Query psy14840
Match_columns 119
No_of_seqs 171 out of 1718
Neff 8.6
Searched_HMMs 46136
Date Fri Aug 16 22:08:05 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy14840.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/14840hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PHA03234 DNA packaging protein 99.3 1.2E-11 2.6E-16 92.4 6.3 60 57-117 31-92 (338)
2 KOG4219|consensus 99.2 6.8E-12 1.5E-16 94.4 2.7 66 51-116 28-93 (423)
3 PHA02638 CC chemokine receptor 98.9 2.4E-09 5.2E-14 82.1 6.8 59 57-117 97-155 (417)
4 PHA02834 chemokine receptor-li 98.9 3.4E-09 7.3E-14 78.6 6.7 57 58-116 28-84 (323)
5 PHA03235 DNA packaging protein 98.8 1.3E-08 2.9E-13 77.9 7.9 59 57-116 31-91 (409)
6 PHA03087 G protein-coupled che 98.8 1.1E-08 2.3E-13 75.8 5.5 58 57-116 39-96 (335)
7 KOG4220|consensus 98.7 5.6E-10 1.2E-14 84.7 -3.4 61 58-118 30-90 (503)
8 PF00001 7tm_1: 7 transmembran 98.3 6.3E-07 1.4E-11 62.2 3.9 42 75-116 1-42 (257)
9 PF10320 7TM_GPCR_Srsx: Serpen 98.2 5.3E-07 1.2E-11 65.1 0.9 46 70-115 2-47 (257)
10 KOG2087|consensus 96.6 0.00058 1.3E-08 51.5 0.5 50 61-110 27-76 (363)
11 PF05296 TAS2R: Mammalian tast 95.4 0.14 3E-06 38.0 8.0 54 57-110 5-61 (303)
12 PF10328 7TM_GPCR_Srx: Serpent 95.3 0.036 7.8E-07 40.1 4.6 43 68-110 3-45 (274)
13 PF10324 7TM_GPCR_Srw: Serpent 94.3 0.047 1E-06 40.2 3.0 48 68-116 6-54 (318)
14 PF05462 Dicty_CAR: Slime mold 93.9 0.28 6.1E-06 36.5 6.6 52 58-109 6-57 (303)
15 PF10321 7TM_GPCR_Srt: Serpent 92.8 0.8 1.7E-05 34.3 7.5 52 58-109 32-83 (313)
16 PF10317 7TM_GPCR_Srd: Serpent 88.7 1.5 3.2E-05 32.2 5.6 47 64-110 4-51 (292)
17 PF11710 Git3: G protein-coupl 85.2 3.7 7.9E-05 28.7 5.7 25 87-111 30-54 (201)
18 PF01102 Glycophorin_A: Glycop 61.0 15 0.00033 23.8 3.4 21 72-92 76-96 (122)
19 PF09882 DUF2109: Predicted me 57.5 38 0.00083 20.1 4.4 46 69-114 4-49 (78)
20 PF00002 7tm_2: 7 transmembran 56.5 8.5 0.00018 26.9 1.9 42 68-109 10-51 (242)
21 PF10323 7TM_GPCR_Srv: Serpent 47.3 17 0.00036 26.6 2.2 34 77-110 13-50 (283)
22 PF02009 Rifin_STEVOR: Rifin/s 42.4 29 0.00063 26.0 2.8 28 63-90 258-285 (299)
23 PHA03164 hypothetical protein; 42.0 34 0.00074 20.3 2.5 8 97-104 63-70 (88)
24 TIGR01477 RIFIN variant surfac 41.8 45 0.00097 25.6 3.8 30 62-91 311-340 (353)
25 PF11446 DUF2897: Protein of u 41.7 41 0.00088 18.6 2.7 18 67-84 10-27 (55)
26 PF10316 7TM_GPCR_Srbc: Serpen 40.1 63 0.0014 23.7 4.3 52 63-114 10-61 (273)
27 PF10327 7TM_GPCR_Sri: Serpent 39.8 57 0.0012 24.1 4.1 57 58-114 8-68 (303)
28 PTZ00046 rifin; Provisional 39.4 52 0.0011 25.4 3.8 29 62-90 316-344 (358)
29 PF10326 7TM_GPCR_Str: Serpent 34.0 30 0.00065 25.2 1.8 44 66-109 6-50 (307)
30 PF10192 GpcrRhopsn4: Rhodopsi 33.9 1.8E+02 0.0039 20.9 7.9 37 68-104 38-74 (257)
31 PF15330 SIT: SHP2-interacting 32.2 94 0.002 19.6 3.6 25 61-85 3-27 (107)
32 PF10329 DUF2417: Region of un 31.7 96 0.0021 22.4 4.0 37 73-109 84-120 (232)
33 PF02532 PsbI: Photosystem II 30.1 80 0.0017 15.9 2.4 18 59-76 9-26 (36)
34 PF10319 7TM_GPCR_Srj: Serpent 27.6 95 0.0021 23.5 3.5 50 67-116 13-65 (310)
35 PF08114 PMP1_2: ATPase proteo 25.7 23 0.0005 18.4 0.0 21 67-87 13-33 (43)
36 PHA03283 envelope glycoprotein 20.6 1.5E+02 0.0032 24.2 3.5 34 58-91 397-430 (542)
No 1
>PHA03234 DNA packaging protein UL33; Provisional
Probab=99.25 E-value=1.2e-11 Score=92.40 Aligned_cols=60 Identities=18% Similarity=0.281 Sum_probs=51.1
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHH--HhcCCCCchHHHHHHHHHHHHHHHHhhhhccccc
Q psy14840 57 FRYSVISFYSVIFVMSLLGNGLVCYAV--LVSQKMKTVTNFFIINLSTNDIILTLFCVPFSRL 117 (119)
Q Consensus 57 ~~~~~~~~~~~i~~~~~~gN~lvi~v~--~~~~~l~~~~~~fl~nLa~~Dll~~~~~~P~~~~ 117 (119)
.+.++.++|.+++++|++||++|++++ .+++++|+++|+|+.|||++|+++++ +.|+.+.
T Consensus 31 ~~~~~~~~y~~vf~~gl~gN~lvl~v~~~~~~~~~rt~tn~fi~NLAvaDLL~~l-~lp~~~~ 92 (338)
T PHA03234 31 AQILESAINGIMLTLIIPMIIIVICTLIIYHKVAKHNATSFYLITLFASDFLHML-CVFFLTL 92 (338)
T ss_pred HHHHhhHHHHHHHHHHhhhHHHHHHHHHHHhccccccHHHHHHHHHHHHHHHHHH-HHHHHHH
Confidence 467889999999999999999999955 45567799999999999999999987 5666543
No 2
>KOG4219|consensus
Probab=99.20 E-value=6.8e-12 Score=94.43 Aligned_cols=66 Identities=24% Similarity=0.478 Sum_probs=59.8
Q ss_pred CCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHHHHHHHHHHHhhhhcccc
Q psy14840 51 VMAVPLFRYSVISFYSVIFVMSLLGNGLVCYAVLVSQKMKTVTNFFIINLSTNDIILTLFCVPFSR 116 (119)
Q Consensus 51 ~~~~~~~~~~~~~~~~~i~~~~~~gN~lvi~v~~~~~~l~~~~~~fl~nLa~~Dll~~~~~~P~~~ 116 (119)
+....+.+.+..++|.++.+++++||++|+|++..+|++|+.+|+|++|||+||++.++++.|+..
T Consensus 28 f~lp~~~~~~wai~yg~l~~vAv~GN~iVlwIil~hrrMRtvtnyfL~NLAfADl~~s~Fn~~f~f 93 (423)
T KOG4219|consen 28 FVLPAWQQALWAIAYGLLVFVAVVGNLIVLWIILAHRRMRTVTNYFLVNLAFADLSMSIFNTVFNF 93 (423)
T ss_pred ccCCHHHHHHHHHHHHHHHHHHHhcCceEEEEEeehhehhhhHHHHHHHHHHHHHHHHHHhhHHHH
Confidence 444556678899999999999999999999999999999999999999999999999999888743
No 3
>PHA02638 CC chemokine receptor-like protein; Provisional
Probab=98.94 E-value=2.4e-09 Score=82.15 Aligned_cols=59 Identities=31% Similarity=0.644 Sum_probs=51.5
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHHHHHHHHHHHhhhhccccc
Q psy14840 57 FRYSVISFYSVIFVMSLLGNGLVCYAVLVSQKMKTVTNFFIINLSTNDIILTLFCVPFSRL 117 (119)
Q Consensus 57 ~~~~~~~~~~~i~~~~~~gN~lvi~v~~~~~~l~~~~~~fl~nLa~~Dll~~~~~~P~~~~ 117 (119)
....+..++.+++++|++||+++++++.+ |++|++++++++|||++|+++.. +.|+++.
T Consensus 97 ~~~~l~~~y~lvfvlgliGN~LVl~il~~-k~lrt~t~i~llnLAisDLl~~l-~lPf~i~ 155 (417)
T PHA02638 97 ISEYIKIFYIIIFILGLFGNAAIIMILFC-KKIKTITDIYIFNLAISDLIFVI-DFPFIIY 155 (417)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHh-ccCCCHhHHHHHHHHHHHHHHHH-HHHHHHH
Confidence 46778888999999999999999987654 78899999999999999999865 8898764
No 4
>PHA02834 chemokine receptor-like protein; Provisional
Probab=98.92 E-value=3.4e-09 Score=78.58 Aligned_cols=57 Identities=35% Similarity=0.725 Sum_probs=49.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHHHHHHHHHHHhhhhcccc
Q psy14840 58 RYSVISFYSVIFVMSLLGNGLVCYAVLVSQKMKTVTNFFIINLSTNDIILTLFCVPFSR 116 (119)
Q Consensus 58 ~~~~~~~~~~i~~~~~~gN~lvi~v~~~~~~l~~~~~~fl~nLa~~Dll~~~~~~P~~~ 116 (119)
+.+..+++.+++++|++||+++++++.+++++ +++|+|+.|||++|++. ..++|+.+
T Consensus 28 ~~~~~~~~~li~v~~~~gN~lVi~vi~~~~~~-~~~n~~i~nLAiaDll~-~~~lP~~i 84 (323)
T PHA02834 28 NYFVIVFYILLFIFGLIGNVLVIAVLIVKRFM-FVVDVYLFNIAMSDLML-VFSFPFII 84 (323)
T ss_pred hhhHHHHHHHHHHHHHhhHHHHHHHHHhcccc-chhhhhhHHHHHHHHHH-HHHHHHHH
Confidence 56788999999999999999999998886664 57899999999999987 44888754
No 5
>PHA03235 DNA packaging protein UL33; Provisional
Probab=98.84 E-value=1.3e-08 Score=77.94 Aligned_cols=59 Identities=17% Similarity=0.257 Sum_probs=47.5
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC--CchHHHHHHHHHHHHHHHHhhhhcccc
Q psy14840 57 FRYSVISFYSVIFVMSLLGNGLVCYAVLVSQKM--KTVTNFFIINLSTNDIILTLFCVPFSR 116 (119)
Q Consensus 57 ~~~~~~~~~~~i~~~~~~gN~lvi~v~~~~~~l--~~~~~~fl~nLa~~Dll~~~~~~P~~~ 116 (119)
.+....+++.+++++|++||+++++++.+++++ ++..++|++|||++|++. ++++|+.+
T Consensus 31 ~~~~~~~~~~li~vvGiigN~lVL~~~~~~~r~~~~~~~~~~I~NLAvsDLl~-l~~lP~~i 91 (409)
T PHA03235 31 ARTTETFINLLIISVGGPLNLIVLVTQLLANRVHGFSTPTLYMTNLYLANLLT-VFVLPFIM 91 (409)
T ss_pred hHhHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccCCccHHHHHHHHHHHHHH-HHHHHHHH
Confidence 467888999999999999999999986543332 356679999999999987 45888764
No 6
>PHA03087 G protein-coupled chemokine receptor-like protein; Provisional
Probab=98.78 E-value=1.1e-08 Score=75.81 Aligned_cols=58 Identities=31% Similarity=0.618 Sum_probs=50.3
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHHHHHHHHHHHhhhhcccc
Q psy14840 57 FRYSVISFYSVIFVMSLLGNGLVCYAVLVSQKMKTVTNFFIINLSTNDIILTLFCVPFSR 116 (119)
Q Consensus 57 ~~~~~~~~~~~i~~~~~~gN~lvi~v~~~~~~l~~~~~~fl~nLa~~Dll~~~~~~P~~~ 116 (119)
.+....+++.+++++|++||+++++++.++ ++|++.++++.|||++|++.++ ..|..+
T Consensus 39 ~~~~~~~~~~~i~~~gl~gN~lvl~~~~~~-~~~~~~~~ll~~laisDll~~~-~~~~~~ 96 (335)
T PHA03087 39 NSTILIVVYSTIFFFGLVGNIIVIYVLTKT-KIKTPMDIYLLNLAVSDLLFVM-TLPFQI 96 (335)
T ss_pred hhhHHHHHHHHHHHHHHHhhHhEEeeehhc-cccCchHHHHHHHHHHHHHHHH-hHHHHH
Confidence 466788899999999999999999998888 8899999999999999998876 566543
No 7
>KOG4220|consensus
Probab=98.71 E-value=5.6e-10 Score=84.66 Aligned_cols=61 Identities=21% Similarity=0.425 Sum_probs=55.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHHHHHHHHHHHhhhhcccccc
Q psy14840 58 RYSVISFYSVIFVMSLLGNGLVCYAVLVSQKMKTVTNFFIINLSTNDIILTLFCVPFSRLL 118 (119)
Q Consensus 58 ~~~~~~~~~~i~~~~~~gN~lvi~v~~~~~~l~~~~~~fl~nLa~~Dll~~~~~~P~~~~~ 118 (119)
...+.++...+.++.++||++|++.+..+++||+..|||+++||+|||+++.+.+|+..+|
T Consensus 30 ~v~i~~v~~~lsLVTv~GNlLVmiSfKvnrqLqTVnNYfLfSLAcADliIG~~SMnl~t~Y 90 (503)
T KOG4220|consen 30 VVFIVVVTGSLSLVTVVGNLLVMISFKVNRQLQTVNNYFLFSLACADLIIGAFSMNLYTTY 90 (503)
T ss_pred EEeeehhhhHHHHHhhhccEEEEEEEEecceeeeecceeehHHHHhhhhhheeechHHHHH
Confidence 4566778888999999999999999999999999999999999999999999999987654
No 8
>PF00001 7tm_1: 7 transmembrane receptor (rhodopsin family) Rhodopsin-like GPCR superfamily signature 5-hydroxytryptamine 7 receptor signature bradykinin receptor signature gastrin receptor signature melatonin receptor signature olfactory receptor signature; InterPro: IPR000276 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/). The rhodopsin-like GPCRs themselves represent a widespread protein family that includes hormone, neurotransmitter and light receptors, all of which transduce extracellular signals through interaction with guanine nucleotide-binding (G) proteins. Although their activating ligands vary widely in structure and character, the amino acid sequences of the receptors are very similar and are believed to adopt a common structural framework comprising 7 transmembrane (TM) helices [, , ].; GO: 0007186 G-protein coupled receptor protein signaling pathway, 0016021 integral to membrane; PDB: 2KI9_A 3QAK_A 2YDV_A 3VGA_A 3PWH_A 3RFM_A 3EML_A 3VG9_A 3REY_A 3UZA_A ....
Probab=98.32 E-value=6.3e-07 Score=62.18 Aligned_cols=42 Identities=38% Similarity=0.789 Sum_probs=37.7
Q ss_pred HHHHHHHHHHhcCCCCchHHHHHHHHHHHHHHHHhhhhcccc
Q psy14840 75 GNGLVCYAVLVSQKMKTVTNFFIINLSTNDIILTLFCVPFSR 116 (119)
Q Consensus 75 gN~lvi~v~~~~~~l~~~~~~fl~nLa~~Dll~~~~~~P~~~ 116 (119)
||.++++++.++|++|++.++|+.|||++|++.++...|..+
T Consensus 1 GN~lvi~~~~~~~~~~~~~~~~l~~Lav~Dll~~~~~~~~~~ 42 (257)
T PF00001_consen 1 GNILVILVILRSKRLRTPSNILLLNLAVADLLVGLFCIPFYI 42 (257)
T ss_dssp HHHHHHHHHHHSGGG-SHHHHHHHHHHHHHHHHHHTHHHHHH
T ss_pred CchhehhhhhhhccCCChhHHHHHHHHHHHHhhccccccccc
Confidence 899999999999999999999999999999999997777644
No 9
>PF10320 7TM_GPCR_Srsx: Serpentine type 7TM GPCR chemoreceptor Srsx; InterPro: IPR019424 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/). The nematode Caenorhabditis elegans has only 14 types of chemosensory neuron, yet is able to sense and respond to several hundred different chemicals because each neuron detects several stimuli []. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf' []. Chemoreception in C. elegans is mediated by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs). More than 1300 potential chemoreceptor genes have been identified in C. elegans, which are generally prefixed sr for serpentine receptor. The receptor superfamilies include Sra (Sra, Srb, Srab, Sre), Str (Srh, Str, Sri, Srd, Srj, Srm, Srn) and Srg (Srx, Srt, Srg, Sru, Srv, Srxa), as well as the families Srw, Srz, Srbc, Srsx and Srr [, , ]. Many of these proteins have homologues in Caenorhabditis briggsae. This entry represents serpentine receptor class sx (Srsx), which is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf' [].
Probab=98.17 E-value=5.3e-07 Score=65.10 Aligned_cols=46 Identities=24% Similarity=0.410 Sum_probs=42.2
Q ss_pred HHHHHHHHHHHHHHHhcCCCCchHHHHHHHHHHHHHHHHhhhhccc
Q psy14840 70 VMSLLGNGLVCYAVLVSQKMKTVTNFFIINLSTNDIILTLFCVPFS 115 (119)
Q Consensus 70 ~~~~~gN~lvi~v~~~~~~l~~~~~~fl~nLa~~Dll~~~~~~P~~ 115 (119)
++|++||..++.++.++|++|+|++++++.+|++|++.....+|..
T Consensus 2 ~ig~~gN~~~i~~~~~~~~Lrs~~~~li~~~~~~d~~~~~~~~~~~ 47 (257)
T PF10320_consen 2 IIGLFGNLLLIILIFRNKSLRSPCYILICILCFADLICLLGTLPFM 47 (257)
T ss_pred EEEEEccHHHHHHHHhccccccchHHHHHHHHHHHHHHHhhHHHHH
Confidence 4688999999999999999999999999999999999988777754
No 10
>KOG2087|consensus
Probab=96.64 E-value=0.00058 Score=51.48 Aligned_cols=50 Identities=24% Similarity=0.358 Sum_probs=42.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHHHHHHHHHHHhh
Q psy14840 61 VISFYSVIFVMSLLGNGLVCYAVLVSQKMKTVTNFFIINLSTNDIILTLF 110 (119)
Q Consensus 61 ~~~~~~~i~~~~~~gN~lvi~v~~~~~~l~~~~~~fl~nLa~~Dll~~~~ 110 (119)
+-+.-.++.++++.||.+|++.....+...+...++++|||++|++.++.
T Consensus 27 lRi~vW~i~~lAi~gN~~Vl~~~~~~~~~~~~~~~li~~la~ad~~mGiY 76 (363)
T KOG2087|consen 27 LRISVWVIALLAIVGNLLVLLTRFTSRYELNSHRFLICNLAFADLLMGIY 76 (363)
T ss_pred eeehhhhhhhHHhccCeeeeeeeeehhhhccchHHHHHHHHHHHHHcchH
Confidence 33445677888999999999998888877788899999999999999863
No 11
>PF05296 TAS2R: Mammalian taste receptor protein (TAS2R); InterPro: IPR007960 This family consists of several forms of mammalian taste receptor proteins (TAS2Rs). TAS2Rs are G protein-coupled receptors expressed in subsets of taste receptor cells of the tongue and palate epithelia and are organised in the genome in clusters. The proteins are genetically linked to loci that influence bitter perception in mice and humans [].; GO: 0004930 G-protein coupled receptor activity, 0007186 G-protein coupled receptor protein signaling pathway, 0050909 sensory perception of taste, 0016021 integral to membrane
Probab=95.38 E-value=0.14 Score=37.97 Aligned_cols=54 Identities=19% Similarity=0.391 Sum_probs=42.5
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHH---hcCCCCchHHHHHHHHHHHHHHHHhh
Q psy14840 57 FRYSVISFYSVIFVMSLLGNGLVCYAVL---VSQKMKTVTNFFIINLSTNDIILTLF 110 (119)
Q Consensus 57 ~~~~~~~~~~~i~~~~~~gN~lvi~v~~---~~~~l~~~~~~fl~nLa~~Dll~~~~ 110 (119)
.+....++..+.+++|++||+.++.+.. +++|.-.|.+..+.+||++.++.-..
T Consensus 5 ~~~i~~~i~~~~~~~Gi~~N~FI~~vn~~~w~k~~~l~~~d~IL~~La~sr~~l~~~ 61 (303)
T PF05296_consen 5 LEIIFLIILVVEFIIGILGNGFIVLVNCSDWVKSRKLSPSDQILTSLAISRILLQWV 61 (303)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHcCCCCChHHHHHHHHHHHHHHHHHH
Confidence 3566778888999999999999887654 33444468999999999999887653
No 12
>PF10328 7TM_GPCR_Srx: Serpentine type 7TM GPCR chemoreceptor Srx; InterPro: IPR019430 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/). The nematode Caenorhabditis elegans has only 14 types of chemosensory neuron, yet is able to sense and respond to several hundred different chemicals because each neuron detects several stimuli []. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf' []. Chemoreception in C. elegans is mediated by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs). More than 1300 potential chemoreceptor genes have been identified in C. elegans, which are generally prefixed sr for serpentine receptor. The receptor superfamilies include Sra (Sra, Srb, Srab, Sre), Str (Srh, Str, Sri, Srd, Srj, Srm, Srn) and Srg (Srx, Srt, Srg, Sru, Srv, Srxa), as well as the families Srw, Srz, Srbc, Srsx and Srr [, , ]. Many of these proteins have homologues in Caenorhabditis briggsae. This entry represents serpentine receptor class x (Srx) from the Srg superfamily [, ]. Srg receptors contain seven hydrophobic, putative transmembrane, regions and can be distinguished from other 7TM GPCR receptors by their own characteristic TM signatures.
Probab=95.30 E-value=0.036 Score=40.11 Aligned_cols=43 Identities=16% Similarity=0.292 Sum_probs=39.2
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCCchHHHHHHHHHHHHHHHHhh
Q psy14840 68 IFVMSLLGNGLVCYAVLVSQKMKTVTNFFIINLSTNDIILTLF 110 (119)
Q Consensus 68 i~~~~~~gN~lvi~v~~~~~~l~~~~~~fl~nLa~~Dll~~~~ 110 (119)
+.+.|++.|.++++.+.+.+++|++.+..-.+.|++|.+.+++
T Consensus 3 ~s~~G~~~N~~v~~~~~~~~~~~~sF~~l~~~~a~~n~i~~~~ 45 (274)
T PF10328_consen 3 ISIIGIILNWLVFIIIFKLKSLRNSFGILCASQAIANIIICLI 45 (274)
T ss_pred eeHHHHHHHHHHHHHHHhcccccCCHHHHHHHHHHHHHHHHHH
Confidence 4567999999999999999999999999999999999998873
No 13
>PF10324 7TM_GPCR_Srw: Serpentine type 7TM GPCR chemoreceptor Srw; InterPro: IPR019427 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/). The nematode Caenorhabditis elegans has only 14 types of chemosensory neuron, yet is able to sense and respond to several hundred different chemicals because each neuron detects several stimuli []. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf' []. Chemoreception in C. elegans is mediated by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs). More than 1300 potential chemoreceptor genes have been identified in C. elegans, which are generally prefixed sr for serpentine receptor. The receptor superfamilies include Sra (Sra, Srb, Srab, Sre), Str (Srh, Str, Sri, Srd, Srj, Srm, Srn) and Srg (Srx, Srt, Srg, Sru, Srv, Srxa), as well as the families Srw, Srz, Srbc, Srsx and Srr [, , ]. Many of these proteins have homologues in Caenorhabditis briggsae. This entry represents serpentine receptor class w (Srw), which is a solo family amongst the superfamilies of chemoreceptors. The genes encoding Srw do not appear to be under as strong an adaptive evolutionary pressure as those of Srz [].
Probab=94.26 E-value=0.047 Score=40.16 Aligned_cols=48 Identities=15% Similarity=0.279 Sum_probs=38.2
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCCc-hHHHHHHHHHHHHHHHHhhhhcccc
Q psy14840 68 IFVMSLLGNGLVCYAVLVSQKMKT-VTNFFIINLSTNDIILTLFCVPFSR 116 (119)
Q Consensus 68 i~~~~~~gN~lvi~v~~~~~~l~~-~~~~fl~nLa~~Dll~~~~~~P~~~ 116 (119)
+.++|+++|..-+.+. .+|.+|+ ++|.++..+|++|++..+..++..+
T Consensus 6 ~~~~g~~~N~~h~~VL-trk~mR~~~in~~l~~Iai~Dl~~~~~~~~~~~ 54 (318)
T PF10324_consen 6 LSIFGLFINIFHLIVL-TRKSMRSSSINILLIGIAICDLLYMLSILIWEL 54 (318)
T ss_pred EeHHHHHHHHHHhhhc-CChhhhcCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4567999999887666 4566775 8999999999999999887666543
No 14
>PF05462 Dicty_CAR: Slime mold cyclic AMP receptor
Probab=93.91 E-value=0.28 Score=36.53 Aligned_cols=52 Identities=19% Similarity=0.268 Sum_probs=44.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHHHHHHHHHHHh
Q psy14840 58 RYSVISFYSVIFVMSLLGNGLVCYAVLVSQKMKTVTNFFIINLSTNDIILTL 109 (119)
Q Consensus 58 ~~~~~~~~~~i~~~~~~gN~lvi~v~~~~~~l~~~~~~fl~nLa~~Dll~~~ 109 (119)
...+.++..+...++++|-++++....+.|++|++.+-++.-++++|++..+
T Consensus 6 ~~~~~~i~~~~s~lSllGclfiI~tf~~~k~~r~~~~rli~yl~~~~ll~~v 57 (303)
T PF05462_consen 6 IRTLYAIELVASVLSLLGCLFIIITFCLFKRLRKPINRLIFYLSIANLLTNV 57 (303)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCccHHHHHHHHHHHHHHHHH
Confidence 3455666677788899999999999999999999999999999999998654
No 15
>PF10321 7TM_GPCR_Srt: Serpentine type 7TM GPCR chemoreceptor Srt; InterPro: IPR019425 Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type []. Srt is a member of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf' [].
Probab=92.81 E-value=0.8 Score=34.27 Aligned_cols=52 Identities=13% Similarity=0.097 Sum_probs=43.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHHHHHHHHHHHh
Q psy14840 58 RYSVISFYSVIFVMSLLGNGLVCYAVLVSQKMKTVTNFFIINLSTNDIILTL 109 (119)
Q Consensus 58 ~~~~~~~~~~i~~~~~~gN~lvi~v~~~~~~l~~~~~~fl~nLa~~Dll~~~ 109 (119)
+..+...+.+..++..+-....+.++.++++.|.+.|-...-||+.|++...
T Consensus 32 ~p~~G~~~~~~g~~~~~lY~p~~~~i~~~~~~k~~~ykiM~~L~i~Di~~l~ 83 (313)
T PF10321_consen 32 RPILGIYFLIFGIIIIILYIPCLIAIFKKKLFKMSCYKIMFFLAIFDIIQLF 83 (313)
T ss_pred ccchhHHHHHHHHHHHHHHHHHHHHHHHhccccCcHHHHHHHHHHHHHHHHH
Confidence 5666677777777777778888888888888889999999999999999865
No 16
>PF10317 7TM_GPCR_Srd: Serpentine type 7TM GPCR chemoreceptor Srd; InterPro: IPR019421 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/). The nematode Caenorhabditis elegans has only 14 types of chemosensory neuron, yet is able to sense and respond to several hundred different chemicals because each neuron detects several stimuli []. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf' []. Chemoreception in C. elegans is mediated by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs). More than 1300 potential chemoreceptor genes have been identified in C. elegans, which are generally prefixed sr for serpentine receptor. The receptor superfamilies include Sra (Sra, Srb, Srab, Sre), Str (Srh, Str, Sri, Srd, Srj, Srm, Srn) and Srg (Srx, Srt, Srg, Sru, Srv, Srxa), as well as the families Srw, Srz, Srbc, Srsx and Srr [, , ]. Many of these proteins have homologues in Caenorhabditis briggsae. This entry represents the chemoreceptor Srd [].
Probab=88.73 E-value=1.5 Score=32.16 Aligned_cols=47 Identities=15% Similarity=0.357 Sum_probs=37.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCC-CchHHHHHHHHHHHHHHHHhh
Q psy14840 64 FYSVIFVMSLLGNGLVCYAVLVSQKM-KTVTNFFIINLSTNDIILTLF 110 (119)
Q Consensus 64 ~~~~i~~~~~~gN~lvi~v~~~~~~l-~~~~~~fl~nLa~~Dll~~~~ 110 (119)
++.+.+.+|+.-|.++++.+.++.-. -....+++.|-|+.|++.++.
T Consensus 4 ~~~~~~~~~~~~n~~Ll~~i~~~tp~~l~~~~~~l~~~~~~~~~~~~~ 51 (292)
T PF10317_consen 4 YHPIFFILGIILNILLLYLIIFKTPKSLRTYSILLLNTAIFDLISIIS 51 (292)
T ss_pred eHHHHHHHHHHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45677889999999999887765533 356788999999999998763
No 17
>PF11710 Git3: G protein-coupled glucose receptor regulating Gpa2; InterPro: IPR023041 This entry contains a functionally uncharacterised region belonging to the Git3 G-protein coupled receptor. Git3 is one of six proteins required for glucose-triggered adenylate cyclase activation, and is a G protein-coupled receptor responsible for the activation of adenylate cyclase through Gpa2 - heterotrimeric G protein alpha subunit, part of the glucose-detection pathway. Git3 contains seven predicted transmembrane domains, a third cytoplasmic loop and a cytoplasmic tail []. This is the conserved N-terminal domain of the member proteins.
Probab=85.20 E-value=3.7 Score=28.71 Aligned_cols=25 Identities=24% Similarity=0.328 Sum_probs=19.2
Q ss_pred CCCCchHHHHHHHHHHHHHHHHhhh
Q psy14840 87 QKMKTVTNFFIINLSTNDIILTLFC 111 (119)
Q Consensus 87 ~~l~~~~~~fl~nLa~~Dll~~~~~ 111 (119)
+++|..-+.++.||.++|++-++..
T Consensus 30 ~r~~~fR~~LIl~L~~aD~~qal~~ 54 (201)
T PF11710_consen 30 YRRRSFRHQLILNLLLADFIQALAF 54 (201)
T ss_pred hhhhhHHHHHHHHHHHHHHHHHHHH
Confidence 4445656679999999999988753
No 18
>PF01102 Glycophorin_A: Glycophorin A; InterPro: IPR001195 Proteins in this group are responsible for the molecular basis of the blood group antigens, surface markers on the outside of the red blood cell membrane. Most of these markers are proteins, but some are carbohydrates attached to lipids or proteins [Reid M.E., Lomas-Francis C. The Blood Group Antigen FactsBook Academic Press, London / San Diego, (1997)]. Glycophorin A (PAS-2) and glycophorin B (PAS-3) belong to the MNS blood group system and are associated with antigens that include M/N, S/s, U, He, Mi(a), M(c), Vw, Mur, M(g), Vr, M(e), Mt(a), St(a), Ri(a), Cl(a), Ny(a), Hut, Hil, M(v), Far, Mit, Dantu, Hop, Nob, En(a), ENKT, amongst others. Glycophorin A is the major sialoglycoprotein of the erythrocyte membrane []. Structurally, glycophorin A consists of an N-terminal extracellular domain, heavily glycosylated on serine and threonine residues, followed by a transmembrane region and a C-terminal cytoplasmic domain. Other glycophorins in this entry such as Glycophorin B and Glycophorin E represent minor sialoglycoproteins in the erythrocyte membrane.; GO: 0016021 integral to membrane; PDB: 2KPF_B 1AFO_B 2KPE_A.
Probab=61.03 E-value=15 Score=23.78 Aligned_cols=21 Identities=14% Similarity=0.143 Sum_probs=8.6
Q ss_pred HHHHHHHHHHHHHhcCCCCch
Q psy14840 72 SLLGNGLVCYAVLVSQKMKTV 92 (119)
Q Consensus 72 ~~~gN~lvi~v~~~~~~l~~~ 92 (119)
|++|=+++|+.++++++.|.+
T Consensus 76 GvIg~Illi~y~irR~~Kk~~ 96 (122)
T PF01102_consen 76 GVIGIILLISYCIRRLRKKSS 96 (122)
T ss_dssp HHHHHHHHHHHHHHHHS----
T ss_pred HHHHHHHHHHHHHHHHhccCC
Confidence 555555555444444444443
No 19
>PF09882 DUF2109: Predicted membrane protein (DUF2109); InterPro: IPR019214 This entry is found in various hypothetical archaeal proteins and has no known function.
Probab=57.50 E-value=38 Score=20.14 Aligned_cols=46 Identities=11% Similarity=0.261 Sum_probs=32.2
Q ss_pred HHHHHHHHHHHHHHHHhcCCCCchHHHHHHHHHHHHHHHHhhhhcc
Q psy14840 69 FVMSLLGNGLVCYAVLVSQKMKTVTNFFIINLSTNDIILTLFCVPF 114 (119)
Q Consensus 69 ~~~~~~gN~lvi~v~~~~~~l~~~~~~fl~nLa~~Dll~~~~~~P~ 114 (119)
.+.|+++=..++-++..+.+.+.-.|.-..|-+++-++....--|+
T Consensus 4 ~i~g~Iai~~~iR~~~~~~r~~KL~yLnv~~F~iaalIaL~i~~P~ 49 (78)
T PF09882_consen 4 IIIGIIAILMAIRIFLTKSRARKLLYLNVINFAIAALIALYIKSPM 49 (78)
T ss_pred HHHHHHHHHHHHHHHHhHhHHHhhhHHHHHHHHHHHHHHHHhCCcH
Confidence 3445555555666666666667777888888899988887766665
No 20
>PF00002 7tm_2: 7 transmembrane receptor (Secretin family); InterPro: IPR000832 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/). The secretin-like GPCRs include secretin [], calcitonin [], parathyroid hormone/parathyroid hormone-related peptides [] and vasoactive intestinal peptide [], all of which activate adenylyl cyclase and the phosphatidyl-inositol-calcium pathway. These receptors contain seven transmembrane regions, in a manner reminiscent of the rhodopsins and other receptors believed to interact with G-proteins (however there is no significant sequence identity between these families, the secretin-like receptors thus bear their own unique '7TM' signature). Their N terminus is probably located on the extracellular side of the membrane and potentially glycosylated. This N-terminal region contains a long conserved region which allow the binding of large peptidic ligand such as glucagon, secretin, VIP and PACAP; this region contains five conserved cysteines residues which could be involved in disulphide bond. The C-terminal region of these receptor is probably cytoplasmic. Every receptor gene in this family is encoded on multiple exons, and several of these genes are alternatively spliced to yield functionally distinct products. ; GO: 0004930 G-protein coupled receptor activity, 0007186 G-protein coupled receptor protein signaling pathway, 0016021 integral to membrane; PDB: 3L2J_A 1BL1_A.
Probab=56.54 E-value=8.5 Score=26.93 Aligned_cols=42 Identities=19% Similarity=0.206 Sum_probs=1.1
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCCchHHHHHHHHHHHHHHHHh
Q psy14840 68 IFVMSLLGNGLVCYAVLVSQKMKTVTNFFIINLSTNDIILTL 109 (119)
Q Consensus 68 i~~~~~~gN~lvi~v~~~~~~l~~~~~~fl~nLa~~Dll~~~ 109 (119)
-..+++++-.+++......|++|+..+....||++++++..+
T Consensus 10 g~~~Si~~ll~~i~~~~~~r~lr~~~~~i~~~l~~sll~~~~ 51 (242)
T PF00002_consen 10 GCSLSIICLLLTIITYLLFRKLRSFRNKIHLNLCLSLLLANL 51 (242)
T ss_dssp HHH---------------------------------------
T ss_pred HHHHHHHHHHHHHHHHHHHHhhcccchhhhhhhHHHHHHHHH
Confidence 334445555555555555577777667788899999887654
No 21
>PF10323 7TM_GPCR_Srv: Serpentine type 7TM GPCR chemoreceptor Srv; InterPro: IPR019426 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/). The nematode Caenorhabditis elegans has only 14 types of chemosensory neuron, yet is able to sense and respond to several hundred different chemicals because each neuron detects several stimuli []. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf' []. Chemoreception in C. elegans is mediated by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs). More than 1300 potential chemoreceptor genes have been identified in C. elegans, which are generally prefixed sr for serpentine receptor. The receptor superfamilies include Sra (Sra, Srb, Srab, Sre), Str (Srh, Str, Sri, Srd, Srj, Srm, Srn) and Srg (Srx, Srt, Srg, Sru, Srv, Srxa), as well as the families Srw, Srz, Srbc, Srsx and Srr [, , ]. Many of these proteins have homologues in Caenorhabditis briggsae. This entry represents serpentine receptor class v (Srv) from the Srg superfamily [, ]. Srg receptors contain seven hydrophobic, putative transmembrane, regions and can be distinguished from other 7TM GPCR receptors by their own characteristic TM signatures.
Probab=47.27 E-value=17 Score=26.58 Aligned_cols=34 Identities=26% Similarity=0.405 Sum_probs=24.4
Q ss_pred HHHHHHHHhcCC----CCchHHHHHHHHHHHHHHHHhh
Q psy14840 77 GLVCYAVLVSQK----MKTVTNFFIINLSTNDIILTLF 110 (119)
Q Consensus 77 ~lvi~v~~~~~~----l~~~~~~fl~nLa~~Dll~~~~ 110 (119)
..+++++.+.|+ .+++-+-.+.+-+++|++....
T Consensus 13 ~~il~~l~~~r~~~~~~~~~Fy~l~~~~~iaDi~~~~~ 50 (283)
T PF10323_consen 13 IFILYCLLKLRKRSKTFKSTFYTLLIQHCIADILSMLF 50 (283)
T ss_pred HHHHHHHHHcccCccccCCHHHHHHHHHHHHHHHHHHH
Confidence 444455555443 4689999999999999998653
No 22
>PF02009 Rifin_STEVOR: Rifin/stevor family; InterPro: IPR002858 Malaria is still a major cause of mortality in many areas of the world. Plasmodium falciparum causes the most severe human form of the disease and is responsible for most fatalities. Severe cases of malaria can occur when the parasite invades and then proliferates within red blood cell erythrocytes. The parasite produces many variant antigenic proteins, encoded by multigene families, which are present on the surface of the infected erythrocyte and play important roles in virulence. A crucial survival mechanism for the malaria parasite is its ability to evade the immune response by switching these variant surface antigens. The high virulence of P. falciparum relative to other malarial parasites is in large part due to the fact that in this organism many of these surface antigens mediate the binding of infected erythrocytes to the vascular endothelium (cytoadherence) and non-infected erythrocytes (rosetting). This can lead to the accumulation of infected cells in the vasculature of a variety of organs, blocking the blood flow and reducing the oxygen supply. Clinical symptoms of severe infection can include fever, progressive anaemia, multi-organ dysfunction and coma. For more information see []. Several multicopy gene families have been described in Plasmodium falciparum, including the stevor family of subtelomeric open reading frames and the rif interspersed repetitive elements. Both families contain three predicted transmembrane segments. It has been proposed that stevor and rif are members of a larger superfamily that code for variant surface antigens [].
Probab=42.41 E-value=29 Score=25.98 Aligned_cols=28 Identities=18% Similarity=0.259 Sum_probs=18.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCCC
Q psy14840 63 SFYSVIFVMSLLGNGLVCYAVLVSQKMK 90 (119)
Q Consensus 63 ~~~~~i~~~~~~gN~lvi~v~~~~~~l~ 90 (119)
+...++.++.++--.++|+.++|+||.+
T Consensus 258 I~aSiiaIliIVLIMvIIYLILRYRRKK 285 (299)
T PF02009_consen 258 IIASIIAILIIVLIMVIIYLILRYRRKK 285 (299)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3445555555666677788888877643
No 23
>PHA03164 hypothetical protein; Provisional
Probab=42.00 E-value=34 Score=20.33 Aligned_cols=8 Identities=13% Similarity=0.160 Sum_probs=3.0
Q ss_pred HHHHHHHH
Q psy14840 97 IINLSTND 104 (119)
Q Consensus 97 l~nLa~~D 104 (119)
+..||++=
T Consensus 63 LtgLaIam 70 (88)
T PHA03164 63 LTGLAIAM 70 (88)
T ss_pred HHHHHHHH
Confidence 33333333
No 24
>TIGR01477 RIFIN variant surface antigen, rifin family. This model represents the rifin branch of the rifin/stevor family (pfam02009) of predicted variant surface antigens as found in Plasmodium falciparum. This model is based on a set of rifin sequences kindly provided by Matt Berriman from the Sanger Center. This is a global model and assesses a penalty for incomplete sequence. Additional fragmentary sequences may be found with the fragment model and a cutoff of 20 bits.
Probab=41.77 E-value=45 Score=25.63 Aligned_cols=30 Identities=17% Similarity=0.214 Sum_probs=21.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcCCCCc
Q psy14840 62 ISFYSVIFVMSLLGNGLVCYAVLVSQKMKT 91 (119)
Q Consensus 62 ~~~~~~i~~~~~~gN~lvi~v~~~~~~l~~ 91 (119)
.+...++.++.++--.++|+.+.|+||.+.
T Consensus 311 ~IiaSiIAIvvIVLIMvIIYLILRYRRKKK 340 (353)
T TIGR01477 311 PIIASIIAILIIVLIMVIIYLILRYRRKKK 340 (353)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhcch
Confidence 345566666777777788888888887543
No 25
>PF11446 DUF2897: Protein of unknown function (DUF2897); InterPro: IPR021550 This is a bacterial family of uncharacterised proteins.
Probab=41.74 E-value=41 Score=18.62 Aligned_cols=18 Identities=22% Similarity=0.135 Sum_probs=10.7
Q ss_pred HHHHHHHHHHHHHHHHHH
Q psy14840 67 VIFVMSLLGNGLVCYAVL 84 (119)
Q Consensus 67 ~i~~~~~~gN~lvi~v~~ 84 (119)
++.+--++||+.++--..
T Consensus 10 viVlgvIigNia~LK~sA 27 (55)
T PF11446_consen 10 VIVLGVIIGNIAALKYSA 27 (55)
T ss_pred HHHHHHHHhHHHHHHHhc
Confidence 333344579998874443
No 26
>PF10316 7TM_GPCR_Srbc: Serpentine type 7TM GPCR chemoreceptor Srbc ; InterPro: IPR019420 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/). The nematode Caenorhabditis elegans has only 14 types of chemosensory neuron, yet is able to sense and respond to several hundred different chemicals because each neuron detects several stimuli []. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf' []. Chemoreception in C. elegans is mediated by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs). More than 1300 potential chemoreceptor genes have been identified in C. elegans, which are generally prefixed sr for serpentine receptor. The receptor superfamilies include Sra (Sra, Srb, Srab, Sre), Str (Srh, Str, Sri, Srd, Srj, Srm, Srn) and Srg (Srx, Srt, Srg, Sru, Srv, Srxa), as well as the families Srw, Srz, Srbc, Srsx and Srr [, , ]. Many of these proteins have homologues in Caenorhabditis briggsae. This entry represents serpentine receptor class b (Srb) from the Sra superfamily []. Srb receptors contain 6-8 hydrophobic, putative transmembrane, regions and can be distinguished from other 7TM GPCR receptors by their own characteristic TM signatures. Srbc is a solo family amongst the superfamilies of chemoreceptors.
Probab=40.06 E-value=63 Score=23.75 Aligned_cols=52 Identities=13% Similarity=0.094 Sum_probs=32.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHHHHHHHHHHHhhhhcc
Q psy14840 63 SFYSVIFVMSLLGNGLVCYAVLVSQKMKTVTNFFIINLSTNDIILTLFCVPF 114 (119)
Q Consensus 63 ~~~~~i~~~~~~gN~lvi~v~~~~~~l~~~~~~fl~nLa~~Dll~~~~~~P~ 114 (119)
.+-.+........|...++.+...|+.|++--.++--..+.|.+.+....+.
T Consensus 10 ~i~i~~s~~~~~iN~~lL~~if~~Kk~kk~~l~LfY~Rf~~D~~~~~~~~~~ 61 (273)
T PF10316_consen 10 IIGIIFSIITCLINFYLLYSIFYSKKKKKPDLSLFYFRFAIDVFYGFSVFIY 61 (273)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhccccCCCCEEeeHHHHHHHHHHHHHHHHH
Confidence 3334445567778998888887555544443333344567898888765443
No 27
>PF10327 7TM_GPCR_Sri: Serpentine type 7TM GPCR chemoreceptor Sri; InterPro: IPR019429 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/). The nematode Caenorhabditis elegans has only 14 types of chemosensory neuron, yet is able to sense and respond to several hundred different chemicals because each neuron detects several stimuli []. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf' []. Chemoreception in C. elegans is mediated by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs). More than 1300 potential chemoreceptor genes have been identified in C. elegans, which are generally prefixed sr for serpentine receptor. The receptor superfamilies include Sra (Sra, Srb, Srab, Sre), Str (Srh, Str, Sri, Srd, Srj, Srm, Srn) and Srg (Srx, Srt, Srg, Sru, Srv, Srxa), as well as the families Srw, Srz, Srbc, Srsx and Srr [, , ]. Many of these proteins have homologues in Caenorhabditis briggsae. This entry represents Sri, which is part of the Str superfamily of chemoreceptors.
Probab=39.81 E-value=57 Score=24.11 Aligned_cols=57 Identities=28% Similarity=0.498 Sum_probs=39.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHh-cCCCCchHHHHH---HHHHHHHHHHHhhhhcc
Q psy14840 58 RYSVISFYSVIFVMSLLGNGLVCYAVLV-SQKMKTVTNFFI---INLSTNDIILTLFCVPF 114 (119)
Q Consensus 58 ~~~~~~~~~~i~~~~~~gN~lvi~v~~~-~~~l~~~~~~fl---~nLa~~Dll~~~~~~P~ 114 (119)
..++...+-+++.++++-|.+.++.+.. .+++.+.-|+++ ....+.|+-.+...-|.
T Consensus 8 P~~li~~~~~ig~iS~~~n~~~iyLi~fks~k~~~fry~ll~~Qi~~~l~di~~t~L~qpi 68 (303)
T PF10327_consen 8 PQWLINYYHIIGVISFILNSLGIYLIIFKSPKLDNFRYYLLYFQISCTLTDIHLTFLMQPI 68 (303)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHheeEEEecCCccchhhHHHHHHHHHHHhhhhhhhhccch
Confidence 4567778889999999999999987665 444454434333 23456788887766554
No 28
>PTZ00046 rifin; Provisional
Probab=39.42 E-value=52 Score=25.36 Aligned_cols=29 Identities=14% Similarity=0.226 Sum_probs=20.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcCCCC
Q psy14840 62 ISFYSVIFVMSLLGNGLVCYAVLVSQKMK 90 (119)
Q Consensus 62 ~~~~~~i~~~~~~gN~lvi~v~~~~~~l~ 90 (119)
.+...++.++-++--.++|+.+.|+||.+
T Consensus 316 aIiaSiiAIvVIVLIMvIIYLILRYRRKK 344 (358)
T PTZ00046 316 AIIASIVAIVVIVLIMVIIYLILRYRRKK 344 (358)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhcc
Confidence 34556666666666778888888888754
No 29
>PF10326 7TM_GPCR_Str: Serpentine type 7TM GPCR chemoreceptor Str; InterPro: IPR019428 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/). The nematode Caenorhabditis elegans has only 14 types of chemosensory neuron, yet is able to sense and respond to several hundred different chemicals because each neuron detects several stimuli []. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf' []. Chemoreception in C. elegans is mediated by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs). More than 1300 potential chemoreceptor genes have been identified in C. elegans, which are generally prefixed sr for serpentine receptor. The receptor superfamilies include Sra (Sra, Srb, Srab, Sre), Str (Srh, Str, Sri, Srd, Srj, Srm, Srn) and Srg (Srx, Srt, Srg, Sru, Srv, Srxa), as well as the families Srw, Srz, Srbc, Srsx and Srr [, , ]. Many of these proteins have homologues in Caenorhabditis briggsae. This entry represents serpentine receptor class r (Str) from the Str superfamily [, ]. Almost a quarter (22.5%) of str and srj family genes and pseudogenes in C. elegans appear to have been newly formed by gene duplications since the species split [].
Probab=34.04 E-value=30 Score=25.20 Aligned_cols=44 Identities=27% Similarity=0.391 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHHHHHHHHHhcCCCCchHHH-HHHHHHHHHHHHHh
Q psy14840 66 SVIFVMSLLGNGLVCYAVLVSQKMKTVTNF-FIINLSTNDIILTL 109 (119)
Q Consensus 66 ~~i~~~~~~gN~lvi~v~~~~~~l~~~~~~-fl~nLa~~Dll~~~ 109 (119)
.+.++++++.|.+.++.+.++.+.+...|- ++.-.|+.|+.++.
T Consensus 6 ~~~~~~s~~~N~~Li~Li~~~s~k~~G~Yk~Lm~~fs~~~i~fs~ 50 (307)
T PF10326_consen 6 YIGFVLSLFLNSLLIYLILTKSPKSLGSYKYLMIYFSIFEIIFSI 50 (307)
T ss_pred HHHHHHHHHHHHHHHHHHHhccCCCCCCEEEEEehhHHHHHHHHH
Confidence 456678899999999888766554444332 33345666777665
No 30
>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=33.90 E-value=1.8e+02 Score=20.89 Aligned_cols=37 Identities=11% Similarity=0.050 Sum_probs=20.0
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCCchHHHHHHHHHHHH
Q psy14840 68 IFVMSLLGNGLVCYAVLVSQKMKTVTNFFIINLSTND 104 (119)
Q Consensus 68 i~~~~~~gN~lvi~v~~~~~~l~~~~~~fl~nLa~~D 104 (119)
++.+..+-+...+....+++.+|.....+...+.+-=
T Consensus 38 ~y~vl~~~~~~~~~~l~~~~~~h~~~~l~~~~l~l~~ 74 (257)
T PF10192_consen 38 LYIVLSIISIYSIQSLKKRGLMHPVYKLFSAALLLQF 74 (257)
T ss_pred HHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHH
Confidence 3333333344444455666666777777766666443
No 31
>PF15330 SIT: SHP2-interacting transmembrane adaptor protein, SIT
Probab=32.21 E-value=94 Score=19.57 Aligned_cols=25 Identities=12% Similarity=0.210 Sum_probs=14.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHh
Q psy14840 61 VISFYSVIFVMSLLGNGLVCYAVLV 85 (119)
Q Consensus 61 ~~~~~~~i~~~~~~gN~lvi~v~~~ 85 (119)
+..++.+..++.++.|++...-..+
T Consensus 3 Ll~il~llLll~l~asl~~wr~~~r 27 (107)
T PF15330_consen 3 LLGILALLLLLSLAASLLAWRMKQR 27 (107)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 4455666666777777765433333
No 32
>PF10329 DUF2417: Region of unknown function (DUF2417); InterPro: IPR019431 This entry represents a family of fungal proteins with no known function. In some cases these proteins also contain an alpha/beta hydrolase fold (IPR000073 from INTERPRO).
Probab=31.71 E-value=96 Score=22.39 Aligned_cols=37 Identities=27% Similarity=0.346 Sum_probs=16.0
Q ss_pred HHHHHHHHHHHHhcCCCCchHHHHHHHHHHHHHHHHh
Q psy14840 73 LLGNGLVCYAVLVSQKMKTVTNFFIINLSTNDIILTL 109 (119)
Q Consensus 73 ~~gN~lvi~v~~~~~~l~~~~~~fl~nLa~~Dll~~~ 109 (119)
++.|.+.++.+....+.-...++.++-|-+.|++...
T Consensus 84 l~~~~~~L~Ff~vpS~~~r~l~~vl~~Lllvdlilil 120 (232)
T PF10329_consen 84 LITNLFNLWFFGVPSKLERILNIVLAGLLLVDLILIL 120 (232)
T ss_pred HHHHHHHHHheecCcHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344444444333333333344455555555555544
No 33
>PF02532 PsbI: Photosystem II reaction centre I protein (PSII 4.8 kDa protein); InterPro: IPR003686 Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product. PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane [, ]. Within the core of the complex, the chlorophyll and beta-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10 kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection []. This family represents the low molecular weight transmembrane protein PsbI, which is tightly associated with the D1/D2 heterodimer in PSII. The function of PsbI is unknown, but it may be involved in the assembly, dimerisation or stabilisation of PSII dimers [].; GO: 0015979 photosynthesis, 0009523 photosystem II, 0009539 photosystem II reaction center, 0016020 membrane; PDB: 3A0H_i 3ARC_I 3A0B_i 3BZ2_I 3PRQ_I 3KZI_I 3PRR_I 2AXT_i 4FBY_I 1S5L_i ....
Probab=30.09 E-value=80 Score=15.86 Aligned_cols=18 Identities=33% Similarity=0.910 Sum_probs=9.0
Q ss_pred HHHHHHHHHHHHHHHHHH
Q psy14840 59 YSVISFYSVIFVMSLLGN 76 (119)
Q Consensus 59 ~~~~~~~~~i~~~~~~gN 76 (119)
+....++..+++.|...|
T Consensus 9 y~vV~ffv~LFifGflsn 26 (36)
T PF02532_consen 9 YTVVIFFVSLFIFGFLSN 26 (36)
T ss_dssp HHHHHHHHHHHHHHHHTT
T ss_pred hhhHHHHHHHHhccccCC
Confidence 334445555555555544
No 34
>PF10319 7TM_GPCR_Srj: Serpentine type 7TM GPCR chemoreceptor Srj; InterPro: IPR019423 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/). The nematode Caenorhabditis elegans has only 14 types of chemosensory neuron, yet is able to sense and respond to several hundred different chemicals because each neuron detects several stimuli []. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf' []. Chemoreception in C. elegans is mediated by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs). More than 1300 potential chemoreceptor genes have been identified in C. elegans, which are generally prefixed sr for serpentine receptor. The receptor superfamilies include Sra (Sra, Srb, Srab, Sre), Str (Srh, Str, Sri, Srd, Srj, Srm, Srn) and Srg (Srx, Srt, Srg, Sru, Srv, Srxa), as well as the families Srw, Srz, Srbc, Srsx and Srr [, , ]. Many of these proteins have homologues in Caenorhabditis briggsae. This entry represents serpentine receptor class j (Srj) from the Str superfamily [, ]. The Srj family is designated as the out-group based on its location in preliminary phylogenetic analyses of the entire superfamily [].
Probab=27.57 E-value=95 Score=23.45 Aligned_cols=50 Identities=14% Similarity=0.365 Sum_probs=36.2
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCCCchH-HHHHHHHHHHHHHHHhh--hhcccc
Q psy14840 67 VIFVMSLLGNGLVCYAVLVSQKMKTVT-NFFIINLSTNDIILTLF--CVPFSR 116 (119)
Q Consensus 67 ~i~~~~~~gN~lvi~v~~~~~~l~~~~-~~fl~nLa~~Dll~~~~--~~P~~~ 116 (119)
+.++++.+-|.+.++.+..+|+.+-.- .++++--|+-|++.++. .+|..+
T Consensus 13 ~~~~lsf~~Np~fiyli~~~~~~~~G~Yr~LL~~Fa~fn~~~S~~~~~vp~~v 65 (310)
T PF10319_consen 13 IFGILSFIVNPIFIYLIFTEKKSQFGNYRYLLLFFAIFNLIYSVVDLLVPICV 65 (310)
T ss_pred HHHHHHHHHhhhhheeEEcccccccccHHHHHHHHHHHHHHHHHHHHHhhhee
Confidence 445667889999999999888876544 45666778888888763 455544
No 35
>PF08114 PMP1_2: ATPase proteolipid family; InterPro: IPR012589 This family consists of small proteolipids associated with the plasma membrane H+ ATPase. Two proteolipids (PMP1 and PMP2) are associated with the ATPase and both genes are similarly expressed in the wild-type strain of yeast. No modification of the level of transcription of one PMP gene is detected in a strain deleted of the other. Though both proteolipids show similarity with other small proteolipids associated with other cation -transporting ATPases, their functions remain unclear [].
Probab=25.74 E-value=23 Score=18.44 Aligned_cols=21 Identities=24% Similarity=0.422 Sum_probs=11.2
Q ss_pred HHHHHHHHHHHHHHHHHHhcC
Q psy14840 67 VIFVMSLLGNGLVCYAVLVSQ 87 (119)
Q Consensus 67 ~i~~~~~~gN~lvi~v~~~~~ 87 (119)
+.+++|++|-.++...++|+.
T Consensus 13 VF~lVglv~i~iva~~iYRKw 33 (43)
T PF08114_consen 13 VFCLVGLVGIGIVALFIYRKW 33 (43)
T ss_pred ehHHHHHHHHHHHHHHHHHHH
Confidence 344556666666555555443
No 36
>PHA03283 envelope glycoprotein E; Provisional
Probab=20.56 E-value=1.5e+02 Score=24.18 Aligned_cols=34 Identities=15% Similarity=0.229 Sum_probs=21.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCc
Q psy14840 58 RYSVISFYSVIFVMSLLGNGLVCYAVLVSQKMKT 91 (119)
Q Consensus 58 ~~~~~~~~~~i~~~~~~gN~lvi~v~~~~~~l~~ 91 (119)
..++.++..+++.+|++.-++++|...++++.+.
T Consensus 397 ~~~l~~~~~~~~~~~~~~~~l~vw~c~~~r~~~~ 430 (542)
T PHA03283 397 RHYLAFLLAIICTCAALLVALVVWGCILYRRSNR 430 (542)
T ss_pred cccchhHHHHHHHHHHHHHHHhhhheeeehhhcC
Confidence 4455566666667776666677777777555443
Done!