHHHHHHHHHhhcccccccccchhHHHHHHHHhcccccc-chhhHHHHHHHHHHHHHHHHHHHHHHh
Q 028001 1 MNIFRLAGDMTHLASVLVLLLKIHTIKSCAGISLKTQELYALVFATRYLDIF-TNYISFYNTIMKLIFLGSSFSIVWYIK 79 (215)
Q Consensus 1 mn~fr~~gd~~hl~s~~iLl~Ki~~~kS~~GlSlkTQ~ly~ivf~~Ryldl~-~~~~s~Yn~~mk~~~i~ss~~ivyl~~ 79 (215)
||.||++||++|++|+.+|+.||+++|+|+|+|+|||.+|++||++||+|++ +.+.|+||.+||++||+++.+|+++|+
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 8999999999999999999999999999999999999999999999999999 467899999999999999999999999
Q ss_pred hccccccccccccccchhHHhHHHHhhhhhhccCCcchhHHHHHHHHHHHHHHhhhHHHHHhhcCccchhHHHHHHHHHH
Q 028001 80 RHKIVHRSYDKDQDTFRHWFIVLPCLVLALLINERFTFKEVMWTFSLYLEAVAILPQLVLLQRTRNIDNLTGQYVFLLGA 159 (215)
Q Consensus 80 ~~~~~~~Tyd~~~D~f~~~~liip~~vla~l~~~~~~~~ei~WtFSiyLEsvAILPQL~mlqk~~~ve~~tshYv~~Lg~ 159 (215)
.+ +++|||+..|||+...+++||+++|+++|++.++.+++||||+|||||||||||+|+||.||-|++|+||+++||+
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 95 6899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhhheeeeecCCcchhHHHHHHHHHHHHHhceeeeEEeeeecCccccCCC
Q 028001 160 YRALYILNWIYRYFTEDHYIHWITWIAGLVQTLLYADFFYYYFQSWKNNAKLELPA 215 (215)
Q Consensus 160 yR~ly~~~Wi~~y~~~~~~~~~~~~~~givQt~l~~DF~y~Y~~~~~~G~~~~Lp~ 215 (215)
||++|++|||+|+..+.+-.+-+++.+|++||++|.|||+.|.|.|.+||+++||+
T Consensus 159 YRalYip~wI~r~~~~~kk~~~iai~aGivQTlLY~DFf~iYyr~V~rGk~f~LP~ 214 (214)
T COG5196 159 YRALYIPYWILRKVYDIKKTGNIAIAAGIVQTLLYLDFFAIYYRYVFRGKSFSLPS 214 (214)
T ss_pred HHHhhhhHHHHHhhhcccccccchhHHHHHHHHHHHHhHHhhhhhhhcccccCCCC
Confidence 99999999999998875557889999999999999999999999999999999996
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=1e-57 Score=371.96 Aligned_cols=143 Identities=59% Similarity=1.089 Sum_probs=138.2
Q ss_pred cccccccchhHHHHHHHHhccccc--cchhhHHHHHHHHHHHHHHHHHHHHHHhhccccccccccccccchhHHhHHHHh
Q 028001 28 SCAGISLKTQELYALVFATRYLDI--FTNYISFYNTIMKLIFLGSSFSIVWYIKRHKIVHRSYDKDQDTFRHWFIVLPCL 105 (215)
Q Consensus 28 S~~GlSlkTQ~ly~ivf~~Ryldl--~~~~~s~Yn~~mk~~~i~ss~~ivyl~~~~~~~~~Tyd~~~D~f~~~~liip~~ 105 (215)
||+|+|+|||+||++|+++||+|+ +.++.+.||++||+++++++++++|+|.. ++|+|||+++|+|+..++++||+
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 77888999999999999999999999966 58999999999999999999999
Q ss_pred hhhhhcc--CCcchhHHHHHHHHHHHHHHhhhHHHHHhhcCccchhHHHHHHHHHHHHHHHHhhhheee
Q 028001 106 VLALLIN--ERFTFKEVMWTFSLYLEAVAILPQLVLLQRTRNIDNLTGQYVFLLGAYRALYILNWIYRY 172 (215)
Q Consensus 106 vla~l~~--~~~~~~ei~WtFSiyLEsvAILPQL~mlqk~~~ve~~tshYv~~Lg~yR~ly~~~Wi~~y 172 (215)
+||+++| +++++.|++||||+|||||||+|||+|+||+||+|++|+||+++||+||++|++|||+||
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 567899999999999999999999999999999999999999999999999999999997
No 4
>PF04193 PQ-loop: PQ loop repeat
Probab=94.14 E-value=0.23 Score=33.80 Aligned_cols=54 Identities=19% Similarity=0.282 Sum_probs=47.7
Q ss_pred hHHHHHHHHHHHHHHhhhHHHHHhhcCccchhHHHHHHHHHHHHHHHHhhhhee
Q 028001 118 KEVMWTFSLYLEAVAILPQLVLLQRTRNIDNLTGQYVFLLGAYRALYILNWIYR 171 (215)
Q Consensus 118 ~ei~WtFSiyLEsvAILPQL~mlqk~~~ve~~tshYv~~Lg~yR~ly~~~Wi~~ 171 (215)
.+++...+.-+++++-+||+....|++++|.+.--++.......++.+++.+..
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 467788899999999999999999999999999999998888888888777654
No 5
>TIGR00951 2A43 Lysosomal Cystine Transporter.
Probab=93.67 E-value=4.2 Score=35.22 Aligned_cols=50 Identities=18% Similarity=0.222 Sum_probs=32.4
Q ss_pred chhHHHHHHHHHHHHHHhhhHHHHHhhcCccchhHHHHHH--HHH-HHHHHHH
Q 028001 116 TFKEVMWTFSLYLEAVAILPQLVLLQRTRNIDNLTGQYVF--LLG-AYRALYI 165 (215)
Q Consensus 116 ~~~ei~WtFSiyLEsvAILPQL~mlqk~~~ve~~tshYv~--~Lg-~yR~ly~ 165 (215)
.+.+.++...+-+-.++-+||..+-.|.|..+.+-..-++ +.| +-|++--
T Consensus 137 ~~l~~l~~iki~is~ikyiPQi~~Ny~~ksT~glSi~~i~Ld~~G~lqri~ts 189 (220)
T TIGR00951 137 AFVTMLSYIKVAVTLVKYFPQAATNYHNKSTGQLSIITVFLDFTGLLQRIFQS 189 (220)
T ss_pred HHHHHHHHHHHHHHHHHHhHHHHHHHhcCCCCcCCHHHHHHHHHHHHHHHHHH
Confidence 3566777777888888999999999987655544333332 233 3455443
No 6
>PF04193 PQ-loop: PQ loop repeat
Probab=90.36 E-value=0.44 Score=32.37 Aligned_cols=42 Identities=21% Similarity=0.093 Sum_probs=30.7
Q ss_pred hhhHHHHHHHHHHHHHHhhcccccccccchhHHHHHHHHhcc
Q 028001 7 AGDMTHLASVLVLLLKIHTIKSCAGISLKTQELYALVFATRY 48 (215)
Q Consensus 7 ~gd~~hl~s~~iLl~Ki~~~kS~~GlSlkTQ~ly~ivf~~Ry 48 (215)
.|=..-+.+.+==+.|.+|+||+.|+|..+..+..+..+++.
T Consensus 8 i~~~~~~~~~lPQi~~~~k~ks~~glS~~~~~l~~~g~~~~~ 49 (61)
T PF04193_consen 8 ISIVLWIISFLPQIIKNYKRKSTGGLSLWFLLLWLIGSILWV 49 (61)
T ss_pred HHHHHHHHHHHhHHHHHHHccccccccHHHHHHHHHHHHHHH
Confidence 333444455555569999999999999998888777665544
No 7
>KOG3211 consensus Predicted endoplasmic reticulum membrane protein Lec35/MPDU1 involved in monosaccharide-P-dolichol utilization [General function prediction only]
Probab=85.79 E-value=16 Score=31.98 Aligned_cols=168 Identities=15% Similarity=0.136 Sum_probs=87.8
Q ss_pred HHHHhhcccccccccchhHHHHHHHHh--ccccccchhhHHHHHHHHHHHHHHHHHHHHHHhhccccccccccccccchh
Q 028001 20 LLKIHTIKSCAGISLKTQELYALVFAT--RYLDIFTNYISFYNTIMKLIFLGSSFSIVWYIKRHKIVHRSYDKDQDTFRH 97 (215)
Q Consensus 20 l~Ki~~~kS~~GlSlkTQ~ly~ivf~~--Ryldl~~~~~s~Yn~~mk~~~i~ss~~ivyl~~~~~~~~~Tyd~~~D~f~~ 97 (215)
+.||...||+.|+|+.+|+|=++.++. +|.-- .+| ...+.+...|+..+..++-.+.++ |+ -..-+.|.|-.
T Consensus 50 I~kI~aakSa~GLSv~s~~LElvgytvtl~Y~~~-~g~--pFss~gE~~fLl~Q~vili~~if~--f~-~~~~~~v~~l~ 123 (230)
T KOG3211|consen 50 IMKIRAAKSARGLSVVSLLLELVGYTVTLSYSYT-SGY--PFSSYGEYPFLLLQAVILILCIFH--FS-GQTVTVVQFLG 123 (230)
T ss_pred HHHHHhhcccccccHHHHHHHHHHHHheeeehhh-cCC--CchhHHHHHHHHHHHHHHHHHHHH--hc-cceeehhhHHH
Confidence 489999999999999999988877753 33110 011 112345566676676666555553 33 11123444444
Q ss_pred HHhHHHHhhhhhhccCCcchhHHHHHHHHHHHHHHhhhHHHHHhhc---CccchhHHHHHHHHHHHHHHHHhhhheeeee
Q 028001 98 WFIVLPCLVLALLINERFTFKEVMWTFSLYLEAVAILPQLVLLQRT---RNIDNLTGQYVFLLGAYRALYILNWIYRYFT 174 (215)
Q Consensus 98 ~~liip~~vla~l~~~~~~~~ei~WtFSiyLEsvAILPQL~mlqk~---~~ve~~tshYv~~Lg~yR~ly~~~Wi~~y~~ 174 (215)
.+.+++..+.+.. .| ..+.+..=+-.+-.-.++=+||..-..|+ |...-+|.---+.=.+.|.++-+ .+
T Consensus 124 ~~~~v~~~~~sk~-~p-~~~~~L~~~~~l~i~v~sr~~Qi~~n~~~~~tgqls~it~fLsf~g~lARiftsi------q~ 195 (230)
T KOG3211|consen 124 YIALVVSVLASKA-LP-LWIITLAQNLCLPIVVVSRLLQIQCNYHNRSTGQLSLITVFLSFGGCLARIFTSI------QE 195 (230)
T ss_pred HHHHHHHHHHHhh-hh-HHHHHHHHhcCchhhhHHHHHHHHHHhcccccchhHHHHHHHHhhhHHHHHHHHH------Hh
Confidence 4444443322211 11 11122222222223347889999988875 45555554444656677776533 33
Q ss_pred cCCcchhH-HHHHHHHHHHHHhceeeeE
Q 028001 175 EDHYIHWI-TWIAGLVQTLLYADFFYYY 201 (215)
Q Consensus 175 ~~~~~~~~-~~~~givQt~l~~DF~y~Y 201 (215)
.+++.-.. -+++-..+..+.+.++.|+
T Consensus 196 t~d~~mll~~v~s~~~Ng~i~aq~l~Y~ 223 (230)
T KOG3211|consen 196 TGDFLMLLRFVISLALNGLITAQVLRYW 223 (230)
T ss_pred cCChhhHHHHHHHHHHhHHHHHHHHHHH
Confidence 33321111 1134445556666655544
No 8
>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=83.94 E-value=0.62 Score=27.66 Aligned_cols=23 Identities=26% Similarity=0.251 Sum_probs=18.6
Q ss_pred HHHHHhhcccccccccchhHHHH
Q 028001 19 LLLKIHTIKSCAGISLKTQELYA 41 (215)
Q Consensus 19 Ll~Ki~~~kS~~GlSlkTQ~ly~ 41 (215)
-++|++|+||+.|+|.-...+-.
T Consensus 6 Qi~~~~~~ks~~glS~~~~~l~~ 28 (32)
T smart00679 6 QIIKNYRRKSTEGLSILFVLLWL 28 (32)
T ss_pred HHHHHHHcCCcCcCCHHHHHHHH
Confidence 36899999999999987665543
No 9
>PHA02246 hypothetical protein
Probab=79.32 E-value=16 Score=30.77 Aligned_cols=145 Identities=23% Similarity=0.336 Sum_probs=77.7
Q ss_pred HHHHhhcccccccccchhHHHHHHHHhccccccchhhHHHHHHH------HH----HHHHHHHHHHHHHhhccccccccc
Q 028001 20 LLKIHTIKSCAGISLKTQELYALVFATRYLDIFTNYISFYNTIM------KL----IFLGSSFSIVWYIKRHKIVHRSYD 89 (215)
Q Consensus 20 l~Ki~~~kS~~GlSlkTQ~ly~ivf~~Ryldl~~~~~s~Yn~~m------k~----~~i~ss~~ivyl~~~~~~~~~Tyd 89 (215)
+..+.++||..|+|- -.-|++++.. -.|.||... .+ ..+ ..-++-+.. ..|
T Consensus 24 L~slvk~~nv~GvS~--~FWYLi~~tv--------giSfyNlL~T~~~~fqi~svg~nl--~lgivcLlv------~~~- 84 (192)
T PHA02246 24 LVALVKAESVKGVSN--YFWYLIVATV--------GISFYNLLLTDASVFQIVSVGLNL--TLGIVCLLV------ASY- 84 (192)
T ss_pred HHHHhhhcccccHHH--HHHHHHHHHH--------HHHHHHHHhcCCceEEEeeeehhh--hhhhhheee------ehh-
Confidence 367889999999984 3566666543 345666421 11 111 111121111 122
Q ss_pred cccccchhHHhHHHHhhhhhhccCCcchhHHHHHHHHHHHHHHhhhHHHHHhhcCccchhHHHHHHHHHHHHHHHHhhhh
Q 028001 90 KDQDTFRHWFIVLPCLVLALLINERFTFKEVMWTFSLYLEAVAILPQLVLLQRTRNIDNLTGQYVFLLGAYRALYILNWI 169 (215)
Q Consensus 90 ~~~D~f~~~~liip~~vla~l~~~~~~~~ei~WtFSiyLEsvAILPQL~mlqk~~~ve~~tshYv~~Lg~yR~ly~~~Wi 169 (215)
|++|-|...++++-++.+-.+ . +..|+.-+.+.----.|-.||...+.|++..|......-..+|..-++-..+-.
T Consensus 85 rkkd~f~~~fiiifSLllfll-~---~~~evtQtVat~tIiLaYi~QIIqfyKTK~SEg~n~~l~lii~~GL~~L~~~m~ 160 (192)
T PHA02246 85 RKKDYFSIPFIIVFSLLLFLL-S---DFTALTQTVATITIILAYVTQITTFYKTKSAEGTNRFLFLIIGLGLASLIVSMV 160 (192)
T ss_pred hccccccchHHHHHHHHHHHH-h---hhHHHHHHHHHHHHHHHHHHHHHHHhhhcccCCCChhHHHHHHHHHHHHHHHHh
Confidence 235677766766655544332 1 123444444444445688999999999999888766554445544443333322
Q ss_pred eeeeecCCcchhHHHHHHHHHHHH
Q 028001 170 YRYFTEDHYIHWITWIAGLVQTLL 193 (215)
Q Consensus 170 ~~y~~~~~~~~~~~~~~givQt~l 193 (215)
.. + +....+++|+++.++
T Consensus 161 Lt---h---v~~hIiiTEf~N~iL 178 (192)
T PHA02246 161 LT---H---TYVHIIATEFVNFVL 178 (192)
T ss_pred hh---C---CcceeeHHHHHHHHH
Confidence 21 1 122245788877644
No 10
>TIGR00951 2A43 Lysosomal Cystine Transporter.
Probab=68.75 E-value=5.5 Score=34.47 Aligned_cols=44 Identities=18% Similarity=0.370 Sum_probs=32.5
Q ss_pred HHHHHhhhHHHHHhhcCccchhHHHHHHH-------HHHHHHHHHhhhhee
Q 028001 128 LEAVAILPQLVLLQRTRNIDNLTGQYVFL-------LGAYRALYILNWIYR 171 (215)
Q Consensus 128 LEsvAILPQL~mlqk~~~ve~~tshYv~~-------Lg~yR~ly~~~Wi~~ 171 (215)
.=+++-+||.....|++.+|.+.-.++.. .+.|-+....+|-.+
T Consensus 14 ~~~~~~~PQi~~n~k~ks~~GlS~~~~~l~~~g~~~~~~yn~~~~~~~~~~ 64 (220)
T TIGR00951 14 AWSISFYPQIIKNWRRKSAEGLSFDFVMLNLVGFTAYVIFNFLQLYCWSIT 64 (220)
T ss_pred HHHHHHhhHHHHHHhccccCCcCHHHHHHHHHHHHHHHHHHHHHhcchhhh
Confidence 33568899999999999999998888873 445555555555555
No 11
>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=66.77 E-value=4.7 Score=23.73 Aligned_cols=26 Identities=31% Similarity=0.580 Sum_probs=21.4
Q ss_pred HHhhhHHHHHhhcCccchhHHHHHHH
Q 028001 131 VAILPQLVLLQRTRNIDNLTGQYVFL 156 (215)
Q Consensus 131 vAILPQL~mlqk~~~ve~~tshYv~~ 156 (215)
++-+||.....|++.++.+-..+++.
T Consensus 1 ~~~~PQi~~~~~~ks~~glS~~~~~l 26 (32)
T smart00679 1 VSLLPQIIKNYRRKSTEGLSILFVLL 26 (32)
T ss_pred CcchhHHHHHHHcCCcCcCCHHHHHH
Confidence 36799999999999999887766654
No 12
>KOG1623 consensus Multitransmembrane protein [General function prediction only]
Probab=58.81 E-value=97 Score=27.57 Aligned_cols=65 Identities=18% Similarity=0.505 Sum_probs=37.8
Q ss_pred HHHHHHHHHHhhhHHHHHhhcCccchhHHHHHHHHHHHHHHHHhhh-heeeeecCCcc---hhHHHHHHHHHHHHH
Q 028001 123 TFSLYLEAVAILPQLVLLQRTRNIDNLTGQYVFLLGAYRALYILNW-IYRYFTEDHYI---HWITWIAGLVQTLLY 194 (215)
Q Consensus 123 tFSiyLEsvAILPQL~mlqk~~~ve~~tshYv~~Lg~yR~ly~~~W-i~~y~~~~~~~---~~~~~~~givQt~l~ 194 (215)
+.++|.-..+.++ .-=|++++|.+=--- -+.-++-..-| +|...-++.+. +-+..+.|++|..+|
T Consensus 136 nI~~~~sPL~~m~---~VIktkSvE~mPf~L----s~a~fl~a~~W~lYGlli~D~~IaipN~iG~~l~~~QL~Ly 204 (243)
T KOG1623|consen 136 NISMFAAPLSVIR---KVIKTKSVEYMPFPL----SFALFLVAVQWLLYGLLIKDFFIAIPNVLGFLLGLIQLILY 204 (243)
T ss_pred hHHhhhccHHhhh---hheecCceeeechHH----HHHHHHHHHHHHHHHHHhcCeEEEcccHHHHHHHHHHHHHh
Confidence 4555666666666 333567777664333 33344445556 44443343332 245678999999999
No 13
>PTZ00154 40S ribosomal protein S17; Provisional
Probab=54.79 E-value=8.6 Score=31.18 Aligned_cols=27 Identities=48% Similarity=0.539 Sum_probs=19.8
Q ss_pred hhhhhHHHHHHHHHHHHHHhhcccccccccchhH
Q 028001 5 RLAGDMTHLASVLVLLLKIHTIKSCAGISLKTQE 38 (215)
Q Consensus 5 r~~gd~~hl~s~~iLl~Ki~~~kS~~GlSlkTQ~ 38 (215)
|++|...|+. |-.+...+.|||+|.|+
T Consensus 49 rIAGYIThlm-------kri~~gpvrgis~klqe 75 (134)
T PTZ00154 49 KIAGFVTHLM-------KRIQKGPVRGISLKLQE 75 (134)
T ss_pred HHHHHHHHHH-------hhhccCCccccceehhH
Confidence 5677777753 44456689999999997
No 14
>COG4095 Uncharacterized conserved protein [Function unknown]
Probab=50.19 E-value=1.1e+02 Score=23.20 Aligned_cols=49 Identities=24% Similarity=0.339 Sum_probs=40.2
Q ss_pred HHHHHHHHHHhhhHHHHHhhcCccchhHHHHHHHHHHHHHHHHhhhhee
Q 028001 123 TFSLYLEAVAILPQLVLLQRTRNIDNLTGQYVFLLGAYRALYILNWIYR 171 (215)
Q Consensus 123 tFSiyLEsvAILPQL~mlqk~~~ve~~tshYv~~Lg~yR~ly~~~Wi~~ 171 (215)
..+--+-.+|.+||+.-.-|+++..+++--....+..++++-+++-+..
T Consensus 10 ~ia~ilttf~flPQ~iki~ktK~t~~Isl~~fii~~ia~~lwliygILi 58 (89)
T COG4095 10 TIAGILTTFAFLPQLIKIIKTKNTASISLPMFIILNIALFLWLIYGILI 58 (89)
T ss_pred HHHHHHHHHHHHHHHHHHHhccccccccHHHHHHHHHHHHHHHHHHHHH
Confidence 3344466889999999999999999999888888999998877766655
No 15
>COG4095 Uncharacterized conserved protein [Function unknown]
Probab=35.13 E-value=75 Score=24.11 Aligned_cols=45 Identities=22% Similarity=0.199 Sum_probs=31.4
Q ss_pred hhhHHHHHHHHHHHHHHhhcccccccccchhHHHHHHHHhccccccch
Q 028001 7 AGDMTHLASVLVLLLKIHTIKSCAGISLKTQELYALVFATRYLDIFTN 54 (215)
Q Consensus 7 ~gd~~hl~s~~iLl~Ki~~~kS~~GlSlkTQ~ly~ivf~~Ryldl~~~ 54 (215)
.|...-.++++--+.|+.|+||.+++|+-.-+... .++.+.++.+
T Consensus 11 ia~ilttf~flPQ~iki~ktK~t~~Isl~~fii~~---ia~~lwliyg 55 (89)
T COG4095 11 IAGILTTFAFLPQLIKIIKTKNTASISLPMFIILN---IALFLWLIYG 55 (89)
T ss_pred HHHHHHHHHHHHHHHHHHhccccccccHHHHHHHH---HHHHHHHHHH
Confidence 34455567787888999999999999987554444 4445555543
No 16
>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=33.19 E-value=73 Score=22.43 Aligned_cols=20 Identities=15% Similarity=0.426 Sum_probs=13.2
Q ss_pred chhHHhHHHHhhhhhhccCC
Q 028001 95 FRHWFIVLPCLVLALLINER 114 (215)
Q Consensus 95 f~~~~liip~~vla~l~~~~ 114 (215)
.-..+-++|++++..+.-|+
T Consensus 62 lE~~WTiiP~iiLl~l~~pS 81 (84)
T PF02790_consen 62 LEIIWTIIPAIILLFLAFPS 81 (84)
T ss_dssp HHHHHHHHHHHHHHHHHHHH
T ss_pred hhhhhhHHHHHHHHHHHhhh
Confidence 33446688998887765544
No 17
>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=25.32 E-value=1.1e+02 Score=21.95 Aligned_cols=34 Identities=12% Similarity=0.201 Sum_probs=24.3
Q ss_pred hhhhhhHHHHHHH---HHHHHHHhhcccccccccchh
Q 028001 4 FRLAGDMTHLASV---LVLLLKIHTIKSCAGISLKTQ 37 (215)
Q Consensus 4 fr~~gd~~hl~s~---~iLl~Ki~~~kS~~GlSlkTQ 37 (215)
+..+|..+.++.+ +--+.|++|+||..++|.-..
T Consensus 3 lg~~~~~~~i~~~~spl~~i~~v~k~ks~~~~~~~~~ 39 (87)
T PF03083_consen 3 LGILASVSSIIMFLSPLPQIRQVIKTKSTGSVSFPPF 39 (87)
T ss_pred eeHHHHHHHHHHHHHHHHHHHHHHhCCCCCccceehh
Confidence 3455666655433 466799999999999998754
No 18
>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=23.62 E-value=3.3e+02 Score=23.66 Aligned_cols=16 Identities=38% Similarity=1.059 Sum_probs=8.7
Q ss_pred HHhHHHHhhh-hhhccC
Q 028001 98 WFIVLPCLVL-ALLINE 113 (215)
Q Consensus 98 ~~liip~~vl-a~l~~~ 113 (215)
+++..|..++ |.+++|
T Consensus 219 WFl~~Pv~~~ia~~v~~ 235 (257)
T PF10192_consen 219 WFLSLPVIVIIAHFVDP 235 (257)
T ss_pred HHHHHHHHHHHHHhccH
Confidence 4666676543 445444
No 19
>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=20.42 E-value=81 Score=25.23 Aligned_cols=27 Identities=44% Similarity=0.585 Sum_probs=19.2
Q ss_pred hhhhhHHHHHHHHHHHHHHhhcccccccccchhH
Q 028001 5 RLAGDMTHLASVLVLLLKIHTIKSCAGISLKTQE 38 (215)
Q Consensus 5 r~~gd~~hl~s~~iLl~Ki~~~kS~~GlSlkTQ~ 38 (215)
|++|...|+ .|-.+.....|+|+|.|+
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 354566678899999986
Done!