Query psy6616
Match_columns 71
No_of_seqs 101 out of 596
Neff 6.8
Searched_HMMs 46136
Date Fri Aug 16 22:40:36 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6616.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6616hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0085|consensus 99.9 3.4E-24 7.3E-29 147.6 6.7 69 2-71 290-359 (359)
2 KOG0082|consensus 99.9 1.3E-23 2.7E-28 149.1 6.9 69 2-71 286-354 (354)
3 smart00275 G_alpha G protein a 99.8 1.2E-20 2.5E-25 133.0 7.5 67 2-69 275-342 (342)
4 cd00066 G-alpha G protein alph 99.8 1.7E-20 3.7E-25 130.7 7.2 65 2-67 252-317 (317)
5 KOG0099|consensus 99.8 5.3E-19 1.1E-23 123.3 4.4 58 14-71 319-379 (379)
6 PF00503 G-alpha: G-protein al 99.7 9.1E-17 2E-21 113.9 5.4 58 2-60 328-389 (389)
7 cd04152 Arl4_Arl7 Arl4/Arl7 su 72.6 7.6 0.00016 24.4 3.8 27 35-61 144-170 (183)
8 KOG0087|consensus 69.2 8.2 0.00018 26.5 3.5 31 35-65 150-180 (222)
9 PLN00223 ADP-ribosylation fact 53.1 45 0.00098 20.9 4.7 31 33-63 150-180 (181)
10 smart00188 IL10 Interleukin-10 50.9 5.2 0.00011 25.5 0.1 38 4-43 59-97 (137)
11 COG3598 RepA RecA-family ATPas 44.0 27 0.00059 25.8 2.8 37 7-43 206-243 (402)
12 cd04133 Rop_like Rop subfamily 41.8 27 0.00058 22.1 2.3 24 39-62 151-174 (176)
13 PF12017 Tnp_P_element: Transp 39.2 30 0.00065 23.7 2.3 22 33-54 182-203 (236)
14 PRK15467 ethanolamine utilizat 39.0 35 0.00077 21.0 2.5 28 37-64 123-150 (158)
15 PF02208 Sorb: Sorbin homologo 38.7 27 0.00058 18.4 1.6 18 13-30 21-38 (47)
16 cd04149 Arf6 Arf6 subfamily. 37.9 66 0.0014 19.8 3.6 24 34-57 143-166 (168)
17 KOG0703|consensus 34.9 49 0.0011 23.6 2.9 24 4-27 97-120 (287)
18 cd01897 NOG NOG1 is a nucleola 34.9 40 0.00087 20.2 2.2 27 35-61 142-168 (168)
19 cd04126 Rab20 Rab20 subfamily. 34.6 83 0.0018 20.8 3.9 31 36-66 165-195 (220)
20 cd01862 Rab7 Rab7 subfamily. 34.6 69 0.0015 19.1 3.3 29 36-64 142-170 (172)
21 PTZ00133 ADP-ribosylation fact 34.3 94 0.002 19.4 4.0 31 33-63 150-180 (182)
22 smart00176 RAN Ran (Ras-relate 34.1 71 0.0015 20.7 3.4 29 35-63 128-156 (200)
23 KOG0086|consensus 33.4 76 0.0016 21.2 3.4 31 32-62 142-172 (214)
24 PLN02941 inositol-tetrakisphos 33.2 51 0.0011 23.6 2.8 24 2-26 301-325 (328)
25 smart00177 ARF ARF-like small 33.1 1.2E+02 0.0025 18.7 4.2 28 33-60 146-173 (175)
26 COG1586 SpeD S-adenosylmethion 33.0 51 0.0011 21.1 2.5 16 12-27 97-112 (136)
27 cd00881 GTP_translation_factor 32.7 1.1E+02 0.0025 18.3 4.6 48 13-60 131-186 (189)
28 cd04119 RJL RJL (RabJ-Like) su 32.7 61 0.0013 19.1 2.8 26 36-61 142-167 (168)
29 PF08885 GSCFA: GSCFA family; 32.2 31 0.00068 23.8 1.6 12 14-25 240-251 (251)
30 cd00877 Ran Ran (Ras-related n 30.8 92 0.002 19.0 3.4 27 36-62 134-160 (166)
31 COG0163 UbiX 3-polyprenyl-4-hy 29.6 61 0.0013 21.8 2.5 25 4-28 151-175 (191)
32 cd02685 MIT_C MIT_C; domain fo 28.9 1.6E+02 0.0036 18.9 4.9 34 31-64 48-84 (148)
33 smart00175 RAB Rab subfamily o 28.6 93 0.002 18.3 3.1 25 38-62 139-163 (164)
34 cd04134 Rho3 Rho3 subfamily. 28.2 1.1E+02 0.0023 19.1 3.5 29 36-64 149-177 (189)
35 cd01892 Miro2 Miro2 subfamily. 27.7 63 0.0014 19.8 2.3 24 39-62 144-167 (169)
36 cd01867 Rab8_Rab10_Rab13_like 27.7 1.1E+02 0.0025 18.3 3.4 27 36-62 140-166 (167)
37 PF03681 UPF0150: Uncharacteri 27.1 70 0.0015 15.8 2.0 21 3-24 17-41 (48)
38 cd01893 Miro1 Miro1 subfamily. 27.1 55 0.0012 19.8 1.9 25 38-62 141-165 (166)
39 cd04121 Rab40 Rab40 subfamily. 27.0 1.1E+02 0.0023 19.6 3.4 27 36-62 142-168 (189)
40 cd04127 Rab27A Rab27a subfamil 26.7 1.1E+02 0.0025 18.4 3.3 27 36-62 152-178 (180)
41 PRK00454 engB GTP-binding prot 26.0 88 0.0019 19.2 2.7 22 39-60 172-193 (196)
42 cd08811 CARD_IPS1 Caspase acti 26.0 24 0.00052 20.7 0.1 33 16-48 3-35 (84)
43 cd04132 Rho4_like Rho4-like su 25.9 1.2E+02 0.0027 18.5 3.4 28 38-65 144-171 (187)
44 cd01875 RhoG RhoG subfamily. 25.7 1E+02 0.0022 19.4 3.0 27 38-64 154-180 (191)
45 cd04174 Rnd1_Rho6 Rnd1/Rho6 su 25.5 83 0.0018 21.1 2.7 28 39-66 165-193 (232)
46 PF00025 Arf: ADP-ribosylation 25.2 1.7E+02 0.0037 18.2 4.0 29 32-60 147-175 (175)
47 cd04107 Rab32_Rab38 Rab38/Rab3 25.2 1.2E+02 0.0025 19.2 3.2 28 36-63 143-170 (201)
48 cd04112 Rab26 Rab26 subfamily. 25.1 1.3E+02 0.0029 18.7 3.5 30 37-66 139-168 (191)
49 cd04124 RabL2 RabL2 subfamily. 24.9 1.2E+02 0.0026 18.2 3.2 26 37-62 134-159 (161)
50 cd01876 YihA_EngB The YihA (En 24.4 77 0.0017 18.4 2.2 23 37-59 147-169 (170)
51 smart00174 RHO Rho (Ras homolo 24.2 1E+02 0.0022 18.5 2.7 25 38-62 149-173 (174)
52 PF10406 TAF8_C: Transcription 23.8 49 0.0011 17.2 1.1 12 2-14 5-16 (51)
53 cd04123 Rab21 Rab21 subfamily. 23.8 90 0.002 18.2 2.4 23 38-60 139-161 (162)
54 PF00071 Ras: Ras family; Int 23.7 1E+02 0.0022 18.2 2.7 26 36-61 136-161 (162)
55 PRK02770 S-adenosylmethionine 23.3 1.1E+02 0.0024 19.3 2.8 15 13-27 101-115 (139)
56 PF02829 3H: 3H domain; Inter 23.0 1.8E+02 0.0038 17.3 4.1 45 13-57 45-92 (98)
57 cd04150 Arf1_5_like Arf1-Arf5- 23.0 1.8E+02 0.004 17.5 3.8 24 33-56 133-156 (159)
58 PRK13441 F0F1 ATP synthase sub 22.8 2.1E+02 0.0045 18.2 4.1 42 16-57 88-131 (180)
59 cd01869 Rab1_Ypt1 Rab1/Ypt1 su 22.8 1.4E+02 0.0029 17.8 3.1 26 36-61 139-164 (166)
60 PF12261 T_hemolysin: Thermost 22.8 91 0.002 20.5 2.4 36 10-45 6-41 (179)
61 cd01865 Rab3 Rab3 subfamily. 22.7 1.4E+02 0.003 17.9 3.1 26 36-61 138-163 (165)
62 cd04142 RRP22 RRP22 subfamily. 22.7 1.2E+02 0.0025 19.5 2.9 27 36-62 149-175 (198)
63 cd04109 Rab28 Rab28 subfamily. 22.7 1.4E+02 0.0031 19.1 3.3 29 36-64 141-169 (215)
64 cd04120 Rab12 Rab12 subfamily. 22.5 1.7E+02 0.0037 18.9 3.7 27 36-62 138-164 (202)
65 cd04135 Tc10 TC10 subfamily. 22.3 1E+02 0.0022 18.5 2.5 22 39-60 152-173 (174)
66 cd04136 Rap_like Rap-like subf 22.1 92 0.002 18.3 2.2 23 38-60 140-162 (163)
67 PF09670 Cas_Cas02710: CRISPR- 22.0 2.5E+02 0.0054 20.3 4.7 46 10-55 47-92 (379)
68 PF11411 DNA_ligase_IV: DNA li 21.7 20 0.00043 17.9 -0.7 19 40-58 17-35 (36)
69 cd04137 RheB Rheb (Ras Homolog 21.3 1.7E+02 0.0036 17.7 3.3 31 36-66 138-168 (180)
70 cd01866 Rab2 Rab2 subfamily. 21.1 1.8E+02 0.0038 17.5 3.4 27 36-62 141-167 (168)
71 PLN03110 Rab GTPase; Provision 21.0 1.6E+02 0.0036 18.9 3.4 27 36-62 149-175 (216)
72 COG5036 SPX domain-containing 20.4 68 0.0015 24.5 1.6 30 38-67 322-351 (509)
73 PF13232 Complex1_LYR_1: Compl 20.1 1.5E+02 0.0033 15.3 4.0 40 3-58 16-55 (61)
No 1
>KOG0085|consensus
Probab=99.90 E-value=3.4e-24 Score=147.57 Aligned_cols=69 Identities=43% Similarity=0.702 Sum_probs=65.8
Q ss_pred cccCCCCCCC-CChHHHHHHHHHHHHhhccCCCCCeeEeecccccCccHHHHHHHHHHHHHHhhhhhcCCC
Q psy6616 2 KYFTELLSGA-QEYGEAAAYIQAQFEAKNKSTTKEIYCHMTCATDTNNIQFVFDAVTDVIIANNLRGCGLY 71 (71)
Q Consensus 2 ~~Fp~~y~G~-~~~~~~~~fi~~kF~~~~~~~~r~iy~h~T~AtDt~ni~~vf~~V~d~Il~~nl~~~~l~ 71 (71)
+|||+ |+|| .|..+|.+||.++|.+.+++..|.+|+||||||||+||++||.+|+|+||+.||++++|+
T Consensus 290 ~YFPe-~~GP~qDa~AAreFILkm~~d~nPd~dKii~SHfTcATDT~NIRfVFaaVkDtiLq~~LkE~NLv 359 (359)
T KOG0085|consen 290 DYFPE-FDGPKQDAQAAREFILKMYVDMNPDSDKIIYSHFTCATDTENIRFVFAAVKDTILQLNLKEYNLV 359 (359)
T ss_pred HhCcc-cCCCcccHHHHHHHHHHHHHhhCCCccceeeeeeeecccchhHHHHHHHHHHHHHHhhhHhhccC
Confidence 69999 9998 688899999999999999888999999999999999999999999999999999999875
No 2
>KOG0082|consensus
Probab=99.89 E-value=1.3e-23 Score=149.13 Aligned_cols=69 Identities=57% Similarity=0.922 Sum_probs=66.5
Q ss_pred cccCCCCCCCCChHHHHHHHHHHHHhhccCCCCCeeEeecccccCccHHHHHHHHHHHHHHhhhhhcCCC
Q psy6616 2 KYFTELLSGAQEYGEAAAYIQAQFEAKNKSTTKEIYCHMTCATDTNNIQFVFDAVTDVIIANNLRGCGLY 71 (71)
Q Consensus 2 ~~Fp~~y~G~~~~~~~~~fi~~kF~~~~~~~~r~iy~h~T~AtDt~ni~~vf~~V~d~Il~~nl~~~~l~ 71 (71)
+|||| |+|++++++|.+||+.+|.+++.++.|++|+|+||||||+||+.||++|.|+|++.||+..||+
T Consensus 286 ~~Fpd-y~G~~~~~~a~~yI~~kF~~l~~~~~k~iy~h~T~AtDT~nv~~vf~av~d~Ii~~nlk~~gl~ 354 (354)
T KOG0082|consen 286 DCFPD-YKGVNTYEEAAKYIRKKFEELNKNKDKKIYVHFTCATDTQNVQFVFDAVTDTIIQNNLKDAGLI 354 (354)
T ss_pred hhCcC-CCCCCChHHHHHHHHHHHHHHhcccCCcceEEEEeeccHHHHHHHHHHHHHHHHHHHHHHhcCC
Confidence 69999 9999999999999999999999887799999999999999999999999999999999999985
No 3
>smart00275 G_alpha G protein alpha subunit. Subunit of G proteins that contains the guanine nucleotide binding site
Probab=99.83 E-value=1.2e-20 Score=132.99 Aligned_cols=67 Identities=46% Similarity=0.859 Sum_probs=63.2
Q ss_pred cccCCCCCCCCChHHHHHHHHHHHHhhccC-CCCCeeEeecccccCccHHHHHHHHHHHHHHhhhhhcC
Q psy6616 2 KYFTELLSGAQEYGEAAAYIQAQFEAKNKS-TTKEIYCHMTCATDTNNIQFVFDAVTDVIIANNLRGCG 69 (71)
Q Consensus 2 ~~Fp~~y~G~~~~~~~~~fi~~kF~~~~~~-~~r~iy~h~T~AtDt~ni~~vf~~V~d~Il~~nl~~~~ 69 (71)
+|||+ |+|++++++|.+||+++|.+++++ ++|.+|+|+||||||++++.||++|+++|++.||+..|
T Consensus 275 ~~fp~-y~g~~~~~~~~~yi~~~F~~~~~~~~~r~~y~h~t~a~Dt~~~~~v~~~v~~~I~~~~l~~~~ 342 (342)
T smart00275 275 DYFPD-YKGPNDYEAAAKFIKQKFLRLNRNSSRKSIYHHFTCATDTRNIRVVFDAVKDIILQRNLKDAG 342 (342)
T ss_pred ccCCC-CCCCCCHHHHHHHHHHHHHHhccCCCCceEEEEEeeecccHHHHHHHHHHHHHHHHHHHHhcC
Confidence 59999 999999999999999999999875 67999999999999999999999999999999998765
No 4
>cd00066 G-alpha G protein alpha subunit. The alpha subunit of G proteins contains the guanine nucleotide binding site. The heterotrimeric GNP-binding proteins are signal transducers that communicate signals from many hormones, neurotransmitters, chemokines, and autocrine and paracrine factors. Extracellular signals are received by receptors, which activate the G proteins, which in turn route the signals to several distinct intracellular signaling pathways. The alpha subunit of G proteins is a weak GTPase. In the resting state, heterotrimeric G proteins are associated at the cytosolic face of the plasma membrane and the alpha subunit binds to GDP. Upon activation by a receptor GDP is replaced with GTP, and the G-alpha/GTP complex dissociates from the beta and gamma subunits. This results in activation of downstream signaling pathways, such as cAMP synthesis by adenylyl cyclase, which is terminated when GTP is hydrolized and the heterotrimers reconstitute.
Probab=99.83 E-value=1.7e-20 Score=130.67 Aligned_cols=65 Identities=52% Similarity=0.936 Sum_probs=61.3
Q ss_pred cccCCCCCC-CCChHHHHHHHHHHHHhhccCCCCCeeEeecccccCccHHHHHHHHHHHHHHhhhhh
Q psy6616 2 KYFTELLSG-AQEYGEAAAYIQAQFEAKNKSTTKEIYCHMTCATDTNNIQFVFDAVTDVIIANNLRG 67 (71)
Q Consensus 2 ~~Fp~~y~G-~~~~~~~~~fi~~kF~~~~~~~~r~iy~h~T~AtDt~ni~~vf~~V~d~Il~~nl~~ 67 (71)
+|||+ |+| ++++++|.+||+++|.++++.++|.+|+|+||||||++|+.||++|+++|++.||+.
T Consensus 252 ~~fp~-y~g~~~~~~~~~~~i~~~F~~~~~~~~~~~~~~~t~a~Dt~~i~~vf~~v~~~i~~~~l~~ 317 (317)
T cd00066 252 DYFPD-YTGPPNDYEEAAKFIRKKFLDLNRNPNKEIYPHFTCATDTENIRFVFDAVKDIILQNNLKD 317 (317)
T ss_pred ccCCC-CCCCCCCHHHHHHHHHHHHHHhhcCCCCeEEEEeccccchHHHHHHHHHHHHHHHHHHhcC
Confidence 69999 999 899999999999999999877789999999999999999999999999999999863
No 5
>KOG0099|consensus
Probab=99.76 E-value=5.3e-19 Score=123.29 Aligned_cols=58 Identities=33% Similarity=0.473 Sum_probs=52.6
Q ss_pred hHHHHHHHHHHHHhhcc---CCCCCeeEeecccccCccHHHHHHHHHHHHHHhhhhhcCCC
Q psy6616 14 YGEAAAYIQAQFEAKNK---STTKEIYCHMTCATDTNNIQFVFDAVTDVIIANNLRGCGLY 71 (71)
Q Consensus 14 ~~~~~~fi~~kF~~~~~---~~~r~iy~h~T~AtDt~ni~~vf~~V~d~Il~~nl~~~~l~ 71 (71)
+..|.-||++.|.++.+ +..+.+|+|||||+||+||+.||++|+|+|++.||++++|+
T Consensus 319 v~raK~fird~FlRiSta~~Dg~h~CYpHFTcAvDTenIrrVFnDcrdiIqr~hlrqyeLl 379 (379)
T KOG0099|consen 319 VTRAKYFIRDEFLRISTASGDGRHYCYPHFTCAVDTENIRRVFNDCRDIIQRMHLRQYELL 379 (379)
T ss_pred hHHHHHhhhhhHhhhccccCCCceecccceeEeechHHHHHHHHHHHHHHHHHHHHHhccC
Confidence 56677899999998864 35789999999999999999999999999999999999985
No 6
>PF00503 G-alpha: G-protein alpha subunit; InterPro: IPR001019 Guanine nucleotide binding proteins (G proteins) are membrane-associated, heterotrimeric proteins composed of three subunits: alpha (IPR001019 from INTERPRO), beta (IPR001632 from INTERPRO) and gamma (IPR001770 from INTERPRO) []. G proteins and their receptors (GPCRs) form one of the most prevalent signalling systems in mammalian cells, regulating systems as diverse as sensory perception, cell growth and hormonal regulation []. At the cell surface, the binding of ligands such as hormones and neurotransmitters to a GPCR activates the receptor by causing a conformational change, which in turn activates the bound G protein on the intracellular-side of the membrane. The activated receptor promotes the exchange of bound GDP for GTP on the G protein alpha subunit. GTP binding changes the conformation of switch regions within the alpha subunit, which allows the bound trimeric G protein (inactive) to be released from the receptor, and to dissociate into active alpha subunit (GTP-bound) and beta/gamma dimer. The alpha subunit and the beta/gamma dimer go on to activate distinct downstream effectors, such as adenylyl cyclase, phosphodiesterases, phospholipase C, and ion channels. These effectors in turn regulate the intracellular concentrations of secondary messengers, such as cAMP, diacylglycerol, sodium or calcium cations, which ultimately lead to a physiological response, usually via the downstream regulation of gene transcription. The cycle is completed by the hydrolysis of alpha subunit-bound GTP to GDP, resulting in the re-association of the alpha and beta/gamma subunits and their binding to the receptor, which terminates the signal []. The length of the G protein signal is controlled by the duration of the GTP-bound alpha subunit, which can be regulated by RGS (regulator of G protein signalling) proteins (IPR000342 from INTERPRO) or by covalent modifications []. There are several isoforms of each subunit, many of which have splice variants, which together can make up hundreds of combinations of G proteins. The specific combination of subunits in heterotrimeric G proteins affects not only which receptor it can bind to, but also which downstream target is affected, providing the means to target specific physiological processes in response to specific external stimuli [, ]. G proteins carry lipid modifications on one or more of their subunits to target them to the plasma membrane and to contribute to protein interactions. This family consists of the G protein alpha subunit, which acts as a weak GTPase. G protein classes are defined based on the sequence and function of their alpha subunits, which in mammals fall into four main categories: G(S)alpha, G(Q)alpha, G(I)alpha and G(12)alpha; there are also fungal and plant classes of alpha subunits. The alpha subunit consists of two domains: a GTP-binding domain and a helical insertion domain (IPR011025 from INTERPRO). The GTP-binding domain is homologous to Ras-like small GTPases, and includes switch regions I and II, which change conformation during activation. The switch regions are loops of alpha-helices with conformations sensitive to guanine nucleotides. The helical insertion domain is inserted into the GTP-binding domain before switch region I and is unique to heterotrimeric G proteins. This helical insertion domain functions to sequester the guanine nucleotide at the interface with the GTP-binding domain and must be displaced to enable nucleotide dissociation.; GO: 0004871 signal transducer activity, 0019001 guanyl nucleotide binding, 0007186 G-protein coupled receptor protein signaling pathway; PDB: 3QI2_B 3QE0_A 2IK8_A 2OM2_A 2GTP_B 2XNS_B 3ONW_B 1KJY_A 2EBC_A 1Y3A_B ....
Probab=99.66 E-value=9.1e-17 Score=113.94 Aligned_cols=58 Identities=43% Similarity=0.810 Sum_probs=52.9
Q ss_pred cccCCCCCCC--CChHHHHHHHHHHHHhhccCCC--CCeeEeecccccCccHHHHHHHHHHHH
Q psy6616 2 KYFTELLSGA--QEYGEAAAYIQAQFEAKNKSTT--KEIYCHMTCATDTNNIQFVFDAVTDVI 60 (71)
Q Consensus 2 ~~Fp~~y~G~--~~~~~~~~fi~~kF~~~~~~~~--r~iy~h~T~AtDt~ni~~vf~~V~d~I 60 (71)
+|||+ |+|+ +++++|.+||+++|.++.+... |.+|+|+||||||++|+.||++|+|+|
T Consensus 328 ~~fp~-y~g~~~~~~~~~~~~i~~~f~~~~~~~~~~~~~~~h~t~a~d~~~~~~v~~~v~~~i 389 (389)
T PF00503_consen 328 KYFPD-YTGDRPNDVDSAIKFIKNKFLRLNRNNSPSRRIYVHFTCATDTENIRKVFNAVKDII 389 (389)
T ss_dssp GTSTT-GGSH-TSSHHHHHHHHHHHHHCTHSTTTTCS-EEEEEESTTSHHHHHHHHHHHHHHH
T ss_pred hhCCC-CCCCcccCHHHHHHHHHHHHHHhccCCCCCcceEEEEeeecccHHHHHHHHHhcCcC
Confidence 69999 9986 8999999999999999876544 999999999999999999999999997
No 7
>cd04152 Arl4_Arl7 Arl4/Arl7 subfamily. Arl4 (Arf-like 4) is highly expressed in testicular germ cells, and is found in the nucleus and nucleolus. In mice, Arl4 is developmentally expressed during embryogenesis, and a role in somite formation and central nervous system differentiation has been proposed. Arl7 has been identified as the only Arf/Arl protein to be induced by agonists of liver X-receptor and retinoid X-receptor and by cholesterol loading in human macrophages. Arl7 is proposed to play a role in transport between a perinuclear compartment and the plasma membrane, apparently linked to the ABCA1-mediated cholesterol secretion pathway. Older literature suggests that Arl6 is a part of the Arl4/Arl7 subfamily, but analyses based on more recent sequence data place Arl6 in its own subfamily.
Probab=72.60 E-value=7.6 Score=24.39 Aligned_cols=27 Identities=15% Similarity=0.226 Sum_probs=23.9
Q ss_pred CeeEeecccccCccHHHHHHHHHHHHH
Q psy6616 35 EIYCHMTCATDTNNIQFVFDAVTDVII 61 (71)
Q Consensus 35 ~iy~h~T~AtDt~ni~~vf~~V~d~Il 61 (71)
.+.++.+||.+.+++..+|..+.+.++
T Consensus 144 ~~~~~~~SA~~~~gi~~l~~~l~~~l~ 170 (183)
T cd04152 144 PWHVQPACAIIGEGLQEGLEKLYEMIL 170 (183)
T ss_pred ceEEEEeecccCCCHHHHHHHHHHHHH
Confidence 456789999999999999999988885
No 8
>KOG0087|consensus
Probab=69.16 E-value=8.2 Score=26.49 Aligned_cols=31 Identities=23% Similarity=0.243 Sum_probs=26.7
Q ss_pred CeeEeecccccCccHHHHHHHHHHHHHHhhh
Q psy6616 35 EIYCHMTCATDTNNIQFVFDAVTDVIIANNL 65 (71)
Q Consensus 35 ~iy~h~T~AtDt~ni~~vf~~V~d~Il~~nl 65 (71)
.++.+.|+|.|..|++..|..|-..|.+..-
T Consensus 150 ~l~f~EtSAl~~tNVe~aF~~~l~~I~~~vs 180 (222)
T KOG0087|consen 150 GLFFLETSALDATNVEKAFERVLTEIYKIVS 180 (222)
T ss_pred CceEEEecccccccHHHHHHHHHHHHHHHHH
Confidence 5888999999999999999998888875443
No 9
>PLN00223 ADP-ribosylation factor; Provisional
Probab=53.10 E-value=45 Score=20.92 Aligned_cols=31 Identities=23% Similarity=0.339 Sum_probs=24.3
Q ss_pred CCCeeEeecccccCccHHHHHHHHHHHHHHh
Q psy6616 33 TKEIYCHMTCATDTNNIQFVFDAVTDVIIAN 63 (71)
Q Consensus 33 ~r~iy~h~T~AtDt~ni~~vf~~V~d~Il~~ 63 (71)
.|.+|.-.|||.+-+++..+|+.+-+.+..+
T Consensus 150 ~~~~~~~~~Sa~~g~gv~e~~~~l~~~~~~~ 180 (181)
T PLN00223 150 QRHWYIQSTCATSGEGLYEGLDWLSNNIANK 180 (181)
T ss_pred CCceEEEeccCCCCCCHHHHHHHHHHHHhhc
Confidence 3556666799999999999999887776643
No 10
>smart00188 IL10 Interleukin-10 family. Interleukin-10 inhibits the synthesis of a number of cytokines, including IFN-gamma, IL-2, IL-3, TNF and GM-CSF produced by activated macrophages and by helper T cells.
Probab=50.92 E-value=5.2 Score=25.48 Aligned_cols=38 Identities=5% Similarity=0.151 Sum_probs=25.6
Q ss_pred cCCCCCCC-CChHHHHHHHHHHHHhhccCCCCCeeEeeccc
Q psy6616 4 FTELLSGA-QEYGEAAAYIQAQFEAKNKSTTKEIYCHMTCA 43 (71)
Q Consensus 4 Fp~~y~G~-~~~~~~~~fi~~kF~~~~~~~~r~iy~h~T~A 43 (71)
||. +.-. .+....+..|.+.|..+.+. -+.+..|+.|.
T Consensus 59 ~p~-a~~~~~~~k~~i~Sl~~~f~~lk~~-l~~C~~~~~Ce 97 (137)
T smart00188 59 MPQ-AENHGPDIKEHVNSLGEKLKTLRLR-LRRCHRFLPCE 97 (137)
T ss_pred HHH-HhcCCcchhhhHHHHHHHHHHHHHH-HHHCccccCcc
Confidence 566 5322 35677788899999877543 45677788883
No 11
>COG3598 RepA RecA-family ATPase [DNA replication, recombination, and repair]
Probab=44.01 E-value=27 Score=25.83 Aligned_cols=37 Identities=14% Similarity=0.084 Sum_probs=25.1
Q ss_pred CCCCCCChHHHHHHHHHHHHhhcc-CCCCCeeEeeccc
Q psy6616 7 LLSGAQEYGEAAAYIQAQFEAKNK-STTKEIYCHMTCA 43 (71)
Q Consensus 7 ~y~G~~~~~~~~~fi~~kF~~~~~-~~~r~iy~h~T~A 43 (71)
||.|........+-|.++++++.. ....-+|+|-|+-
T Consensus 206 f~~G~s~s~vqv~~fi~~~rkla~~l~caIiy~hHtsk 243 (402)
T COG3598 206 FYEGKSISDVQVKEFIKKTRKLARNLECAIIYIHHTSK 243 (402)
T ss_pred hcCCccchhHHHHHHHHHHHHHHHhcCCeEEEEecccc
Confidence 467765555556666677888754 3467899998864
No 12
>cd04133 Rop_like Rop subfamily. The Rop (Rho-related protein from plants) subfamily plays a role in diverse cellular processes, including cytoskeletal organization, pollen and vegetative cell growth, hormone responses, stress responses, and pathogen resistance. Rops are able to regulate several downstream pathways to amplify a specific signal by acting as master switches early in the signaling cascade. They transmit a variety of extracellular and intracellular signals. Rops are involved in establishing cell polarity in root-hair development, root-hair elongation, pollen-tube growth, cell-shape formation, responses to hormones such as abscisic acid (ABA) and auxin, responses to abiotic stresses such as oxygen deprivation, and disease resistance and disease susceptibility. An individual Rop can have a unique function or an overlapping function shared with other Rop proteins; in addition, a given Rop-regulated function can be controlled by one or multiple Rop proteins. For example,
Probab=41.81 E-value=27 Score=22.14 Aligned_cols=24 Identities=25% Similarity=0.418 Sum_probs=20.9
Q ss_pred eecccccCccHHHHHHHHHHHHHH
Q psy6616 39 HMTCATDTNNIQFVFDAVTDVIIA 62 (71)
Q Consensus 39 h~T~AtDt~ni~~vf~~V~d~Il~ 62 (71)
-.|||.+.+||+.+|..+.+.+++
T Consensus 151 ~E~SAk~~~nV~~~F~~~~~~~~~ 174 (176)
T cd04133 151 IECSSKTQQNVKAVFDAAIKVVLQ 174 (176)
T ss_pred EECCCCcccCHHHHHHHHHHHHhc
Confidence 489999999999999999887654
No 13
>PF12017 Tnp_P_element: Transposase protein; InterPro: IPR021896 Protein in this family are transposases found in insects. This region is about 230 amino acids in length and is found associated with PF05485 from PFAM.
Probab=39.25 E-value=30 Score=23.74 Aligned_cols=22 Identities=14% Similarity=0.407 Sum_probs=16.2
Q ss_pred CCCeeEeecccccCccHHHHHH
Q psy6616 33 TKEIYCHMTCATDTNNIQFVFD 54 (71)
Q Consensus 33 ~r~iy~h~T~AtDt~ni~~vf~ 54 (71)
..+||.+|.+.+|.+.++.++.
T Consensus 182 KQpi~~~f~t~m~~~~l~~iI~ 203 (236)
T PF12017_consen 182 KQPIYFDFDTSMDADILKNIIE 203 (236)
T ss_pred CccEEEEecCcCCHHHHHHHHH
Confidence 5689999999888766654443
No 14
>PRK15467 ethanolamine utilization protein EutP; Provisional
Probab=39.05 E-value=35 Score=21.01 Aligned_cols=28 Identities=11% Similarity=0.109 Sum_probs=23.1
Q ss_pred eEeecccccCccHHHHHHHHHHHHHHhh
Q psy6616 37 YCHMTCATDTNNIQFVFDAVTDVIIANN 64 (71)
Q Consensus 37 y~h~T~AtDt~ni~~vf~~V~d~Il~~n 64 (71)
-+.+|+|.+.++|..+|+.+.+.+-+.+
T Consensus 123 p~~~~Sa~~g~gi~~l~~~l~~~~~~~~ 150 (158)
T PRK15467 123 PIFELNSHDPQSVQQLVDYLASLTKQEE 150 (158)
T ss_pred CEEEEECCCccCHHHHHHHHHHhchhhh
Confidence 3558999999999999999988776543
No 15
>PF02208 Sorb: Sorbin homologous domain; InterPro: IPR003127 Sorbin is an active peptide present in the digestive tract, where it has pro-absorptive and anti-secretory effects in different parts of the intestine, including the ability to decrease VIP (vasoactive intestinal peptide) and cholera toxin-induced secretion. It is expressed in some intestinal and pancreatic endocrine tumours in humans []. Sorbin-homology domains are found in adaptor proteins such as vinexin, CAP/ponsin and argBP2, which regulate various cellular functions, including cell adhesion, cytoskeletal organisation, and growth factor signalling []. In addition to the sorbin domain, these proteins contain three SH3 (src homology 3) domains. The sorbin homology domain mediates the interaction of vinexin and CAP with flotillin, which is crucial for the localisation of SH3-binding proteins to the lipid raft, a region of the plasma membrane rich in cholesterol and sphingolipids that acts to concentrate certain signalling molecules. The sorbin homology domain of adaptor proteins may mediate interactions with the lipid raft that are crucial to intracellular communication [].
Probab=38.66 E-value=27 Score=18.36 Aligned_cols=18 Identities=11% Similarity=0.274 Sum_probs=15.2
Q ss_pred ChHHHHHHHHHHHHhhcc
Q psy6616 13 EYGEAAAYIQAQFEAKNK 30 (71)
Q Consensus 13 ~~~~~~~fi~~kF~~~~~ 30 (71)
+++....+-+.+|+++++
T Consensus 21 ~vd~~kDWYktMFkqIHk 38 (47)
T PF02208_consen 21 NVDRPKDWYKTMFKQIHK 38 (47)
T ss_pred cccchhHHHHHHHHHHHh
Confidence 467788999999999875
No 16
>cd04149 Arf6 Arf6 subfamily. Arf6 (ADP ribosylation factor 6) proteins localize to the plasma membrane, where they perform a wide variety of functions. In its active, GTP-bound form, Arf6 is involved in cell spreading, Rac-induced formation of plasma membrane ruffles, cell migration, wound healing, and Fc-mediated phagocytosis. Arf6 appears to change the actin structure at the plasma membrane by activating Rac, a Rho family protein involved in membrane ruffling. Arf6 is required for and enhances Rac formation of ruffles. Arf6 can regulate dendritic branching in hippocampal neurons, and in yeast it localizes to the growing bud, where it plays a role in polarized growth and bud site selection. In leukocytes, Arf6 is required for chemokine-stimulated migration across endothelial cells. Arf6 also plays a role in down-regulation of beta2-adrenergic receptors and luteinizing hormone receptors by facilitating the release of sequestered arrestin to allow endocytosis. Arf6 is believed t
Probab=37.87 E-value=66 Score=19.75 Aligned_cols=24 Identities=17% Similarity=0.333 Sum_probs=19.0
Q ss_pred CCeeEeecccccCccHHHHHHHHH
Q psy6616 34 KEIYCHMTCATDTNNIQFVFDAVT 57 (71)
Q Consensus 34 r~iy~h~T~AtDt~ni~~vf~~V~ 57 (71)
+.+..+.|||.+-+++..+|..+.
T Consensus 143 ~~~~~~~~SAk~g~gv~~~~~~l~ 166 (168)
T cd04149 143 RNWYVQPSCATSGDGLYEGLTWLS 166 (168)
T ss_pred CcEEEEEeeCCCCCChHHHHHHHh
Confidence 445677899999999998887553
No 17
>KOG0703|consensus
Probab=34.90 E-value=49 Score=23.58 Aligned_cols=24 Identities=8% Similarity=0.230 Sum_probs=16.0
Q ss_pred cCCCCCCCCChHHHHHHHHHHHHh
Q psy6616 4 FTELLSGAQEYGEAAAYIQAQFEA 27 (71)
Q Consensus 4 Fp~~y~G~~~~~~~~~fi~~kF~~ 27 (71)
.|+.|.+|.+-.....||++||+.
T Consensus 97 ~p~~~~~p~~d~~~e~FIR~KYE~ 120 (287)
T KOG0703|consen 97 LPDPFRRPGPDDLVEQFIRDKYER 120 (287)
T ss_pred CCccccCCChHHHHHHHHHHHHhh
Confidence 466466664434566799999985
No 18
>cd01897 NOG NOG1 is a nucleolar GTP-binding protein present in eukaryotes ranging from trypanosomes to humans. NOG1 is functionally linked to ribosome biogenesis and found in association with the nuclear pore complexes and identified in many preribosomal complexes. Thus, defects in NOG1 can lead to defects in 60S biogenesis. The S. cerevisiae NOG1 gene is essential for cell viability, and mutations in the predicted G motifs abrogate function. It is a member of the ODN family of GTP-binding proteins that also includes the bacterial Obg and DRG proteins.
Probab=34.87 E-value=40 Score=20.15 Aligned_cols=27 Identities=4% Similarity=0.030 Sum_probs=22.3
Q ss_pred CeeEeecccccCccHHHHHHHHHHHHH
Q psy6616 35 EIYCHMTCATDTNNIQFVFDAVTDVII 61 (71)
Q Consensus 35 ~iy~h~T~AtDt~ni~~vf~~V~d~Il 61 (71)
...+..|||.+-++++.+|+.+.+.++
T Consensus 142 ~~~~~~~Sa~~~~gi~~l~~~l~~~~~ 168 (168)
T cd01897 142 GEEVLKISTLTEEGVDEVKNKACELLL 168 (168)
T ss_pred cCceEEEEecccCCHHHHHHHHHHHhC
Confidence 455778999999999999998877653
No 19
>cd04126 Rab20 Rab20 subfamily. Rab20 is one of several Rab proteins that appear to be restricted in expression to the apical domain of murine polarized epithelial cells. It is expressed on the apical side of polarized kidney tubule and intestinal epithelial cells, and in non-polarized cells. It also localizes to vesico-tubular structures below the apical brush border of renal proximal tubule cells and in the apical region of duodenal epithelial cells. Rab20 has also been shown to colocalize with vacuolar H+-ATPases (V-ATPases) in mouse kidney cells, suggesting a role in the regulation of V-ATPase traffic in specific portions of the nephron. It was also shown to be one of several proteins whose expression is upregulated in human myelodysplastic syndrome (MDS) patients. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bo
Probab=34.61 E-value=83 Score=20.82 Aligned_cols=31 Identities=19% Similarity=0.327 Sum_probs=24.8
Q ss_pred eeEeecccccCccHHHHHHHHHHHHHHhhhh
Q psy6616 36 IYCHMTCATDTNNIQFVFDAVTDVIIANNLR 66 (71)
Q Consensus 36 iy~h~T~AtDt~ni~~vf~~V~d~Il~~nl~ 66 (71)
+-...|+|.+.+||+.+|..+-..++...++
T Consensus 165 ~~~~E~SA~tg~~V~elf~~i~~~~~~~~~~ 195 (220)
T cd04126 165 KMCFETSAKTGYNVDELFEYLFNLVLPLILA 195 (220)
T ss_pred ceEEEeeCCCCCCHHHHHHHHHHHHHHHHHh
Confidence 4456899999999999999998888754443
No 20
>cd01862 Rab7 Rab7 subfamily. Rab7 is a small Rab GTPase that regulates vesicular traffic from early to late endosomal stages of the endocytic pathway. The yeast Ypt7 and mammalian Rab7 are both involved in transport to the vacuole/lysosome, whereas Ypt7 is also required for homotypic vacuole fusion. Mammalian Rab7 is an essential participant in the autophagic pathway for sequestration and targeting of cytoplasmic components to the lytic compartment. Mammalian Rab7 is also proposed to function as a tumor suppressor. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-
Probab=34.60 E-value=69 Score=19.06 Aligned_cols=29 Identities=17% Similarity=0.296 Sum_probs=24.5
Q ss_pred eeEeecccccCccHHHHHHHHHHHHHHhh
Q psy6616 36 IYCHMTCATDTNNIQFVFDAVTDVIIANN 64 (71)
Q Consensus 36 iy~h~T~AtDt~ni~~vf~~V~d~Il~~n 64 (71)
+.+..++|....++..+|+.+.+.+++.+
T Consensus 142 ~~~~~~Sa~~~~gv~~l~~~i~~~~~~~~ 170 (172)
T cd01862 142 IPYFETSAKEAINVEQAFETIARKALEQE 170 (172)
T ss_pred ceEEEEECCCCCCHHHHHHHHHHHHHhcc
Confidence 55678999999999999999988887653
No 21
>PTZ00133 ADP-ribosylation factor; Provisional
Probab=34.27 E-value=94 Score=19.41 Aligned_cols=31 Identities=19% Similarity=0.260 Sum_probs=23.9
Q ss_pred CCCeeEeecccccCccHHHHHHHHHHHHHHh
Q psy6616 33 TKEIYCHMTCATDTNNIQFVFDAVTDVIIAN 63 (71)
Q Consensus 33 ~r~iy~h~T~AtDt~ni~~vf~~V~d~Il~~ 63 (71)
.+.++.-.|||.+-++++.+|+.+.+.+.++
T Consensus 150 ~~~~~~~~~Sa~tg~gv~e~~~~l~~~i~~~ 180 (182)
T PTZ00133 150 QRNWYIQGCCATTAQGLYEGLDWLSANIKKS 180 (182)
T ss_pred CCcEEEEeeeCCCCCCHHHHHHHHHHHHHHh
Confidence 3455666799999999999999887766543
No 22
>smart00176 RAN Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases. Ran is involved in the active transport of proteins through nuclear pores.
Probab=34.15 E-value=71 Score=20.71 Aligned_cols=29 Identities=14% Similarity=0.101 Sum_probs=24.4
Q ss_pred CeeEeecccccCccHHHHHHHHHHHHHHh
Q psy6616 35 EIYCHMTCATDTNNIQFVFDAVTDVIIAN 63 (71)
Q Consensus 35 ~iy~h~T~AtDt~ni~~vf~~V~d~Il~~ 63 (71)
.+-...|||.+.++|+.+|..+...+++.
T Consensus 128 ~~~~~e~SAk~~~~v~~~F~~l~~~i~~~ 156 (200)
T smart00176 128 NLQYYDISAKSNYNFEKPFLWLARKLIGD 156 (200)
T ss_pred CCEEEEEeCCCCCCHHHHHHHHHHHHHhc
Confidence 35567899999999999999998887653
No 23
>KOG0086|consensus
Probab=33.37 E-value=76 Score=21.24 Aligned_cols=31 Identities=19% Similarity=0.216 Sum_probs=27.5
Q ss_pred CCCCeeEeecccccCccHHHHHHHHHHHHHH
Q psy6616 32 TTKEIYCHMTCATDTNNIQFVFDAVTDVIIA 62 (71)
Q Consensus 32 ~~r~iy~h~T~AtDt~ni~~vf~~V~d~Il~ 62 (71)
+++++..|-|+|.-.+|++..|-.|-.+||.
T Consensus 142 qEnel~flETSa~TGeNVEEaFl~c~~tIl~ 172 (214)
T KOG0086|consen 142 QENELMFLETSALTGENVEEAFLKCARTILN 172 (214)
T ss_pred cccceeeeeecccccccHHHHHHHHHHHHHH
Confidence 3567888999999999999999999999884
No 24
>PLN02941 inositol-tetrakisphosphate 1-kinase
Probab=33.18 E-value=51 Score=23.64 Aligned_cols=24 Identities=13% Similarity=0.367 Sum_probs=18.5
Q ss_pred cccCCCCCCCCChHHHH-HHHHHHHH
Q psy6616 2 KYFTELLSGAQEYGEAA-AYIQAQFE 26 (71)
Q Consensus 2 ~~Fp~~y~G~~~~~~~~-~fi~~kF~ 26 (71)
+|||+ |+|=.++++.. +||.+...
T Consensus 301 N~fP~-~k~~p~~~~~l~~~~~~~~~ 325 (328)
T PLN02941 301 NYFPG-YAKMPGYETVLTDFLLSLVQ 325 (328)
T ss_pred cCCCc-cccCCchHHHHHHHHHHHHh
Confidence 58999 99976787766 68877654
No 25
>smart00177 ARF ARF-like small GTPases; ARF, ADP-ribosylation factor. Ras homologues involved in vesicular transport. Activator of phospholipase D isoforms. Unlike Ras proteins they lack cysteine residues at their C-termini and therefore are unlikely to be prenylated. ARFs are N-terminally myristoylated. Contains ATP/GTP-binding motif (P-loop).
Probab=33.08 E-value=1.2e+02 Score=18.74 Aligned_cols=28 Identities=18% Similarity=0.318 Sum_probs=22.1
Q ss_pred CCCeeEeecccccCccHHHHHHHHHHHH
Q psy6616 33 TKEIYCHMTCATDTNNIQFVFDAVTDVI 60 (71)
Q Consensus 33 ~r~iy~h~T~AtDt~ni~~vf~~V~d~I 60 (71)
.|.+++-.|||..-+++..+|+.+.+.+
T Consensus 146 ~~~~~~~~~Sa~~g~gv~e~~~~l~~~~ 173 (175)
T smart00177 146 DRNWYIQPTCATSGDGLYEGLTWLSNNL 173 (175)
T ss_pred CCcEEEEEeeCCCCCCHHHHHHHHHHHh
Confidence 3556666799999999999998876653
No 26
>COG1586 SpeD S-adenosylmethionine decarboxylase [Amino acid transport and metabolism]
Probab=33.04 E-value=51 Score=21.05 Aligned_cols=16 Identities=19% Similarity=0.202 Sum_probs=14.0
Q ss_pred CChHHHHHHHHHHHHh
Q psy6616 12 QEYGEAAAYIQAQFEA 27 (71)
Q Consensus 12 ~~~~~~~~fi~~kF~~ 27 (71)
-+...|.+||.++|..
T Consensus 97 ~~p~~A~~yi~~~L~p 112 (136)
T COG1586 97 IDPLKAFNYLVEQLKP 112 (136)
T ss_pred CCHHHHHHHHHHHhCC
Confidence 5788999999999975
No 27
>cd00881 GTP_translation_factor GTP translation factor family. This family consists primarily of translation initiation, elongation, and release factors, which play specific roles in protein translation. In addition, the family includes Snu114p, a component of the U5 small nuclear riboprotein particle which is a component of the spliceosome and is involved in excision of introns, TetM, a tetracycline resistance gene that protects the ribosome from tetracycline binding, and the unusual subfamily CysN/ATPS, which has an unrelated function (ATP sulfurylase) acquired through lateral transfer of the EF1-alpha gene and development of a new function.
Probab=32.74 E-value=1.1e+02 Score=18.29 Aligned_cols=48 Identities=8% Similarity=0.004 Sum_probs=32.3
Q ss_pred ChHHHHHHHHHHHHhhccC--------CCCCeeEeecccccCccHHHHHHHHHHHH
Q psy6616 13 EYGEAAAYIQAQFEAKNKS--------TTKEIYCHMTCATDTNNIQFVFDAVTDVI 60 (71)
Q Consensus 13 ~~~~~~~fi~~kF~~~~~~--------~~r~iy~h~T~AtDt~ni~~vf~~V~d~I 60 (71)
+.....+.+++.+...... ..+...+..++|.+..++..+++.+.+.+
T Consensus 131 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~Sa~~g~gi~~l~~~l~~~l 186 (189)
T cd00881 131 DLEEVLREIKELLGLIGFISTKEEGTRNGLLVPIVPGSALTGIGVEELLEAIVEHL 186 (189)
T ss_pred cHHHHHHHHHHHHccccccchhhhhcccCCcceEEEEecccCcCHHHHHHHHHhhC
Confidence 3445566777666543210 13456678999999999999988877654
No 28
>cd04119 RJL RJL (RabJ-Like) subfamily. RJLs are found in many protists and as chimeras with C-terminal DNAJ domains in deuterostome metazoa. They are not found in plants, fungi, and protostome metazoa, suggesting a horizontal gene transfer between protists and deuterostome metazoa. RJLs lack any known membrane targeting signal and contain a degenerate phosphate/magnesium-binding 3 (PM3) motif, suggesting an impaired ability to hydrolyze GTP. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization.
Probab=32.68 E-value=61 Score=19.07 Aligned_cols=26 Identities=15% Similarity=0.222 Sum_probs=21.9
Q ss_pred eeEeecccccCccHHHHHHHHHHHHH
Q psy6616 36 IYCHMTCATDTNNIQFVFDAVTDVII 61 (71)
Q Consensus 36 iy~h~T~AtDt~ni~~vf~~V~d~Il 61 (71)
+-.+.++|..-+++..+|+.+.+.++
T Consensus 142 ~~~~~~Sa~~~~gi~~l~~~l~~~l~ 167 (168)
T cd04119 142 FKYFETSACTGEGVNEMFQTLFSSIV 167 (168)
T ss_pred CeEEEEECCCCCCHHHHHHHHHHHHh
Confidence 34679999999999999999887776
No 29
>PF08885 GSCFA: GSCFA family; InterPro: IPR014982 This group of proteins are functionally uncharacterised. They have been named GSCFA after a highly conserved N-terminal motif in the alignment, they are functionally uncharacterised.
Probab=32.22 E-value=31 Score=23.81 Aligned_cols=12 Identities=33% Similarity=0.501 Sum_probs=9.0
Q ss_pred hHHHHHHHHHHH
Q psy6616 14 YGEAAAYIQAQF 25 (71)
Q Consensus 14 ~~~~~~fi~~kF 25 (71)
-+.|++||-++|
T Consensus 240 s~~aV~~I~~~F 251 (251)
T PF08885_consen 240 SPQAVDYIWERF 251 (251)
T ss_pred CHHHHHHHHhhC
Confidence 356888888876
No 30
>cd00877 Ran Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases. Ran GTPase is involved in diverse biological functions, such as nuclear transport, spindle formation during mitosis, DNA replication, and cell division. Among the Ras superfamily, Ran is a unique small G protein. It does not have a lipid modification motif at the C-terminus to bind to the membrane, which is often observed within the Ras superfamily. Ran may therefore interact with a wide range of proteins in various intracellular locations. Like other GTPases, Ran exists in GTP- and GDP-bound conformations that interact differently with effectors. Conversion between these forms and the assembly or disassembly of effector complexes requires the interaction of regulator proteins. The intrinsic GTPase activity of Ran is very low, but it is greatly stimulated by a GTPase-activating protein (RanGAP1) located in the cytoplasm. By contrast, RCC1, a guanine nucleotide exchange factor that generates RanGTP, is
Probab=30.81 E-value=92 Score=18.96 Aligned_cols=27 Identities=11% Similarity=0.068 Sum_probs=23.3
Q ss_pred eeEeecccccCccHHHHHHHHHHHHHH
Q psy6616 36 IYCHMTCATDTNNIQFVFDAVTDVIIA 62 (71)
Q Consensus 36 iy~h~T~AtDt~ni~~vf~~V~d~Il~ 62 (71)
+-...|+|.+-+++..+|+.+.+.+++
T Consensus 134 ~~~~e~Sa~~~~~v~~~f~~l~~~~~~ 160 (166)
T cd00877 134 LQYYEISAKSNYNFEKPFLWLARKLLG 160 (166)
T ss_pred CEEEEEeCCCCCChHHHHHHHHHHHHh
Confidence 445699999999999999999988875
No 31
>COG0163 UbiX 3-polyprenyl-4-hydroxybenzoate decarboxylase [Coenzyme metabolism]
Probab=29.62 E-value=61 Score=21.84 Aligned_cols=25 Identities=4% Similarity=0.122 Sum_probs=21.3
Q ss_pred cCCCCCCCCChHHHHHHHHHHHHhh
Q psy6616 4 FTELLSGAQEYGEAAAYIQAQFEAK 28 (71)
Q Consensus 4 Fp~~y~G~~~~~~~~~fi~~kF~~~ 28 (71)
-|.||..|.+.++-.+|+..|-.+.
T Consensus 151 ~PaFY~~P~sieDlvd~~v~rvLD~ 175 (191)
T COG0163 151 MPAFYHKPQSIEDLVDFVVGRVLDL 175 (191)
T ss_pred ChhhhcCCCCHHHHHHHHHHHHHHH
Confidence 3568999999999999999988764
No 32
>cd02685 MIT_C MIT_C; domain found C-terminal to MIT (contained within Microtubule Interacting and Trafficking molecules) domains, as well as in some bacterial proteins. The function of this domain is unknown.
Probab=28.86 E-value=1.6e+02 Score=18.90 Aligned_cols=34 Identities=12% Similarity=0.243 Sum_probs=25.1
Q ss_pred CCCCCeeEeecccccCccH---HHHHHHHHHHHHHhh
Q psy6616 31 STTKEIYCHMTCATDTNNI---QFVFDAVTDVIIANN 64 (71)
Q Consensus 31 ~~~r~iy~h~T~AtDt~ni---~~vf~~V~d~Il~~n 64 (71)
+....+++|.+|.-|..+. +..|+.+++.+.+.+
T Consensus 48 ~~~~~~~i~LvT~~d~~~~~~Q~~~l~~i~~sl~~~g 84 (148)
T cd02685 48 PPCELKYIHLVTGEDEDNGKQQIEALEEIKQSLASHG 84 (148)
T ss_pred CccceEEEEEEecCCCCCHHHHHHHHHHHHHHHHhCC
Confidence 5567999999999998865 455666776666544
No 33
>smart00175 RAB Rab subfamily of small GTPases. Rab GTPases are implicated in vesicle trafficking.
Probab=28.62 E-value=93 Score=18.26 Aligned_cols=25 Identities=20% Similarity=0.325 Sum_probs=21.6
Q ss_pred EeecccccCccHHHHHHHHHHHHHH
Q psy6616 38 CHMTCATDTNNIQFVFDAVTDVIIA 62 (71)
Q Consensus 38 ~h~T~AtDt~ni~~vf~~V~d~Il~ 62 (71)
+..++|..-+++..+|+.+.+.++.
T Consensus 139 ~~e~Sa~~~~~i~~l~~~i~~~~~~ 163 (164)
T smart00175 139 FFETSAKTNTNVEEAFEELAREILK 163 (164)
T ss_pred EEEEeCCCCCCHHHHHHHHHHHHhh
Confidence 5789999999999999999887754
No 34
>cd04134 Rho3 Rho3 subfamily. Rho3 is a member of the Rho family found only in fungi. Rho3 is believed to regulate cell polarity by interacting with the diaphanous/formin family protein For3 to control both the actin cytoskeleton and microtubules. Rho3 is also believed to have a direct role in exocytosis that is independent of its role in regulating actin polarity. The function in exocytosis may be two-pronged: first, in the transport of post-Golgi vesicles from the mother cell to the bud, mediated by myosin (Myo2); second, in the docking and fusion of vesicles to the plasma membrane, mediated by an exocyst (Exo70) protein. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins.
Probab=28.16 E-value=1.1e+02 Score=19.14 Aligned_cols=29 Identities=10% Similarity=0.077 Sum_probs=24.5
Q ss_pred eeEeecccccCccHHHHHHHHHHHHHHhh
Q psy6616 36 IYCHMTCATDTNNIQFVFDAVTDVIIANN 64 (71)
Q Consensus 36 iy~h~T~AtDt~ni~~vf~~V~d~Il~~n 64 (71)
+....++|..-+++..+|..+...++...
T Consensus 149 ~~~~e~SAk~~~~v~e~f~~l~~~~~~~~ 177 (189)
T cd04134 149 LRYLECSAKLNRGVNEAFTEAARVALNVR 177 (189)
T ss_pred CEEEEccCCcCCCHHHHHHHHHHHHhccc
Confidence 44578999999999999999998888544
No 35
>cd01892 Miro2 Miro2 subfamily. Miro (mitochondrial Rho) proteins have tandem GTP-binding domains separated by a linker region containing putative calcium-binding EF hand motifs. Genes encoding Miro-like proteins were found in several eukaryotic organisms. This CD represents the putative GTPase domain in the C terminus of Miro proteins. These atypical Rho GTPases have roles in mitochondrial homeostasis and apoptosis. Most Rho proteins contain a lipid modification site at the C-terminus; however, Miro is one of few Rho subfamilies that lack this feature.
Probab=27.69 E-value=63 Score=19.82 Aligned_cols=24 Identities=4% Similarity=-0.068 Sum_probs=20.7
Q ss_pred eecccccCccHHHHHHHHHHHHHH
Q psy6616 39 HMTCATDTNNIQFVFDAVTDVIIA 62 (71)
Q Consensus 39 h~T~AtDt~ni~~vf~~V~d~Il~ 62 (71)
..++|...+++..+|..+.+.++.
T Consensus 144 ~~~Sa~~~~~v~~lf~~l~~~~~~ 167 (169)
T cd01892 144 LHFSSKLGDSSNELFTKLATAAQY 167 (169)
T ss_pred EEEEeccCccHHHHHHHHHHHhhC
Confidence 578999999999999999888764
No 36
>cd01867 Rab8_Rab10_Rab13_like Rab8/Sec4/Ypt2. Rab8/Sec4/Ypt2 are known or suspected to be involved in post-Golgi transport to the plasma membrane. It is likely that these Rabs have functions that are specific to the mammalian lineage and have no orthologs in plants. Rab8 modulates polarized membrane transport through reorganization of actin and microtubules, induces the formation of new surface extensions, and has an important role in directed membrane transport to cell surfaces. The Ypt2 gene of the fission yeast Schizosaccharomyces pombe encodes a member of the Ypt/Rab family of small GTP-binding proteins, related in sequence to Sec4p of Saccharomyces cerevisiae but closer to mammalian Rab8. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhi
Probab=27.66 E-value=1.1e+02 Score=18.33 Aligned_cols=27 Identities=22% Similarity=0.114 Sum_probs=23.1
Q ss_pred eeEeecccccCccHHHHHHHHHHHHHH
Q psy6616 36 IYCHMTCATDTNNIQFVFDAVTDVIIA 62 (71)
Q Consensus 36 iy~h~T~AtDt~ni~~vf~~V~d~Il~ 62 (71)
+....+||..-.++..+|..+.+.+++
T Consensus 140 ~~~~~~Sa~~~~~v~~~~~~i~~~~~~ 166 (167)
T cd01867 140 IKFLETSAKANINVEEAFFTLAKDIKK 166 (167)
T ss_pred CEEEEEeCCCCCCHHHHHHHHHHHHHh
Confidence 345799999999999999999988875
No 37
>PF03681 UPF0150: Uncharacterised protein family (UPF0150); InterPro: IPR005357 This family of small proteins is uncharacterised. In Q9A3L8 from SWISSPROT this domain is found next to a DNA binding helix-turn-helix domain IPR002145 from INTERPRO, which suggests that this is some kind of ligand binding domain.; PDB: 2DSY_C 2YZT_A 3KWR_A.
Probab=27.12 E-value=70 Score=15.83 Aligned_cols=21 Identities=29% Similarity=0.525 Sum_probs=12.9
Q ss_pred ccCCCCCC----CCChHHHHHHHHHH
Q psy6616 3 YFTELLSG----AQEYGEAAAYIQAQ 24 (71)
Q Consensus 3 ~Fp~~y~G----~~~~~~~~~fi~~k 24 (71)
+||+ +.| +.+.++|.+=+++-
T Consensus 17 ~~pd-lpg~~t~G~t~eea~~~~~ea 41 (48)
T PF03681_consen 17 YFPD-LPGCFTQGDTLEEALENAKEA 41 (48)
T ss_dssp EETT-CCTCEEEESSHHHHHHHHHHH
T ss_pred EeCC-ccChhhcCCCHHHHHHHHHHH
Confidence 4777 655 35677776655543
No 38
>cd01893 Miro1 Miro1 subfamily. Miro (mitochondrial Rho) proteins have tandem GTP-binding domains separated by a linker region containing putative calcium-binding EF hand motifs. Genes encoding Miro-like proteins were found in several eukaryotic organisms. This CD represents the N-terminal GTPase domain of Miro proteins. These atypical Rho GTPases have roles in mitochondrial homeostasis and apoptosis. Most Rho proteins contain a lipid modification site at the C-terminus; however, Miro is one of few Rho subfamilies that lack this feature.
Probab=27.12 E-value=55 Score=19.81 Aligned_cols=25 Identities=20% Similarity=0.267 Sum_probs=21.4
Q ss_pred EeecccccCccHHHHHHHHHHHHHH
Q psy6616 38 CHMTCATDTNNIQFVFDAVTDVIIA 62 (71)
Q Consensus 38 ~h~T~AtDt~ni~~vf~~V~d~Il~ 62 (71)
.-.|+|.+..+++.+|..+...++.
T Consensus 141 ~~e~Sa~~~~~v~~lf~~~~~~~~~ 165 (166)
T cd01893 141 CVECSAKTLINVSEVFYYAQKAVLH 165 (166)
T ss_pred EEEeccccccCHHHHHHHHHHHhcC
Confidence 3489999999999999999888764
No 39
>cd04121 Rab40 Rab40 subfamily. This subfamily contains Rab40a, Rab40b, and Rab40c, which are all highly homologous. In rat, Rab40c is localized to the perinuclear recycling compartment (PRC), and is distributed in a tissue-specific manor, with high expression in brain, heart, kidney, and testis, low expression in lung and liver, and no expression in spleen and skeletal muscle. Rab40c is highly expressed in differentiated oligodendrocytes but minimally expressed in oligodendrocyte progenitors, suggesting a role in the vesicular transport of myelin components. Unlike most other Ras-superfamily proteins, Rab40c was shown to have a much lower affinity for GTP, and an affinity for GDP that is lower than for GTP. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide d
Probab=26.97 E-value=1.1e+02 Score=19.58 Aligned_cols=27 Identities=11% Similarity=0.141 Sum_probs=23.1
Q ss_pred eeEeecccccCccHHHHHHHHHHHHHH
Q psy6616 36 IYCHMTCATDTNNIQFVFDAVTDVIIA 62 (71)
Q Consensus 36 iy~h~T~AtDt~ni~~vf~~V~d~Il~ 62 (71)
+-...++|.+-.+|+.+|..+.+.++.
T Consensus 142 ~~~~e~SAk~g~~V~~~F~~l~~~i~~ 168 (189)
T cd04121 142 MTFFEVSPLCNFNITESFTELARIVLM 168 (189)
T ss_pred CEEEEecCCCCCCHHHHHHHHHHHHHH
Confidence 446799999999999999999887764
No 40
>cd04127 Rab27A Rab27a subfamily. The Rab27a subfamily consists of Rab27a and its highly homologous isoform, Rab27b. Unlike most Rab proteins whose functions remain poorly defined, Rab27a has many known functions. Rab27a has multiple effector proteins, and depending on which effector it binds, Rab27a has different functions as well as tissue distribution and/or cellular localization. Putative functions have been assigned to Rab27a when associated with the effector proteins Slp1, Slp2, Slp3, Slp4, Slp5, DmSlp, rabphilin, Dm/Ce-rabphilin, Slac2-a, Slac2-b, Slac2-c, Noc2, JFC1, and Munc13-4. Rab27a has been associated with several human diseases, including hemophagocytic syndrome (Griscelli syndrome or GS), Hermansky-Pudlak syndrome, and choroidermia. In the case of GS, a rare, autosomal recessive disease, a Rab27a mutation is directly responsible for the disorder. When Rab27a is localized to the secretory granules of pancreatic beta cells, it is believed to mediate glucose-stimulated
Probab=26.65 E-value=1.1e+02 Score=18.44 Aligned_cols=27 Identities=19% Similarity=0.287 Sum_probs=22.7
Q ss_pred eeEeecccccCccHHHHHHHHHHHHHH
Q psy6616 36 IYCHMTCATDTNNIQFVFDAVTDVIIA 62 (71)
Q Consensus 36 iy~h~T~AtDt~ni~~vf~~V~d~Il~ 62 (71)
+-...++|...++++.+|+.+.+.+++
T Consensus 152 ~~~~e~Sak~~~~v~~l~~~l~~~~~~ 178 (180)
T cd04127 152 IPYFETSAATGTNVEKAVERLLDLVMK 178 (180)
T ss_pred CeEEEEeCCCCCCHHHHHHHHHHHHHh
Confidence 345789999999999999999887764
No 41
>PRK00454 engB GTP-binding protein YsxC; Reviewed
Probab=26.01 E-value=88 Score=19.24 Aligned_cols=22 Identities=9% Similarity=0.095 Sum_probs=18.5
Q ss_pred eecccccCccHHHHHHHHHHHH
Q psy6616 39 HMTCATDTNNIQFVFDAVTDVI 60 (71)
Q Consensus 39 h~T~AtDt~ni~~vf~~V~d~I 60 (71)
..|+|.|.++++.+++.+.+.+
T Consensus 172 ~~~Sa~~~~gi~~l~~~i~~~~ 193 (196)
T PRK00454 172 ILFSSLKKQGIDELRAAIAKWL 193 (196)
T ss_pred EEEEcCCCCCHHHHHHHHHHHh
Confidence 4899999999999998877543
No 42
>cd08811 CARD_IPS1 Caspase activation and recruitment domain (CARD) found in IPS-1. Caspase activation and recruitment domain (CARD) found in IPS-1 (Interferon beta promoter stimulator protein 1), also known as CARDIF, VISA or MAVS. IPS-1 is an adaptor protein that plays an important role in interferon induction in response to viral infection. It is crucial in triggering innate immunity and in developing adaptive immunity against viral pathogens. The CARD of IPS-1 associates with the CARDs of two RNA helicases, RIG-I and MDA5, which bind viral DNA in the cytoplasm during the initial stage of intracellular antiviral response, leading to the induction of type I interferons. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homo
Probab=25.97 E-value=24 Score=20.73 Aligned_cols=33 Identities=18% Similarity=0.286 Sum_probs=22.5
Q ss_pred HHHHHHHHHHHhhccCCCCCeeEeecccccCcc
Q psy6616 16 EAAAYIQAQFEAKNKSTTKEIYCHMTCATDTNN 48 (71)
Q Consensus 16 ~~~~fi~~kF~~~~~~~~r~iy~h~T~AtDt~n 48 (71)
...+||+..+..-..-.-.++-+|..|-||.+.
T Consensus 3 k~~k~I~~n~~~Fc~i~v~eiLP~LpCLT~~Dq 35 (84)
T cd08811 3 KTYKYIRRNMSRFCTVDVVEILPYLPCLTASDQ 35 (84)
T ss_pred HHHHHHHHhhccceeeeHHHhcCccccCchhhH
Confidence 456788887765443345677888888887654
No 43
>cd04132 Rho4_like Rho4-like subfamily. Rho4 is a GTPase that controls septum degradation by regulating secretion of Eng1 or Agn1 during cytokinesis. Rho4 also plays a role in cell morphogenesis. Rho4 regulates septation and cell morphology by controlling the actin cytoskeleton and cytoplasmic microtubules. The localization of Rho4 is modulated by Rdi1, which may function as a GDI, and by Rga9, which is believed to function as a GAP. In S. pombe, both Rho4 deletion and Rho4 overexpression result in a defective cell wall, suggesting a role for Rho4 in maintaining cell wall integrity. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins.
Probab=25.93 E-value=1.2e+02 Score=18.52 Aligned_cols=28 Identities=18% Similarity=0.211 Sum_probs=24.0
Q ss_pred EeecccccCccHHHHHHHHHHHHHHhhh
Q psy6616 38 CHMTCATDTNNIQFVFDAVTDVIIANNL 65 (71)
Q Consensus 38 ~h~T~AtDt~ni~~vf~~V~d~Il~~nl 65 (71)
...++|.+-++|..+|..+.+.++....
T Consensus 144 ~~e~Sa~~~~~v~~~f~~l~~~~~~~~~ 171 (187)
T cd04132 144 YLECSAKTMENVEEVFDTAIEEALKKEG 171 (187)
T ss_pred EEEccCCCCCCHHHHHHHHHHHHHhhhh
Confidence 4688999999999999999999887543
No 44
>cd01875 RhoG RhoG subfamily. RhoG is a GTPase with high sequence similarity to members of the Rac subfamily, including the regions involved in effector recognition and binding. However, RhoG does not bind to known Rac1 and Cdc42 effectors, including proteins containing a Cdc42/Rac interacting binding (CRIB) motif. Instead, RhoG interacts directly with Elmo, an upstream regulator of Rac1, in a GTP-dependent manner and forms a ternary complex with Dock180 to induce activation of Rac1. The RhoG-Elmo-Dock180 pathway is required for activation of Rac1 and cell spreading mediated by integrin, as well as for neurite outgrowth induced by nerve growth factor. Thus RhoG activates Rac1 through Elmo and Dock180 to control cell morphology. RhoG has also been shown to play a role in caveolar trafficking and has a novel role in signaling the neutrophil respiratory burst stimulated by G protein-coupled receptor (GPCR) agonists. Most Rho proteins contain a lipid modification site at the C-termin
Probab=25.65 E-value=1e+02 Score=19.35 Aligned_cols=27 Identities=11% Similarity=0.212 Sum_probs=23.1
Q ss_pred EeecccccCccHHHHHHHHHHHHHHhh
Q psy6616 38 CHMTCATDTNNIQFVFDAVTDVIIANN 64 (71)
Q Consensus 38 ~h~T~AtDt~ni~~vf~~V~d~Il~~n 64 (71)
...|+|.+.+||+.+|..+.+.++..+
T Consensus 154 ~~e~SAk~g~~v~e~f~~l~~~~~~~~ 180 (191)
T cd01875 154 YLECSALNQDGVKEVFAEAVRAVLNPT 180 (191)
T ss_pred EEEeCCCCCCCHHHHHHHHHHHHhccc
Confidence 457999999999999999998887654
No 45
>cd04174 Rnd1_Rho6 Rnd1/Rho6 subfamily. Rnd1/Rho6 is a member of the novel Rho subfamily Rnd, together with Rnd2/Rho7 and Rnd3/RhoE/Rho8. Rnd1/Rho6 binds GTP but does not hydrolyze it to GDP, indicating that it is constitutively active. In rat, Rnd1/Rho6 is highly expressed in the cerebral cortex and hippocampus during synapse formation, and plays a role in spine formation. Rnd1/Rho6 is also expressed in the liver and in endothelial cells, and is upregulated in uterine myometrial cells during pregnancy. Like Rnd3/RhoE/Rho8, Rnd1/Rho6 is believed to function as an antagonist to RhoA. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.
Probab=25.52 E-value=83 Score=21.11 Aligned_cols=28 Identities=11% Similarity=0.099 Sum_probs=23.0
Q ss_pred eecccccCc-cHHHHHHHHHHHHHHhhhh
Q psy6616 39 HMTCATDTN-NIQFVFDAVTDVIIANNLR 66 (71)
Q Consensus 39 h~T~AtDt~-ni~~vf~~V~d~Il~~nl~ 66 (71)
..|+|.+.+ +|..+|..+-..+++..+.
T Consensus 165 ~EtSAktg~~~V~e~F~~~~~~~~~~~~~ 193 (232)
T cd04174 165 LECSAFTSEKSIHSIFRSASLLCLNKLSP 193 (232)
T ss_pred EEccCCcCCcCHHHHHHHHHHHHHHhccc
Confidence 469999886 7999999999888876544
No 46
>PF00025 Arf: ADP-ribosylation factor family The prints entry specific to Sar1 proteins The Prosite entry specific to Sar1 proteins; InterPro: IPR006689 Small GTPases form an independent superfamily within the larger class of regulatory GTP hydrolases. This superfamily contains proteins that control a vast number of important processes and possess a common, structurally preserved GTP-binding domain [, ]. Sequence comparisons of small G proteins from various species have revealed that they are conserved in primary structures at the level of 30-55% similarity []. Crystallographic analysis of various small G proteins revealed the presence of a 20 kDa catalytic domain that is unique for the whole superfamily [, ]. The domain is built of five alpha helices (A1-A5), six beta-strands (B1-B6) and five polypeptide loops (G1-G5). A structural comparison of the GTP- and GDP-bound form, allows one to distinguish two functional loop regions: switch I and switch II that surround the gamma-phosphate group of the nucleotide. The G1 loop (also called the P-loop) that connects the B1 strand and the A1 helix is responsible for the binding of the phosphate groups. The G3 loop provides residues for Mg(2+) and phosphate binding and is located at the N terminus of the A2 helix. The G1 and G3 loops are sequentially similar to Walker A and Walker B boxes that are found in other nucleotide binding motifs. The G2 loop connects the A1 helix and the B2 strand and contains a conserved Thr residue responsible for Mg(2+) binding. The guanine base is recognised by the G4 and G5 loops. The consensus sequence NKXD of the G4 loop contains Lys and Asp residues directly interacting with the nucleotide. Part of the G5 loop located between B6 and A5 acts as a recognition site for the guanine base []. The small GTPase superfamily can be divided into at least 8 different families, including: Arf small GTPases. GTP-binding proteins involved in protein trafficking by modulating vesicle budding and uncoating within the Golgi apparatus. Ran small GTPases. GTP-binding proteins involved in nucleocytoplasmic transport. Required for the import of proteins into the nucleus and also for RNA export. Rab small GTPases. GTP-binding proteins involved in vesicular traffic. Rho small GTPases. GTP-binding proteins that control cytoskeleton reorganisation. Ras small GTPases. GTP-binding proteins involved in signalling pathways. Sar1 small GTPases. Small GTPase component of the coat protein complex II (COPII) which promotes the formation of transport vesicles from the endoplasmic reticulum (ER). Mitochondrial Rho (Miro). Small GTPase domain found in mitochondrial proteins involved in mitochondrial trafficking. Roc small GTPases domain. Small GTPase domain always found associated with the COR domain. This entry represents a branch of the small GTPase superfamily that includes the ADP ribosylation factor Arf, Arl (Arf-like), Arp (Arf-related proteins) and the remotely related Sar (Secretion-associated and Ras-related) proteins. Arf proteins are major regulators of vesicle biogenesis in intracellular traffic []. They cycle between inactive GDP-bound and active GTP-bound forms that bind selectively to effectors. The classical structural GDP/GTP switch is characterised by conformational changes at the so-called switch 1 and switch 2 regions, which bind tightly to the gamma-phosphate of GTP but poorly or not at all to the GDP nucleotide. Structural studies of Arf1 and Arf6 have revealed that although these proteins feature the switch 1 and 2 conformational changes, they depart from other small GTP-binding proteins in that they use an additional, unique switch to propagate structural information from one side of the protein to the other. The GDP/GTP structural cycles of human Arf1 and Arf6 feature a unique conformational change that affects the beta2-beta3 strands connecting switch 1 and switch 2 (interswitch) and also the amphipathic helical N terminus. In GDP-bound Arf1 and Arf6, the interswitch is retracted and forms a pocket to which the N-terminal helix binds, the latter serving as a molecular hasp to maintain the inactive conformation. In the GTP-bound form of these proteins, the interswitch undergoes a two-residue register shift that pulls switch 1 and switch 2 up, restoring an active conformation that can bind GTP. In this conformation, the interswitch projects out of the protein and extrudes the N-terminal hasp by occluding its binding pocket.; GO: 0005525 GTP binding; PDB: 2H57_B 2W83_B 3N5C_B 2J5X_A 3LVR_E 2BAO_A 3LVQ_E 2A5F_A 3PCR_B 1E0S_A ....
Probab=25.24 E-value=1.7e+02 Score=18.17 Aligned_cols=29 Identities=7% Similarity=0.051 Sum_probs=24.2
Q ss_pred CCCCeeEeecccccCccHHHHHHHHHHHH
Q psy6616 32 TTKEIYCHMTCATDTNNIQFVFDAVTDVI 60 (71)
Q Consensus 32 ~~r~iy~h~T~AtDt~ni~~vf~~V~d~I 60 (71)
..+++.+.-+||..-+++...++-+.+.|
T Consensus 147 ~~~~~~v~~~sa~~g~Gv~e~l~WL~~~~ 175 (175)
T PF00025_consen 147 NKRPWSVFSCSAKTGEGVDEGLEWLIEQI 175 (175)
T ss_dssp SSSCEEEEEEBTTTTBTHHHHHHHHHHHH
T ss_pred cCCceEEEeeeccCCcCHHHHHHHHHhcC
Confidence 36889999999999999998888776654
No 47
>cd04107 Rab32_Rab38 Rab38/Rab32 subfamily. Rab32 and Rab38 are members of the Rab family of small GTPases. Human Rab32 was first identified in platelets but it is expressed in a variety of cell types, where it functions as an A-kinase anchoring protein (AKAP). Rab38 has been shown to be melanocyte-specific. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins.
Probab=25.16 E-value=1.2e+02 Score=19.15 Aligned_cols=28 Identities=29% Similarity=0.223 Sum_probs=23.7
Q ss_pred eeEeecccccCccHHHHHHHHHHHHHHh
Q psy6616 36 IYCHMTCATDTNNIQFVFDAVTDVIIAN 63 (71)
Q Consensus 36 iy~h~T~AtDt~ni~~vf~~V~d~Il~~ 63 (71)
.....|+|...++|..+|..+.+.+++.
T Consensus 143 ~~~~e~Sak~~~~v~e~f~~l~~~l~~~ 170 (201)
T cd04107 143 IGWFETSAKEGINIEEAMRFLVKNILAN 170 (201)
T ss_pred ceEEEEeCCCCCCHHHHHHHHHHHHHHh
Confidence 3467899999999999999999888753
No 48
>cd04112 Rab26 Rab26 subfamily. First identified in rat pancreatic acinar cells, Rab26 is believed to play a role in recruiting mature granules to the plasma membrane upon beta-adrenergic stimulation. Rab26 belongs to the Rab functional group III, which are considered key regulators of intracellular vesicle transport during exocytosis. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins.
Probab=25.08 E-value=1.3e+02 Score=18.67 Aligned_cols=30 Identities=20% Similarity=0.201 Sum_probs=25.3
Q ss_pred eEeecccccCccHHHHHHHHHHHHHHhhhh
Q psy6616 37 YCHMTCATDTNNIQFVFDAVTDVIIANNLR 66 (71)
Q Consensus 37 y~h~T~AtDt~ni~~vf~~V~d~Il~~nl~ 66 (71)
-...++|.+.+++..+|..+...++..+..
T Consensus 139 ~~~e~Sa~~~~~v~~l~~~l~~~~~~~~~~ 168 (191)
T cd04112 139 PFMETSAKTGLNVELAFTAVAKELKHRKYE 168 (191)
T ss_pred eEEEEeCCCCCCHHHHHHHHHHHHHHhccc
Confidence 357889999999999999999998876543
No 49
>cd04124 RabL2 RabL2 subfamily. RabL2 (Rab-like2) subfamily. RabL2s are novel Rab proteins identified recently which display features that are distinct from other Rabs, and have been termed Rab-like. RabL2 contains RabL2a and RabL2b, two very similar Rab proteins that share 98% sequence identity in humans. RabL2b maps to the subtelomeric region of chromosome 22q13.3 and RabL2a maps to 2q13, a region that suggests it is also a subtelomeric gene. Both genes are believed to be expressed ubiquitously, suggesting that RabL2s are the first example of duplicated genes in human proximal subtelomeric regions that are both expressed actively. Like other Rab-like proteins, RabL2s lack a prenylation site at the C-terminus. The specific functions of RabL2a and RabL2b remain unknown. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-b
Probab=24.86 E-value=1.2e+02 Score=18.20 Aligned_cols=26 Identities=15% Similarity=0.218 Sum_probs=22.0
Q ss_pred eEeecccccCccHHHHHHHHHHHHHH
Q psy6616 37 YCHMTCATDTNNIQFVFDAVTDVIIA 62 (71)
Q Consensus 37 y~h~T~AtDt~ni~~vf~~V~d~Il~ 62 (71)
....++|.+-.++..+|+.+.+.+++
T Consensus 134 ~~~~~Sa~~~~gv~~l~~~l~~~~~~ 159 (161)
T cd04124 134 PLYYVSAADGTNVVKLFQDAIKLAVS 159 (161)
T ss_pred eEEEEeCCCCCCHHHHHHHHHHHHHh
Confidence 34579999999999999999887765
No 50
>cd01876 YihA_EngB The YihA (EngB) subfamily. This subfamily of GTPases is typified by the E. coli YihA, an essential protein involved in cell division control. YihA and its orthologs are small proteins that typically contain less than 200 amino acid residues and consists of the GTPase domain only (some of the eukaryotic homologs contain an N-terminal extension of about 120 residues that might be involved in organellar targeting). Homologs of yihA are found in most Gram-positive and Gram-negative pathogenic bacteria, with the exception of Mycobacterium tuberculosis. The broad-spectrum nature of YihA and its essentiality for cell viability in bacteria make it an attractive antibacterial target.
Probab=24.40 E-value=77 Score=18.38 Aligned_cols=23 Identities=4% Similarity=-0.090 Sum_probs=18.4
Q ss_pred eEeecccccCccHHHHHHHHHHH
Q psy6616 37 YCHMTCATDTNNIQFVFDAVTDV 59 (71)
Q Consensus 37 y~h~T~AtDt~ni~~vf~~V~d~ 59 (71)
-++.++|.|..+++.+++.+...
T Consensus 147 ~~~~~Sa~~~~~~~~l~~~l~~~ 169 (170)
T cd01876 147 PIILFSSLKGQGIDELRALIEKW 169 (170)
T ss_pred ceEEEecCCCCCHHHHHHHHHHh
Confidence 35599999999999888877653
No 51
>smart00174 RHO Rho (Ras homology) subfamily of Ras-like small GTPases. Members of this subfamily of Ras-like small GTPases include Cdc42 and Rac, as well as Rho isoforms.
Probab=24.20 E-value=1e+02 Score=18.51 Aligned_cols=25 Identities=12% Similarity=0.167 Sum_probs=20.9
Q ss_pred EeecccccCccHHHHHHHHHHHHHH
Q psy6616 38 CHMTCATDTNNIQFVFDAVTDVIIA 62 (71)
Q Consensus 38 ~h~T~AtDt~ni~~vf~~V~d~Il~ 62 (71)
...++|.+.+|+..+|..+.+.+++
T Consensus 149 ~~e~Sa~~~~~v~~lf~~l~~~~~~ 173 (174)
T smart00174 149 YLECSALTQEGVREVFEEAIRAALN 173 (174)
T ss_pred EEEecCCCCCCHHHHHHHHHHHhcC
Confidence 3468999999999999998887764
No 52
>PF10406 TAF8_C: Transcription factor TFIID complex subunit 8 C-term ; InterPro: IPR019473 This entry represents the C-terminal region of subunit 8 (also known as TAF8) of the transcription factor TFIID []. The adjacent N-terminal region generally contains a histone fold domain (IPR006565 from INTERPRO). This subunit is one of the key subunits of TFIID, being one of several general cofactors which are typically involved in gene activation to bring about the communication between gene-specific transcription factors and components of the general transcription machinery [].
Probab=23.81 E-value=49 Score=17.24 Aligned_cols=12 Identities=8% Similarity=0.451 Sum_probs=8.0
Q ss_pred cccCCCCCCCCCh
Q psy6616 2 KYFTELLSGAQEY 14 (71)
Q Consensus 2 ~~Fp~~y~G~~~~ 14 (71)
+|||. |.++..|
T Consensus 5 ~~lP~-fP~~HTY 16 (51)
T PF10406_consen 5 DWLPP-FPPPHTY 16 (51)
T ss_pred ccCCC-CCCCccc
Confidence 57777 7666554
No 53
>cd04123 Rab21 Rab21 subfamily. The localization and function of Rab21 are not clearly defined, with conflicting data reported. Rab21 has been reported to localize in the ER in human intestinal epithelial cells, with partial colocalization with alpha-glucosidase, a late endosomal/lysosomal marker. More recently, Rab21 was shown to colocalize with and affect the morphology of early endosomes. In Dictyostelium, GTP-bound Rab21, together with two novel LIM domain proteins, LimF and ChLim, has been shown to regulate phagocytosis. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site
Probab=23.77 E-value=90 Score=18.17 Aligned_cols=23 Identities=17% Similarity=0.189 Sum_probs=19.3
Q ss_pred EeecccccCccHHHHHHHHHHHH
Q psy6616 38 CHMTCATDTNNIQFVFDAVTDVI 60 (71)
Q Consensus 38 ~h~T~AtDt~ni~~vf~~V~d~I 60 (71)
.+.+||.+.+++..+++.+.+.+
T Consensus 139 ~~~~s~~~~~gi~~~~~~l~~~~ 161 (162)
T cd04123 139 HFETSAKTGKGIEELFLSLAKRM 161 (162)
T ss_pred EEEEeCCCCCCHHHHHHHHHHHh
Confidence 56889999999999999876654
No 54
>PF00071 Ras: Ras family; InterPro: IPR001806 Small GTPases form an independent superfamily within the larger class of regulatory GTP hydrolases. This superfamily contains proteins that control a vast number of important processes and possess a common, structurally preserved GTP-binding domain [, ]. Sequence comparisons of small G proteins from various species have revealed that they are conserved in primary structures at the level of 30-55% similarity []. Crystallographic analysis of various small G proteins revealed the presence of a 20 kDa catalytic domain that is unique for the whole superfamily [, ]. The domain is built of five alpha helices (A1-A5), six beta-strands (B1-B6) and five polypeptide loops (G1-G5). A structural comparison of the GTP- and GDP-bound form, allows one to distinguish two functional loop regions: switch I and switch II that surround the gamma-phosphate group of the nucleotide. The G1 loop (also called the P-loop) that connects the B1 strand and the A1 helix is responsible for the binding of the phosphate groups. The G3 loop provides residues for Mg(2+) and phosphate binding and is located at the N terminus of the A2 helix. The G1 and G3 loops are sequentially similar to Walker A and Walker B boxes that are found in other nucleotide binding motifs. The G2 loop connects the A1 helix and the B2 strand and contains a conserved Thr residue responsible for Mg(2+) binding. The guanine base is recognised by the G4 and G5 loops. The consensus sequence NKXD of the G4 loop contains Lys and Asp residues directly interacting with the nucleotide. Part of the G5 loop located between B6 and A5 acts as a recognition site for the guanine base []. The small GTPase superfamily can be divided into at least 8 different families, including: Arf small GTPases. GTP-binding proteins involved in protein trafficking by modulating vesicle budding and uncoating within the Golgi apparatus. Ran small GTPases. GTP-binding proteins involved in nucleocytoplasmic transport. Required for the import of proteins into the nucleus and also for RNA export. Rab small GTPases. GTP-binding proteins involved in vesicular traffic. Rho small GTPases. GTP-binding proteins that control cytoskeleton reorganisation. Ras small GTPases. GTP-binding proteins involved in signalling pathways. Sar1 small GTPases. Small GTPase component of the coat protein complex II (COPII) which promotes the formation of transport vesicles from the endoplasmic reticulum (ER). Mitochondrial Rho (Miro). Small GTPase domain found in mitochondrial proteins involved in mitochondrial trafficking. Roc small GTPases domain. Small GTPase domain always found associated with the COR domain. ; GO: 0005525 GTP binding, 0007264 small GTPase mediated signal transduction; PDB: 1M7B_A 2V55_B 3EG5_C 3LAW_A 1YHN_A 1T91_B 1HE8_B 3SEA_B 3T5G_A 1XTS_A ....
Probab=23.74 E-value=1e+02 Score=18.17 Aligned_cols=26 Identities=15% Similarity=0.303 Sum_probs=20.9
Q ss_pred eeEeecccccCccHHHHHHHHHHHHH
Q psy6616 36 IYCHMTCATDTNNIQFVFDAVTDVII 61 (71)
Q Consensus 36 iy~h~T~AtDt~ni~~vf~~V~d~Il 61 (71)
+..-.++|.+..+|..+|..+.+.|+
T Consensus 136 ~~~~e~Sa~~~~~v~~~f~~~i~~i~ 161 (162)
T PF00071_consen 136 VPYFEVSAKNGENVKEIFQELIRKIL 161 (162)
T ss_dssp SEEEEEBTTTTTTHHHHHHHHHHHHH
T ss_pred CEEEEEECCCCCCHHHHHHHHHHHHh
Confidence 44456889999999999998887775
No 55
>PRK02770 S-adenosylmethionine decarboxylase proenzyme; Provisional
Probab=23.33 E-value=1.1e+02 Score=19.29 Aligned_cols=15 Identities=20% Similarity=0.242 Sum_probs=13.4
Q ss_pred ChHHHHHHHHHHHHh
Q psy6616 13 EYGEAAAYIQAQFEA 27 (71)
Q Consensus 13 ~~~~~~~fi~~kF~~ 27 (71)
+.+.|.+||++.|..
T Consensus 101 ~p~~a~~~L~~~l~~ 115 (139)
T PRK02770 101 MPEKACQYLIEELMA 115 (139)
T ss_pred CHHHHHHHHHHHhCC
Confidence 788999999999975
No 56
>PF02829 3H: 3H domain; InterPro: IPR004173 The 3H domain is named after its three highly conserved histidine residues. The 3H domain appears to be a small molecule-binding domain, based on its occurrence with other domains []. Several proteins carrying this domain are transcriptional regulators from the biotin repressor family. The transcription regulator TM1602 from Thermotoga maritima is a DNA-binding protein thought to belong to a family of de novo NAD synthesis pathway regulators. TM1602 has an N-terminal DNA-binding domain and a C-terminal 3H regulatory domain. The N-terminal domain appears to bind to the NAD promoter region and repress the de novo NAD biosynthesis operon, while the C-terminal 3H domain may bind to nicotinamide, nicotinic acid, or other substrate/products []. The 3H domain has a 2-layer alpha/beta sandwich fold.; GO: 0005488 binding; PDB: 1J5Y_A.
Probab=23.05 E-value=1.8e+02 Score=17.28 Aligned_cols=45 Identities=18% Similarity=0.235 Sum_probs=29.4
Q ss_pred ChHHHHHHHHHHHHhhccC---CCCCeeEeecccccCccHHHHHHHHH
Q psy6616 13 EYGEAAAYIQAQFEAKNKS---TTKEIYCHMTCATDTNNIQFVFDAVT 57 (71)
Q Consensus 13 ~~~~~~~fi~~kF~~~~~~---~~r~iy~h~T~AtDt~ni~~vf~~V~ 57 (71)
+-.++.+|+.+.=....++ =..-++.|..+|-|-+.+..+.++.+
T Consensus 45 sr~Dv~~Fi~~l~~~~~~~Ls~LT~GvH~HtI~a~~~e~l~~I~~~L~ 92 (98)
T PF02829_consen 45 SRRDVDKFIEKLEKSKAKPLSSLTGGVHYHTIEAPDEEDLDKIEEALK 92 (98)
T ss_dssp SHHHHHHHHHHHHH--S--STTGGGGEEEEEEEESSHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHhccCCcchHHhcCCEeeEEEEECCHHHHHHHHHHHH
Confidence 5677888888765442211 13468999999999888776665544
No 57
>cd04150 Arf1_5_like Arf1-Arf5-like subfamily. This subfamily contains Arf1, Arf2, Arf3, Arf4, Arf5, and related proteins. Arfs1-5 are soluble proteins that are crucial for assembling coat proteins during vesicle formation. Each contains an N-terminal myristoylated amphipathic helix that is folded into the protein in the GDP-bound state. GDP/GTP exchange exposes the helix, which anchors to the membrane. Following GTP hydrolysis, the helix dissociates from the membrane and folds back into the protein. A general feature of Arf1-5 signaling may be the cooperation of two Arfs at the same site. Arfs1-5 are generally considered to be interchangeable in function and location, but some specific functions have been assigned. Arf1 localizes to the early/cis-Golgi, where it is activated by GBF1 and recruits the coat protein COPI. It also localizes to the trans-Golgi network (TGN), where it is activated by BIG1/BIG2 and recruits the AP1, AP3, AP4, and GGA proteins. Humans, but not rodents
Probab=23.02 E-value=1.8e+02 Score=17.45 Aligned_cols=24 Identities=25% Similarity=0.407 Sum_probs=18.3
Q ss_pred CCCeeEeecccccCccHHHHHHHH
Q psy6616 33 TKEIYCHMTCATDTNNIQFVFDAV 56 (71)
Q Consensus 33 ~r~iy~h~T~AtDt~ni~~vf~~V 56 (71)
++.+++..+||...+++..+|+.+
T Consensus 133 ~~~~~~~~~Sak~g~gv~~~~~~l 156 (159)
T cd04150 133 NRNWYIQATCATSGDGLYEGLDWL 156 (159)
T ss_pred CCCEEEEEeeCCCCCCHHHHHHHH
Confidence 455666678999999998888755
No 58
>PRK13441 F0F1 ATP synthase subunit delta; Provisional
Probab=22.84 E-value=2.1e+02 Score=18.18 Aligned_cols=42 Identities=17% Similarity=0.237 Sum_probs=26.5
Q ss_pred HHHHHHHHHHHhhccCCCCCeeEeeccc--ccCccHHHHHHHHH
Q psy6616 16 EAAAYIQAQFEAKNKSTTKEIYCHMTCA--TDTNNIQFVFDAVT 57 (71)
Q Consensus 16 ~~~~fi~~kF~~~~~~~~r~iy~h~T~A--tDt~ni~~vf~~V~ 57 (71)
.....|.+.|.++.......+.+.+||| .+.+.+..+-+.+.
T Consensus 88 ~~l~~I~~~f~~l~~~~~~~~~~~V~sA~~L~~~~~~~i~~~l~ 131 (180)
T PRK13441 88 KLLPQIRALFEYEKILSEQKVPVNLTTAHELSDEELKLLRKFVR 131 (180)
T ss_pred HHHHHHHHHHHHHHHHhcCeeEEEEEecccCCHHHHHHHHHHHH
Confidence 4456677777766544566788899988 55555555544443
No 59
>cd01869 Rab1_Ypt1 Rab1/Ypt1 subfamily. Rab1 is found in every eukaryote and is a key regulatory component for the transport of vesicles from the ER to the Golgi apparatus. Studies on mutations of Ypt1, the yeast homolog of Rab1, showed that this protein is necessary for the budding of vesicles of the ER as well as for their transport to, and fusion with, the Golgi apparatus. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to t
Probab=22.83 E-value=1.4e+02 Score=17.81 Aligned_cols=26 Identities=23% Similarity=0.222 Sum_probs=21.4
Q ss_pred eeEeecccccCccHHHHHHHHHHHHH
Q psy6616 36 IYCHMTCATDTNNIQFVFDAVTDVII 61 (71)
Q Consensus 36 iy~h~T~AtDt~ni~~vf~~V~d~Il 61 (71)
+-...++|.+-+++..+|..+.+.+.
T Consensus 139 ~~~~~~Sa~~~~~v~~~~~~i~~~~~ 164 (166)
T cd01869 139 IPFLETSAKNATNVEQAFMTMAREIK 164 (166)
T ss_pred CeEEEEECCCCcCHHHHHHHHHHHHH
Confidence 34578999999999999998877765
No 60
>PF12261 T_hemolysin: Thermostable hemolysin; InterPro: IPR022050 This family of proteins is found in bacteria. Proteins in this family are typically between 200 and 228 amino acids in length. T_hemolysin is a pore-forming toxin of bacteria, able to lyse erythrocytes from a number of mammalian species.
Probab=22.75 E-value=91 Score=20.52 Aligned_cols=36 Identities=17% Similarity=0.336 Sum_probs=23.2
Q ss_pred CCCChHHHHHHHHHHHHhhccCCCCCeeEeeccccc
Q psy6616 10 GAQEYGEAAAYIQAQFEAKNKSTTKEIYCHMTCATD 45 (71)
Q Consensus 10 G~~~~~~~~~fi~~kF~~~~~~~~r~iy~h~T~AtD 45 (71)
|.....++..||++.|.+.....-+...+.+-+.+|
T Consensus 6 ~~~~r~~~e~fI~~~y~~~~~A~i~~f~P~ll~l~~ 41 (179)
T PF12261_consen 6 GDPERAEVEQFIRQRYAQAYGATIRHFMPQLLALRD 41 (179)
T ss_pred CchhHHHHHHHHHHHHHHHhCCcCCccchHHhhhcc
Confidence 445677888999999998765444444444444433
No 61
>cd01865 Rab3 Rab3 subfamily. The Rab3 subfamily contains Rab3A, Rab3B, Rab3C, and Rab3D. All four isoforms were found in mouse brain and endocrine tissues, with varying levels of expression. Rab3A, Rab3B, and Rab3C localized to synaptic and secretory vesicles; Rab3D was expressed at high levels only in adipose tissue, exocrine glands, and the endocrine pituitary, where it is localized to cytoplasmic secretory granules. Rab3 appears to control Ca2+-regulated exocytosis. The appropriate GDP/GTP exchange cycle of Rab3A is required for Ca2+-regulated exocytosis to occur, and interaction of the GTP-bound form of Rab3A with effector molecule(s) is widely believed to be essential for this process. Functionally, most studies point toward a role for Rab3 in the secretion of hormones and neurotransmitters. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promot
Probab=22.74 E-value=1.4e+02 Score=17.93 Aligned_cols=26 Identities=23% Similarity=0.383 Sum_probs=21.3
Q ss_pred eeEeecccccCccHHHHHHHHHHHHH
Q psy6616 36 IYCHMTCATDTNNIQFVFDAVTDVII 61 (71)
Q Consensus 36 iy~h~T~AtDt~ni~~vf~~V~d~Il 61 (71)
+..+.++|.+..++..+|+.+-+.+.
T Consensus 138 ~~~~~~Sa~~~~gv~~l~~~l~~~~~ 163 (165)
T cd01865 138 FEFFEASAKENINVKQVFERLVDIIC 163 (165)
T ss_pred CEEEEEECCCCCCHHHHHHHHHHHHH
Confidence 34678999999999999998877654
No 62
>cd04142 RRP22 RRP22 subfamily. RRP22 (Ras-related protein on chromosome 22) subfamily consists of proteins that inhibit cell growth and promote caspase-independent cell death. Unlike most Ras proteins, RRP22 is down-regulated in many human tumor cells due to promoter methylation. RRP22 localizes to the nucleolus in a GTP-dependent manner, suggesting a novel function in modulating transport of nucleolar components. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. Like most Ras family proteins, RRP22 is farnesylated.
Probab=22.67 E-value=1.2e+02 Score=19.46 Aligned_cols=27 Identities=11% Similarity=-0.040 Sum_probs=22.6
Q ss_pred eeEeecccccCccHHHHHHHHHHHHHH
Q psy6616 36 IYCHMTCATDTNNIQFVFDAVTDVIIA 62 (71)
Q Consensus 36 iy~h~T~AtDt~ni~~vf~~V~d~Il~ 62 (71)
+-...|+|.+..||..+|..+-..+++
T Consensus 149 ~~~~e~Sak~g~~v~~lf~~i~~~~~~ 175 (198)
T cd04142 149 CGYLECSAKYNWHILLLFKELLISATT 175 (198)
T ss_pred CcEEEecCCCCCCHHHHHHHHHHHhhc
Confidence 334689999999999999999888774
No 63
>cd04109 Rab28 Rab28 subfamily. First identified in maize, Rab28 has been shown to be a late embryogenesis-abundant (Lea) protein that is regulated by the plant hormone abcisic acid (ABA). In Arabidopsis, Rab28 is expressed during embryo development and is generally restricted to provascular tissues in mature embryos. Unlike maize Rab28, it is not ABA-inducible. Characterization of the human Rab28 homolog revealed two isoforms, which differ by a 95-base pair insertion, producing an alternative sequence for the 30 amino acids at the C-terminus. The two human isoforms are presumbly the result of alternative splicing. Since they differ at the C-terminus but not in the GTP-binding region, they are predicted to be targeted to different cellular locations. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs
Probab=22.66 E-value=1.4e+02 Score=19.05 Aligned_cols=29 Identities=7% Similarity=0.312 Sum_probs=24.0
Q ss_pred eeEeecccccCccHHHHHHHHHHHHHHhh
Q psy6616 36 IYCHMTCATDTNNIQFVFDAVTDVIIANN 64 (71)
Q Consensus 36 iy~h~T~AtDt~ni~~vf~~V~d~Il~~n 64 (71)
+....+||..-+++..+|+.+...++...
T Consensus 141 ~~~~~iSAktg~gv~~lf~~l~~~l~~~~ 169 (215)
T cd04109 141 MESCLVSAKTGDRVNLLFQQLAAELLGVD 169 (215)
T ss_pred CEEEEEECCCCCCHHHHHHHHHHHHHhcc
Confidence 33567999999999999999998887643
No 64
>cd04120 Rab12 Rab12 subfamily. Rab12 was first identified in canine cells, where it was localized to the Golgi complex. The specific function of Rab12 remains unknown, and inconsistent results about its cellular localization have been reported. More recent studies have identified Rab12 associated with post-Golgi vesicles, or with other small vesicle-like structures but not with the Golgi complex. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic
Probab=22.46 E-value=1.7e+02 Score=18.92 Aligned_cols=27 Identities=22% Similarity=0.267 Sum_probs=22.6
Q ss_pred eeEeecccccCccHHHHHHHHHHHHHH
Q psy6616 36 IYCHMTCATDTNNIQFVFDAVTDVIIA 62 (71)
Q Consensus 36 iy~h~T~AtDt~ni~~vf~~V~d~Il~ 62 (71)
+....|+|.+-++|..+|..+-+.+++
T Consensus 138 ~~~~etSAktg~gV~e~F~~l~~~~~~ 164 (202)
T cd04120 138 MRFCEASAKDNFNVDEIFLKLVDDILK 164 (202)
T ss_pred CEEEEecCCCCCCHHHHHHHHHHHHHH
Confidence 335589999999999999998887764
No 65
>cd04135 Tc10 TC10 subfamily. TC10 is a Rho family protein that has been shown to induce microspike formation and neurite outgrowth in vitro. Its expression changes dramatically after peripheral nerve injury, suggesting an important role in promoting axonal outgrowth and regeneration. TC10 regulates translocation of insulin-stimulated GLUT4 in adipocytes and has also been shown to bind directly to Golgi COPI coat proteins. GTP-bound TC10 in vitro can bind numerous potential effectors. Depending on its subcellular localization and distinct functional domains, TC10 can differentially regulate two types of filamentous actin in adipocytes. TC10 mRNAs are highly expressed in three types of mouse muscle tissues: leg skeletal muscle, cardiac muscle, and uterus; they were also present in brain, with higher levels in adults than in newborns. TC10 has also been shown to play a role in regulating the expression of cystic fibrosis transmembrane conductance regulator (CFTR) through interacti
Probab=22.28 E-value=1e+02 Score=18.48 Aligned_cols=22 Identities=23% Similarity=0.225 Sum_probs=19.0
Q ss_pred eecccccCccHHHHHHHHHHHH
Q psy6616 39 HMTCATDTNNIQFVFDAVTDVI 60 (71)
Q Consensus 39 h~T~AtDt~ni~~vf~~V~d~I 60 (71)
..++|.+-++++.+|+.+-+.|
T Consensus 152 ~e~Sa~~~~gi~~~f~~~~~~~ 173 (174)
T cd04135 152 VECSALTQKGLKTVFDEAILAI 173 (174)
T ss_pred EEecCCcCCCHHHHHHHHHHHh
Confidence 4689999999999999887765
No 66
>cd04136 Rap_like Rap-like subfamily. The Rap subfamily consists of the Rap1, Rap2, and RSR1. Rap subfamily proteins perform different cellular functions, depending on the isoform and its subcellular localization. For example, in rat salivary gland, neutrophils, and platelets, Rap1 localizes to secretory granules and is believed to regulate exocytosis or the formation of secretory granules. Rap1 has also been shown to localize in the Golgi of rat fibroblasts, zymogen granules, plasma membrane, and microsomal membrane of the pancreatic acini, as well as in the endocytic compartment of skeletal muscle cells and fibroblasts. Rap1 localizes in the nucleus of human oropharyngeal squamous cell carcinomas (SCCs) and cell lines. Rap1 plays a role in phagocytosis by controlling the binding of adhesion receptors (typically integrins) to their ligands. In yeast, Rap1 has been implicated in multiple functions, including activation and silencing of transcription and maintenance of telomeres.
Probab=22.08 E-value=92 Score=18.31 Aligned_cols=23 Identities=26% Similarity=0.228 Sum_probs=18.8
Q ss_pred EeecccccCccHHHHHHHHHHHH
Q psy6616 38 CHMTCATDTNNIQFVFDAVTDVI 60 (71)
Q Consensus 38 ~h~T~AtDt~ni~~vf~~V~d~I 60 (71)
...++|.+-+++..+|..+.+.+
T Consensus 140 ~~~~Sa~~~~~v~~l~~~l~~~~ 162 (163)
T cd04136 140 FYETSAKSKINVDEVFADLVRQI 162 (163)
T ss_pred EEEecCCCCCCHHHHHHHHHHhc
Confidence 45789999999999998876654
No 67
>PF09670 Cas_Cas02710: CRISPR-associated protein (Cas_Cas02710)
Probab=22.01 E-value=2.5e+02 Score=20.29 Aligned_cols=46 Identities=13% Similarity=0.112 Sum_probs=32.0
Q ss_pred CCCChHHHHHHHHHHHHhhccCCCCCeeEeecccccCccHHHHHHH
Q psy6616 10 GAQEYGEAAAYIQAQFEAKNKSTTKEIYCHMTCATDTNNIQFVFDA 55 (71)
Q Consensus 10 G~~~~~~~~~fi~~kF~~~~~~~~r~iy~h~T~AtDt~ni~~vf~~ 55 (71)
.++|..++.+-+.+.+.+....+..+|++.+|..|=+-.+..++.+
T Consensus 47 d~dD~~~~y~~l~~~l~~~~~~~~~~v~vDiTGGTK~Msaglalaa 92 (379)
T PF09670_consen 47 DPDDPLECYRKLREVLEKLRDFPGHEVAVDITGGTKSMSAGLALAA 92 (379)
T ss_pred CCCCHHHHHHHHHHHHHHHhcCCCCeEEEECCCCHHHHHHHHHHHH
Confidence 4567777777787777777334567899999998866555554443
No 68
>PF11411 DNA_ligase_IV: DNA ligase IV; InterPro: IPR021536 DNA ligase IV along with Xrcc4 functions in DNA non-homologous end joining. This process is required to mend double-strand breaks. Upon ligase binding to an Xrcc4 dimer, the helical tails unwind leading to a flat interaction surface []. ; GO: 0003910 DNA ligase (ATP) activity; PDB: 3II6_Y 2E2W_A 1IK9_C.
Probab=21.73 E-value=20 Score=17.87 Aligned_cols=19 Identities=26% Similarity=0.494 Sum_probs=10.2
Q ss_pred ecccccCccHHHHHHHHHH
Q psy6616 40 MTCATDTNNIQFVFDAVTD 58 (71)
Q Consensus 40 ~T~AtDt~ni~~vf~~V~d 58 (71)
++.=||-+.++.||+.+.+
T Consensus 17 Y~~Dtd~~~Lk~vF~~i~~ 35 (36)
T PF11411_consen 17 YTVDTDEDQLKEVFNRIKK 35 (36)
T ss_dssp SSS---HHHHHHHHHCS--
T ss_pred ccccCCHHHHHHHHHHhcc
Confidence 5666777778888876654
No 69
>cd04137 RheB Rheb (Ras Homolog Enriched in Brain) subfamily. Rheb was initially identified in rat brain, where its expression is elevated by seizures or by long-term potentiation. It is expressed ubiquitously, with elevated levels in muscle and brain. Rheb functions as an important mediator between the tuberous sclerosis complex proteins, TSC1 and TSC2, and the mammalian target of rapamycin (TOR) kinase to stimulate cell growth. TOR kinase regulates cell growth by controlling nutrient availability, growth factors, and the energy status of the cell. TSC1 and TSC2 form a dimeric complex that has tumor suppressor activity, and TSC2 is a GTPase activating protein (GAP) for Rheb. The TSC1/TSC2 complex inhibits the activation of TOR kinase through Rheb. Rheb has also been shown to induce the formation of large cytoplasmic vacuoles in a process that is dependent on the GTPase cycle of Rheb, but independent of the TOR kinase, suggesting Rheb plays a role in endocytic trafficking that le
Probab=21.30 E-value=1.7e+02 Score=17.74 Aligned_cols=31 Identities=13% Similarity=0.123 Sum_probs=25.3
Q ss_pred eeEeecccccCccHHHHHHHHHHHHHHhhhh
Q psy6616 36 IYCHMTCATDTNNIQFVFDAVTDVIIANNLR 66 (71)
Q Consensus 36 iy~h~T~AtDt~ni~~vf~~V~d~Il~~nl~ 66 (71)
..+-.++|.+.+++..+|..+.+.+.+.+..
T Consensus 138 ~~~~~~Sa~~~~gv~~l~~~l~~~~~~~~~~ 168 (180)
T cd04137 138 AAFLESSARENENVEEAFELLIEEIEKVENP 168 (180)
T ss_pred CeEEEEeCCCCCCHHHHHHHHHHHHHHhcCC
Confidence 4456799999999999999999988766543
No 70
>cd01866 Rab2 Rab2 subfamily. Rab2 is localized on cis-Golgi membranes and interacts with Golgi matrix proteins. Rab2 is also implicated in the maturation of vesicular tubular clusters (VTCs), which are microtubule-associated intermediates in transport between the ER and Golgi apparatus. In plants, Rab2 regulates vesicle trafficking between the ER and the Golgi bodies and is important to pollen tube growth. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key featur
Probab=21.10 E-value=1.8e+02 Score=17.52 Aligned_cols=27 Identities=19% Similarity=0.185 Sum_probs=21.8
Q ss_pred eeEeecccccCccHHHHHHHHHHHHHH
Q psy6616 36 IYCHMTCATDTNNIQFVFDAVTDVIIA 62 (71)
Q Consensus 36 iy~h~T~AtDt~ni~~vf~~V~d~Il~ 62 (71)
+..-.+||.+.+|+..+|..+.+.+++
T Consensus 141 ~~~~e~Sa~~~~~i~~~~~~~~~~~~~ 167 (168)
T cd01866 141 LIFMETSAKTASNVEEAFINTAKEIYE 167 (168)
T ss_pred CEEEEEeCCCCCCHHHHHHHHHHHHHh
Confidence 345679999999999999888777654
No 71
>PLN03110 Rab GTPase; Provisional
Probab=21.04 E-value=1.6e+02 Score=18.91 Aligned_cols=27 Identities=19% Similarity=0.199 Sum_probs=23.3
Q ss_pred eeEeecccccCccHHHHHHHHHHHHHH
Q psy6616 36 IYCHMTCATDTNNIQFVFDAVTDVIIA 62 (71)
Q Consensus 36 iy~h~T~AtDt~ni~~vf~~V~d~Il~ 62 (71)
+.+..|+|.+-.++..+|+.+-..|.+
T Consensus 149 ~~~~e~SA~~g~~v~~lf~~l~~~i~~ 175 (216)
T PLN03110 149 LSFLETSALEATNVEKAFQTILLEIYH 175 (216)
T ss_pred CEEEEEeCCCCCCHHHHHHHHHHHHHH
Confidence 557799999999999999999877765
No 72
>COG5036 SPX domain-containing protein involved in vacuolar polyphosphate accumulation [Inorganic ion transport and metabolism]
Probab=20.42 E-value=68 Score=24.46 Aligned_cols=30 Identities=23% Similarity=0.344 Sum_probs=26.7
Q ss_pred EeecccccCccHHHHHHHHHHHHHHhhhhh
Q psy6616 38 CHMTCATDTNNIQFVFDAVTDVIIANNLRG 67 (71)
Q Consensus 38 ~h~T~AtDt~ni~~vf~~V~d~Il~~nl~~ 67 (71)
-|-|+|-|-++++..++.|+..|+.+.|+.
T Consensus 322 e~gt~~~d~e~le~l~~evQ~~iv~~~LqP 351 (509)
T COG5036 322 EGGTTAEDLERLERLFEEVQNFIVKRGLQP 351 (509)
T ss_pred hcCCcHHHHHHHHHHHHHHHHHHHHccCch
Confidence 367899999999999999999999988864
No 73
>PF13232 Complex1_LYR_1: Complex1_LYR-like
Probab=20.05 E-value=1.5e+02 Score=15.33 Aligned_cols=40 Identities=18% Similarity=0.196 Sum_probs=23.4
Q ss_pred ccCCCCCCCCChHHHHHHHHHHHHhhccCCCCCeeEeecccccCccHHHHHHHHHH
Q psy6616 3 YFTELLSGAQEYGEAAAYIQAQFEAKNKSTTKEIYCHMTCATDTNNIQFVFDAVTD 58 (71)
Q Consensus 3 ~Fp~~y~G~~~~~~~~~fi~~kF~~~~~~~~r~iy~h~T~AtDt~ni~~vf~~V~d 58 (71)
.||+ |.. -+.+...|+..|..- +. .||.+.|...+..-++
T Consensus 16 ~~~~-~~~---r~~~~~~ir~~Fr~~-----~~-------~td~~~i~~~l~~~~~ 55 (61)
T PF13232_consen 16 KFPD-YNF---RSYFRRRIRDRFRRN-----KN-------VTDPEKIAKLLKEGRK 55 (61)
T ss_pred hcCC-cch---HHHHHHHHHHHHHHc-----CC-------CCCHHHHHHHHHHHHH
Confidence 4566 433 256788999999852 11 4555566655554443
Done!