Query psy12841
Match_columns 88
No_of_seqs 44 out of 46
Neff 2.7
Searched_HMMs 46136
Date Fri Aug 16 21:10:16 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12841.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12841hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4698|consensus 99.4 1.1E-13 2.5E-18 115.2 4.7 80 3-87 178-258 (475)
2 PF04577 DUF563: Protein of un 94.5 0.097 2.1E-06 35.8 4.7 72 6-84 1-74 (206)
3 cd01893 Miro1 Miro1 subfamily. 61.7 17 0.00036 24.0 3.8 34 14-47 16-59 (166)
4 COG2917 Intracellular septatio 49.8 11 0.00024 29.0 1.6 21 7-35 125-145 (180)
5 PRK01904 hypothetical protein; 47.5 22 0.00048 26.6 2.9 54 25-80 72-134 (219)
6 KOG0293|consensus 47.3 13 0.00028 32.5 1.9 50 32-84 331-383 (519)
7 PRK15382 non-LEE encoded effec 47.2 6 0.00013 32.7 -0.1 10 7-16 299-308 (326)
8 KOG0318|consensus 42.1 14 0.00029 33.0 1.2 38 36-74 82-120 (603)
9 cd04101 RabL4 RabL4 (Rab-like4 41.5 27 0.00058 22.5 2.3 27 32-59 49-75 (164)
10 cd01861 Rab6 Rab6 subfamily. 40.6 55 0.0012 20.8 3.6 26 34-60 48-73 (161)
11 cd04138 H_N_K_Ras_like H-Ras/N 40.1 70 0.0015 20.1 4.0 24 35-59 49-72 (162)
12 cd04144 Ras2 Ras2 subfamily. 39.2 53 0.0011 22.4 3.6 20 34-54 46-65 (190)
13 PTZ00099 rab6; Provisional 39.0 22 0.00048 24.8 1.7 22 34-56 28-49 (176)
14 PF12132 DUF3587: Protein of u 38.4 12 0.00025 28.7 0.3 6 7-12 163-168 (199)
15 PRK15384 type III secretion sy 38.3 10 0.00022 31.4 -0.1 10 7-16 304-313 (336)
16 cd01871 Rac1_like Rac1-like su 38.2 28 0.00061 23.6 2.1 22 34-56 48-69 (174)
17 cd04168 TetM_like Tet(M)-like 38.0 36 0.00079 25.1 2.8 26 33-58 62-87 (237)
18 PRK15383 type III secretion sy 37.4 11 0.00023 31.3 -0.1 10 7-16 307-316 (335)
19 cd01890 LepA LepA subfamily. 36.7 40 0.00088 22.0 2.6 21 33-54 65-85 (179)
20 PF12368 DUF3650: Protein of u 36.2 18 0.00039 20.3 0.8 10 16-26 8-17 (28)
21 cd04150 Arf1_5_like Arf1-Arf5- 36.1 40 0.00086 22.3 2.5 24 33-57 42-65 (159)
22 cd04106 Rab23_lke Rab23-like s 35.7 37 0.00081 21.7 2.3 27 32-59 48-74 (162)
23 PF09829 DUF2057: Uncharacteri 34.9 35 0.00076 24.3 2.3 51 28-79 53-111 (189)
24 PRK04517 hypothetical protein; 33.8 49 0.0011 24.8 3.0 55 24-80 73-136 (216)
25 cd04122 Rab14 Rab14 subfamily. 33.8 41 0.00088 22.0 2.3 23 34-57 50-72 (166)
26 KOG1087|consensus 33.3 15 0.00032 31.4 0.1 14 2-17 18-31 (470)
27 cd04119 RJL RJL (RabJ-Like) su 32.3 47 0.001 21.0 2.3 27 33-60 47-73 (168)
28 cd04169 RF3 RF3 subfamily. Pe 32.3 41 0.00089 25.4 2.3 25 33-57 69-93 (267)
29 cd01863 Rab18 Rab18 subfamily. 32.0 45 0.00097 21.3 2.2 24 34-58 48-71 (161)
30 cd04124 RabL2 RabL2 subfamily. 31.2 47 0.001 21.8 2.2 27 33-60 47-73 (161)
31 PTZ00133 ADP-ribosylation fact 30.4 60 0.0013 22.3 2.8 26 33-59 59-84 (182)
32 cd04109 Rab28 Rab28 subfamily. 29.9 54 0.0012 23.0 2.5 25 34-59 49-73 (215)
33 TIGR00231 small_GTP small GTP- 29.6 51 0.0011 19.8 2.0 25 35-60 50-74 (161)
34 COG3221 PhnD ABC-type phosphat 29.6 26 0.00056 27.7 0.9 31 43-77 122-152 (299)
35 PF09730 BicD: Microtubule-ass 29.2 18 0.0004 32.4 0.0 9 5-13 457-465 (717)
36 cd04132 Rho4_like Rho4-like su 29.0 64 0.0014 21.5 2.6 22 34-56 48-69 (187)
37 PLN00223 ADP-ribosylation fact 28.2 61 0.0013 22.3 2.5 25 34-59 60-84 (181)
38 cd04152 Arl4_Arl7 Arl4/Arl7 su 27.9 71 0.0015 21.7 2.7 26 33-59 50-75 (183)
39 cd04126 Rab20 Rab20 subfamily. 27.6 97 0.0021 22.8 3.6 22 34-56 43-64 (220)
40 cd04127 Rab27A Rab27a subfamil 27.1 65 0.0014 21.2 2.3 26 33-59 61-86 (180)
41 cd01889 SelB_euk SelB subfamil 26.8 52 0.0011 22.5 1.9 23 34-56 67-89 (192)
42 smart00094 TR_FER Transferrin. 26.7 26 0.00057 28.0 0.5 19 59-77 96-114 (332)
43 cd04136 Rap_like Rap-like subf 26.6 65 0.0014 20.5 2.2 22 34-56 48-69 (163)
44 cd04149 Arf6 Arf6 subfamily. 26.6 71 0.0015 21.5 2.5 23 33-56 51-73 (168)
45 smart00177 ARF ARF-like small 26.2 85 0.0018 21.1 2.9 26 33-59 55-80 (175)
46 cd01865 Rab3 Rab3 subfamily. 26.0 60 0.0013 21.2 2.0 26 34-60 49-74 (165)
47 cd01885 EF2 EF2 (for archaea a 25.7 75 0.0016 23.6 2.7 27 34-60 72-98 (222)
48 COG3466 ISA1214 Putative trans 25.4 30 0.00066 22.0 0.5 10 65-74 38-47 (52)
49 cd04108 Rab36_Rab34 Rab34/Rab3 24.8 83 0.0018 21.2 2.6 10 35-44 49-58 (170)
50 cd04151 Arl1 Arl1 subfamily. 24.4 83 0.0018 20.3 2.5 26 33-59 41-66 (158)
51 PLN03118 Rab family protein; P 24.4 80 0.0017 21.9 2.5 25 34-59 61-85 (211)
52 TIGR00503 prfC peptide chain r 24.3 64 0.0014 27.2 2.4 27 33-59 78-104 (527)
53 cd01897 NOG NOG1 is a nucleola 24.3 65 0.0014 20.7 1.9 13 34-46 46-58 (168)
54 cd04110 Rab35 Rab35 subfamily. 23.9 1.5E+02 0.0032 20.5 3.8 25 35-60 55-79 (199)
55 cd04107 Rab32_Rab38 Rab38/Rab3 23.4 94 0.002 21.3 2.7 27 33-60 48-74 (201)
56 cd04157 Arl6 Arl6 subfamily. 23.4 1E+02 0.0022 19.5 2.7 26 33-59 43-68 (162)
57 cd01869 Rab1_Ypt1 Rab1/Ypt1 su 22.1 94 0.002 20.1 2.4 24 34-58 50-73 (166)
58 cd00878 Arf_Arl Arf (ADP-ribos 22.0 1.1E+02 0.0023 19.6 2.6 25 34-59 42-66 (158)
59 cd01888 eIF2_gamma eIF2-gamma 21.8 65 0.0014 22.6 1.7 23 35-57 83-105 (203)
60 cd04112 Rab26 Rab26 subfamily. 21.3 87 0.0019 21.3 2.2 23 34-57 49-71 (191)
61 PF12911 OppC_N: N-terminal TM 21.2 55 0.0012 18.8 1.0 16 47-62 3-18 (56)
62 cd01870 RhoA_like RhoA-like su 21.2 65 0.0014 21.0 1.5 12 33-44 47-58 (175)
63 cd04120 Rab12 Rab12 subfamily. 21.1 95 0.0021 22.3 2.4 24 34-58 48-71 (202)
64 smart00175 RAB Rab subfamily o 20.9 93 0.002 19.7 2.1 24 34-58 48-71 (164)
65 smart00062 PBPb Bacterial peri 20.9 54 0.0012 20.4 1.0 19 58-76 95-113 (219)
66 cd00154 Rab Rab family. Rab G 20.6 98 0.0021 18.9 2.1 26 33-59 47-72 (159)
67 cd04176 Rap2 Rap2 subgroup. T 20.4 88 0.0019 20.1 2.0 22 34-56 48-69 (163)
68 cd04175 Rap1 Rap1 subgroup. T 20.4 96 0.0021 20.0 2.1 22 34-56 48-69 (164)
69 cd04123 Rab21 Rab21 subfamily. 20.4 86 0.0019 19.6 1.9 24 33-57 47-70 (162)
70 PF12974 Phosphonate-bd: ABC t 20.2 40 0.00086 23.9 0.3 21 58-78 94-114 (243)
No 1
>KOG4698|consensus
Probab=99.43 E-value=1.1e-13 Score=115.17 Aligned_cols=80 Identities=23% Similarity=0.339 Sum_probs=72.4
Q ss_pred ccccchhhhhhhhHhHhhhhhcCCCCCCcCCceeEEEeeccc-cCcchHHHHhhhhcCCcccccccCCceeeeccccccc
Q psy12841 3 SAVNMYHHFCDFFNLYASQHVNASHPDVFSTDVHIMIWESYT-YASAFADTFKAFTRHPVWDLKTFTGLTVCFKNLVLPL 81 (88)
Q Consensus 3 a~vNMYHHFCDF~NLY~S~HvN~S~~~~F~~Dv~Iv~Wdt~~-Y~d~F~~tw~aFt~~~~~~L~~~~gKrVCFk~a~f~l 81 (88)
.++||||||||++ +.+-+|.++ ..|++|+++++|++.. |...|+|.-++|+++| +-..+=+++++||++|+.+|
T Consensus 178 ~tgn~yhdf~d~~---ipL~it~~~-~~~n~ev~~li~~~~~ww~~kf~Dvv~~lSn~~-~v~~~~~~~ThcF~~~~vgL 252 (475)
T KOG4698|consen 178 YTGNEYHDFNDGI---IPLFITEAE-LRFNKEVQFLITETHSWWDMKFGDVVRQLSNYP-VVDFDAELRTHCFKEAIVGL 252 (475)
T ss_pred cchhhHHHHHhhh---hhhhcccch-hcccccEEEEEEEcchhhhhhHHHHHHhcCCCc-eEEecCCceEEEeeeeeeee
Confidence 4689999999999 777778776 6699999999999977 7779999999999999 66778899999999999999
Q ss_pred cccccc
Q psy12841 82 LPRMIY 87 (88)
Q Consensus 82 LpRm~~ 87 (88)
++++.|
T Consensus 253 ~~h~~y 258 (475)
T KOG4698|consen 253 VSHFPY 258 (475)
T ss_pred eecccc
Confidence 999986
No 2
>PF04577 DUF563: Protein of unknown function (DUF563); InterPro: IPR007657 This is a family of uncharacterised glycosyltransferases belonging to glycosyltransferase family 61. Sequences are further processed into a mature form.; GO: 0016757 transferase activity, transferring glycosyl groups
Probab=94.47 E-value=0.097 Score=35.78 Aligned_cols=72 Identities=19% Similarity=0.265 Sum_probs=47.5
Q ss_pred cch-hhhhhhhHhHhhhhhcCCCCCCcCCceeEEEeeccccC-cchHHHHhhhhcCCcccccccCCceeeeccccccccc
Q psy12841 6 NMY-HHFCDFFNLYASQHVNASHPDVFSTDVHIMIWESYTYA-SAFADTFKAFTRHPVWDLKTFTGLTVCFKNLVLPLLP 83 (88)
Q Consensus 6 NMY-HHFCDF~NLY~S~HvN~S~~~~F~~Dv~Iv~Wdt~~Y~-d~F~~tw~aFt~~~~~~L~~~~gKrVCFk~a~f~lLp 83 (88)
|.| |-.+|++-++.++...+. .++ ..|++ ...... ....+.|+++.- +.-.+.--.++.+||+++++|..+
T Consensus 1 ~~~gH~l~d~l~~l~~~~~~~~----~~~-~~~l~-~~~~~~~~~~~~~l~~lg~-~~~~i~~~~~~~~~~~~l~~~~~~ 73 (206)
T PF04577_consen 1 NNFGHFLIDFLPRLWYLPQYIP----DSD-IIILV-PDDFDNPPFIREILELLGI-PENRIKIDSDEPVCFERLIVPSPP 73 (206)
T ss_pred CCCcEEHHHHHHHHHHHHHHCC----CCC-eEEEE-cCCccccHHHHHHHHHcCC-CccEEEEcCCCeEEECEEEEeCCC
Confidence 445 888999999988886666 333 23332 222222 345689998877 555553335599999999988765
Q ss_pred c
Q psy12841 84 R 84 (88)
Q Consensus 84 R 84 (88)
.
T Consensus 74 ~ 74 (206)
T PF04577_consen 74 Y 74 (206)
T ss_pred c
Confidence 5
No 3
>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=61.71 E-value=17 Score=24.02 Aligned_cols=34 Identities=15% Similarity=0.146 Sum_probs=21.0
Q ss_pred hhHhHhhhhhcCCCCC----------CcCCceeEEEeeccccCc
Q psy12841 14 FFNLYASQHVNASHPD----------VFSTDVHIMIWESYTYAS 47 (88)
Q Consensus 14 F~NLY~S~HvN~S~~~----------~F~~Dv~Iv~Wdt~~Y~d 47 (88)
++|+++..+..+..|. ..+.++++.+|||.+...
T Consensus 16 l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Dt~G~~~ 59 (166)
T cd01893 16 LIMSLVSEEFPENVPRVLPEITIPADVTPERVPTTIVDTSSRPQ 59 (166)
T ss_pred HHHHHHhCcCCccCCCcccceEeeeeecCCeEEEEEEeCCCchh
Confidence 5666666665444332 233567888999966544
No 4
>COG2917 Intracellular septation protein A [Cell division and chromosome partitioning]
Probab=49.82 E-value=11 Score=29.00 Aligned_cols=21 Identities=38% Similarity=0.823 Sum_probs=17.5
Q ss_pred chhhhhhhhHhHhhhhhcCCCCCCcCCce
Q psy12841 7 MYHHFCDFFNLYASQHVNASHPDVFSTDV 35 (88)
Q Consensus 7 MYHHFCDF~NLY~S~HvN~S~~~~F~~Dv 35 (88)
+|-=||-.+|+|++.| ||+|+
T Consensus 125 ~FFlf~ai~N~yV~~~--------fs~d~ 145 (180)
T COG2917 125 LFFLFCAIANEYVARN--------FSTDT 145 (180)
T ss_pred HHHHHHHHHHHHHHHh--------CCCCe
Confidence 3456899999999998 88885
No 5
>PRK01904 hypothetical protein; Provisional
Probab=47.49 E-value=22 Score=26.63 Aligned_cols=54 Identities=20% Similarity=0.326 Sum_probs=40.0
Q ss_pred CCCCCCcCCceeEEEeecc---------ccCcchHHHHhhhhcCCcccccccCCceeeecccccc
Q psy12841 25 ASHPDVFSTDVHIMIWESY---------TYASAFADTFKAFTRHPVWDLKTFTGLTVCFKNLVLP 80 (88)
Q Consensus 25 ~S~~~~F~~Dv~Iv~Wdt~---------~Y~d~F~~tw~aFt~~~~~~L~~~~gKrVCFk~a~f~ 80 (88)
|+....|..|.-|+-.|+. .+.+ ..-=++|.+.|.+.|++=+||.|-++.-.++
T Consensus 72 ~~~~~~~~S~p~IvtF~a~~~~l~l~~P~~~~--~~~a~~F~~~P~~~L~d~~g~~V~~~qd~L~ 134 (219)
T PRK01904 72 GSDRSLFESDPIIVTFQGTTEDIVISAPKLTN--ERDIDKFKKSPNITVKTASGKEISTKQDYLK 134 (219)
T ss_pred CCCccEEeCCCEEEEEecCCeEEEEEcCCCCC--HHHHHHHhhCCcEEEEeCCCCEEEEEEEeec
Confidence 4445568999999988872 2333 2333599999999999999999998865543
No 6
>KOG0293|consensus
Probab=47.26 E-value=13 Score=32.48 Aligned_cols=50 Identities=24% Similarity=0.349 Sum_probs=35.4
Q ss_pred CCceeEEEeeccccCcchHHHHhhhhcCCccccc-ccCCceee--ecccccccccc
Q psy12841 32 STDVHIMIWESYTYASAFADTFKAFTRHPVWDLK-TFTGLTVC--FKNLVLPLLPR 84 (88)
Q Consensus 32 ~~Dv~Iv~Wdt~~Y~d~F~~tw~aFt~~~~~~L~-~~~gKrVC--Fk~a~f~lLpR 84 (88)
++|-+|++||+-+-. -..|+--..--+.+|+ ++|||.|= +.+-...++||
T Consensus 331 s~dr~i~~wdlDgn~---~~~W~gvr~~~v~dlait~Dgk~vl~v~~d~~i~l~~~ 383 (519)
T KOG0293|consen 331 SPDRTIIMWDLDGNI---LGNWEGVRDPKVHDLAITYDGKYVLLVTVDKKIRLYNR 383 (519)
T ss_pred CCCCcEEEecCCcch---hhcccccccceeEEEEEcCCCcEEEEEecccceeeech
Confidence 478999999995543 5678877776788886 99999863 24444444444
No 7
>PRK15382 non-LEE encoded effector protein NleB; Provisional
Probab=47.16 E-value=6 Score=32.65 Aligned_cols=10 Identities=60% Similarity=1.494 Sum_probs=8.5
Q ss_pred chhhhhhhhH
Q psy12841 7 MYHHFCDFFN 16 (88)
Q Consensus 7 MYHHFCDF~N 16 (88)
-|-|||||+-
T Consensus 299 dYn~FCdFIE 308 (326)
T PRK15382 299 NYNHFCDFIE 308 (326)
T ss_pred chhhhcccee
Confidence 4889999985
No 8
>KOG0318|consensus
Probab=42.08 E-value=14 Score=32.98 Aligned_cols=38 Identities=16% Similarity=0.476 Sum_probs=30.0
Q ss_pred eEEEeeccccCcchHHHHhhhhcCCccccc-ccCCceeee
Q psy12841 36 HIMIWESYTYASAFADTFKAFTRHPVWDLK-TFTGLTVCF 74 (88)
Q Consensus 36 ~Iv~Wdt~~Y~d~F~~tw~aFt~~~~~~L~-~~~gKrVCF 74 (88)
+|.+|||..=.-.-+-.+++|. -|+-+|. +++|||.|-
T Consensus 82 ~vRIWdtt~~~hiLKnef~v~a-G~I~Di~Wd~ds~RI~a 120 (603)
T KOG0318|consen 82 KVRIWDTTQKEHILKNEFQVLA-GPIKDISWDFDSKRIAA 120 (603)
T ss_pred cEEEEeccCcceeeeeeeeecc-cccccceeCCCCcEEEE
Confidence 5888999665557777788886 5788886 999999984
No 9
>cd04101 RabL4 RabL4 (Rab-like4) subfamily. RabL4s are novel proteins that have high sequence similarity with Rab family members, but display features that are distinct from Rabs, and have been termed Rab-like. As in other Rab-like proteins, RabL4 lacks a prenylation site at the C-terminus. The specific function of RabL4 remains unknown.
Probab=41.48 E-value=27 Score=22.46 Aligned_cols=27 Identities=15% Similarity=0.343 Sum_probs=17.9
Q ss_pred CCceeEEEeeccccCcchHHHHhhhhcC
Q psy12841 32 STDVHIMIWESYTYASAFADTFKAFTRH 59 (88)
Q Consensus 32 ~~Dv~Iv~Wdt~~Y~d~F~~tw~aFt~~ 59 (88)
+..+++.+|||.+- ..|..+++.+-+.
T Consensus 49 ~~~~~l~i~Dt~G~-~~~~~~~~~~~~~ 75 (164)
T cd04101 49 DNTVELFIFDSAGQ-ELYSDMVSNYWES 75 (164)
T ss_pred CCEEEEEEEECCCH-HHHHHHHHHHhCC
Confidence 34588999999653 4556666666543
No 10
>cd01861 Rab6 Rab6 subfamily. Rab6 is involved in microtubule-dependent transport pathways through the Golgi and from endosomes to the Golgi. Rab6A of mammals is implicated in retrograde transport through the Golgi stack, and is also required for a slow, COPI-independent, retrograde transport pathway from the Golgi to the endoplasmic reticulum (ER). This pathway may allow Golgi residents to be recycled through the ER for scrutiny by ER quality-control systems. Yeast Ypt6p, the homolog of the mammalian Rab6 GTPase, is not essential for cell viability. Ypt6p acts in endosome-to-Golgi, in intra-Golgi retrograde transport, and possibly also in Golgi-to-ER trafficking. 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
Probab=40.58 E-value=55 Score=20.84 Aligned_cols=26 Identities=15% Similarity=0.516 Sum_probs=17.0
Q ss_pred ceeEEEeeccccCcchHHHHhhhhcCC
Q psy12841 34 DVHIMIWESYTYASAFADTFKAFTRHP 60 (88)
Q Consensus 34 Dv~Iv~Wdt~~Y~d~F~~tw~aFt~~~ 60 (88)
++++.+|||.+ ...|...|+.+-++-
T Consensus 48 ~~~l~~~D~~G-~~~~~~~~~~~~~~~ 73 (161)
T cd01861 48 TVRLQLWDTAG-QERFRSLIPSYIRDS 73 (161)
T ss_pred EEEEEEEECCC-cHHHHHHHHHHhccC
Confidence 46788999965 234566677665443
No 11
>cd04138 H_N_K_Ras_like H-Ras/N-Ras/K-Ras subfamily. H-Ras, N-Ras, and K-Ras4A/4B are the prototypical members of the Ras family. These isoforms generate distinct signal outputs despite interacting with a common set of activators and effectors, and are strongly associated with oncogenic progression in tumor initiation. Mutated versions of Ras that are insensitive to GAP stimulation (and are therefore constitutively active) are found in a significant fraction of human cancers. Many Ras guanine nucleotide exchange factors (GEFs) have been identified. They are sequestered in the cytosol until activation by growth factors triggers recruitment to the plasma membrane or Golgi, where the GEF colocalizes with Ras. Active (GTP-bound) Ras interacts with several effector proteins that stimulate a variety of diverse cytoplasmic signaling activities. Some are known to positively mediate the oncogenic properties of Ras, including Raf, phosphatidylinositol 3-kinase (PI3K), RalGEFs, and Tiam1.
Probab=40.15 E-value=70 Score=20.06 Aligned_cols=24 Identities=8% Similarity=0.167 Sum_probs=14.2
Q ss_pred eeEEEeeccccCcchHHHHhhhhcC
Q psy12841 35 VHIMIWESYTYASAFADTFKAFTRH 59 (88)
Q Consensus 35 v~Iv~Wdt~~Y~d~F~~tw~aFt~~ 59 (88)
+.+-+|||.+= +-|+..|..+-+.
T Consensus 49 ~~~~i~Dt~G~-~~~~~l~~~~~~~ 72 (162)
T cd04138 49 CLLDILDTAGQ-EEYSAMRDQYMRT 72 (162)
T ss_pred EEEEEEECCCC-cchHHHHHHHHhc
Confidence 34567999652 3466666655443
No 12
>cd04144 Ras2 Ras2 subfamily. The Ras2 subfamily, found exclusively in fungi, was first identified in Ustilago maydis. In U. maydis, Ras2 is regulated by Sql2, a protein that is homologous to GEFs (guanine nucleotide exchange factors) of the CDC25 family. Ras2 has been shown to induce filamentous growth, but the signaling cascade through which Ras2 and Sql2 regulate cell morphology is not known. 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.
Probab=39.18 E-value=53 Score=22.39 Aligned_cols=20 Identities=0% Similarity=0.036 Sum_probs=11.6
Q ss_pred ceeEEEeeccccCcchHHHHh
Q psy12841 34 DVHIMIWESYTYASAFADTFK 54 (88)
Q Consensus 34 Dv~Iv~Wdt~~Y~d~F~~tw~ 54 (88)
.+.+.+|||.|= +.|...|+
T Consensus 46 ~~~l~i~Dt~G~-~~~~~~~~ 65 (190)
T cd04144 46 PCMLEVLDTAGQ-EEYTALRD 65 (190)
T ss_pred EEEEEEEECCCc-hhhHHHHH
Confidence 456788999552 23444444
No 13
>PTZ00099 rab6; Provisional
Probab=39.02 E-value=22 Score=24.80 Aligned_cols=22 Identities=14% Similarity=0.499 Sum_probs=13.6
Q ss_pred ceeEEEeeccccCcchHHHHhhh
Q psy12841 34 DVHIMIWESYTYASAFADTFKAF 56 (88)
Q Consensus 34 Dv~Iv~Wdt~~Y~d~F~~tw~aF 56 (88)
+++|.+|||.|-. .|...|..|
T Consensus 28 ~v~l~iwDt~G~e-~~~~~~~~~ 49 (176)
T PTZ00099 28 PVRLQLWDTAGQE-RFRSLIPSY 49 (176)
T ss_pred EEEEEEEECCChH-HhhhccHHH
Confidence 5888899996532 344444444
No 14
>PF12132 DUF3587: Protein of unknown function (DUF3587); InterPro: IPR021982 This entry is represented by Hyposoter fugitivus ichnovirus, Gp7; it is a family of uncharacterised viral proteins.
Probab=38.45 E-value=12 Score=28.74 Aligned_cols=6 Identities=50% Similarity=1.796 Sum_probs=5.1
Q ss_pred chhhhh
Q psy12841 7 MYHHFC 12 (88)
Q Consensus 7 MYHHFC 12 (88)
=+||||
T Consensus 163 HfHHyC 168 (199)
T PF12132_consen 163 HFHHYC 168 (199)
T ss_pred CcChhh
Confidence 489999
No 15
>PRK15384 type III secretion system protein; Provisional
Probab=38.26 E-value=10 Score=31.43 Aligned_cols=10 Identities=50% Similarity=1.261 Sum_probs=8.4
Q ss_pred chhhhhhhhH
Q psy12841 7 MYHHFCDFFN 16 (88)
Q Consensus 7 MYHHFCDF~N 16 (88)
=|-|||||+-
T Consensus 304 dYn~FCdFIE 313 (336)
T PRK15384 304 DYNSFCDFIE 313 (336)
T ss_pred chhhhcccee
Confidence 4889999985
No 16
>cd01871 Rac1_like Rac1-like subfamily. The Rac1-like subfamily consists of Rac1, Rac2, and Rac3 proteins, plus the splice variant Rac1b that contains a 19-residue insertion near switch II relative to Rac1. While Rac1 is ubiquitously expressed, Rac2 and Rac3 are largely restricted to hematopoietic and neural tissues respectively. Rac1 stimulates the formation of actin lamellipodia and membrane ruffles. It also plays a role in cell-matrix adhesion and cell anoikis. In intestinal epithelial cells, Rac1 is an important regulator of migration and mediates apoptosis. Rac1 is also essential for RhoA-regulated actin stress fiber and focal adhesion complex formation. In leukocytes, Rac1 and Rac2 have distinct roles in regulating cell morphology, migration, and invasion, but are not essential for macrophage migration or chemotaxis. Rac3 has biochemical properties that are closely related to Rac1, such as effector interaction, nucleotide binding, and hydrolysis; Rac2 has a slower nucleoti
Probab=38.17 E-value=28 Score=23.64 Aligned_cols=22 Identities=9% Similarity=0.247 Sum_probs=12.5
Q ss_pred ceeEEEeeccccCcchHHHHhhh
Q psy12841 34 DVHIMIWESYTYASAFADTFKAF 56 (88)
Q Consensus 34 Dv~Iv~Wdt~~Y~d~F~~tw~aF 56 (88)
++++.+|||.+ .+.|...|+.+
T Consensus 48 ~~~l~i~Dt~G-~~~~~~~~~~~ 69 (174)
T cd01871 48 PVNLGLWDTAG-QEDYDRLRPLS 69 (174)
T ss_pred EEEEEEEECCC-chhhhhhhhhh
Confidence 46788899954 13344444443
No 17
>cd04168 TetM_like Tet(M)-like subfamily. Tet(M), Tet(O), Tet(W), and OtrA are tetracycline resistance genes found in Gram-positive and Gram-negative bacteria. Tetracyclines inhibit protein synthesis by preventing aminoacyl-tRNA from binding to the ribosomal acceptor site. This subfamily contains tetracycline resistance proteins that function through ribosomal protection and are typically found on mobile genetic elements, such as transposons or plasmids, and are often conjugative. Ribosomal protection proteins are homologous to the elongation factors EF-Tu and EF-G. EF-G and Tet(M) compete for binding on the ribosomes. Tet(M) has a higher affinity than EF-G, suggesting these two proteins may have overlapping binding sites and that Tet(M) must be released before EF-G can bind. Tet(M) and Tet(O) have been shown to have ribosome-dependent GTPase activity. These proteins are part of the GTP translation factor family, which includes EF-G, EF-Tu, EF2, LepA, and SelB.
Probab=37.96 E-value=36 Score=25.14 Aligned_cols=26 Identities=8% Similarity=0.129 Sum_probs=20.8
Q ss_pred CceeEEEeeccccCcchHHHHhhhhc
Q psy12841 33 TDVHIMIWESYTYASAFADTFKAFTR 58 (88)
Q Consensus 33 ~Dv~Iv~Wdt~~Y~d~F~~tw~aFt~ 58 (88)
.+.+|.+|||-|+.+..+++.+++..
T Consensus 62 ~~~~i~liDTPG~~~f~~~~~~~l~~ 87 (237)
T cd04168 62 EDTKVNLIDTPGHMDFIAEVERSLSV 87 (237)
T ss_pred CCEEEEEEeCCCccchHHHHHHHHHH
Confidence 47789999999998877777777643
No 18
>PRK15383 type III secretion system protein; Provisional
Probab=37.39 E-value=11 Score=31.31 Aligned_cols=10 Identities=50% Similarity=1.215 Sum_probs=8.4
Q ss_pred chhhhhhhhH
Q psy12841 7 MYHHFCDFFN 16 (88)
Q Consensus 7 MYHHFCDF~N 16 (88)
=|-|||||+-
T Consensus 307 dYn~FCdFIE 316 (335)
T PRK15383 307 DYDAFCDFIE 316 (335)
T ss_pred chhhhcccee
Confidence 4889999985
No 19
>cd01890 LepA LepA subfamily. LepA belongs to the GTPase family of and exhibits significant homology to the translation factors EF-G and EF-Tu, indicating its possible involvement in translation and association with the ribosome. LepA is ubiquitous in bacteria and eukaryota (e.g. yeast GUF1p), but is missing from archaea. This pattern of phyletic distribution suggests that LepA evolved through a duplication of the EF-G gene in bacteria, followed by early transfer into the eukaryotic lineage, most likely from the promitochondrial endosymbiont. Yeast GUF1p is not essential and mutant cells did not reveal any marked phenotype.
Probab=36.67 E-value=40 Score=22.02 Aligned_cols=21 Identities=5% Similarity=0.083 Sum_probs=14.1
Q ss_pred CceeEEEeeccccCcchHHHHh
Q psy12841 33 TDVHIMIWESYTYASAFADTFK 54 (88)
Q Consensus 33 ~Dv~Iv~Wdt~~Y~d~F~~tw~ 54 (88)
.+++|.+|||-|..+ |...|+
T Consensus 65 ~~~~~~l~Dt~G~~~-~~~~~~ 85 (179)
T cd01890 65 QEYLLNLIDTPGHVD-FSYEVS 85 (179)
T ss_pred CcEEEEEEECCCChh-hHHHHH
Confidence 467888999976654 444444
No 20
>PF12368 DUF3650: Protein of unknown function (DUF3650) ; InterPro: IPR022111 This domain family is found in bacteria, and is approximately 30 amino acids in length. The family is found in association with PF00581 from PFAM. There is a single completely conserved residue N that may be functionally important.
Probab=36.25 E-value=18 Score=20.35 Aligned_cols=10 Identities=40% Similarity=0.624 Sum_probs=8.4
Q ss_pred HhHhhhhhcCC
Q psy12841 16 NLYASQHVNAS 26 (88)
Q Consensus 16 NLY~S~HvN~S 26 (88)
|||+..| |-|
T Consensus 8 NrYV~eh-~ls 17 (28)
T PF12368_consen 8 NRYVKEH-GLS 17 (28)
T ss_pred hhhHHhc-CCC
Confidence 8999999 665
No 21
>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=36.07 E-value=40 Score=22.35 Aligned_cols=24 Identities=4% Similarity=0.333 Sum_probs=16.7
Q ss_pred CceeEEEeeccccCcchHHHHhhhh
Q psy12841 33 TDVHIMIWESYTYASAFADTFKAFT 57 (88)
Q Consensus 33 ~Dv~Iv~Wdt~~Y~d~F~~tw~aFt 57 (88)
.++++.+|||.+-. .|...|+.+-
T Consensus 42 ~~~~~~l~D~~G~~-~~~~~~~~~~ 65 (159)
T cd04150 42 KNISFTVWDVGGQD-KIRPLWRHYF 65 (159)
T ss_pred CCEEEEEEECCCCH-hHHHHHHHHh
Confidence 46889999996643 4666777653
No 22
>cd04106 Rab23_lke Rab23-like subfamily. Rab23 is a member of the Rab family of small GTPases. In mouse, Rab23 has been shown to function as a negative regulator in the sonic hedgehog (Shh) signalling pathway. Rab23 mediates the activity of Gli2 and Gli3, transcription factors that regulate Shh signaling in the spinal cord, primarily by preventing Gli2 activation in the absence of Shh ligand. Rab23 also regulates a step in the cytoplasmic signal transduction pathway that mediates the effect of Smoothened (one of two integral membrane proteins that are essential components of the Shh signaling pathway in vertebrates). In humans, Rab23 is expressed in the retina. Mice contain an isoform that shares 93% sequence identity with the human Rab23 and an alternative splicing isoform that is specific to the brain. This isoform causes the murine open brain phenotype, indicating it may have a role in the development of the central nervous system. GTPase activating proteins (GAPs) interact with G
Probab=35.69 E-value=37 Score=21.65 Aligned_cols=27 Identities=30% Similarity=0.597 Sum_probs=17.5
Q ss_pred CCceeEEEeeccccCcchHHHHhhhhcC
Q psy12841 32 STDVHIMIWESYTYASAFADTFKAFTRH 59 (88)
Q Consensus 32 ~~Dv~Iv~Wdt~~Y~d~F~~tw~aFt~~ 59 (88)
+..+.+.+|||.+- +.|...|+.+-+.
T Consensus 48 ~~~~~~~i~D~~G~-~~~~~~~~~~~~~ 74 (162)
T cd04106 48 DEDVRLMLWDTAGQ-EEFDAITKAYYRG 74 (162)
T ss_pred CCEEEEEEeeCCch-HHHHHhHHHHhcC
Confidence 34578899999663 3466666665443
No 23
>PF09829 DUF2057: Uncharacterized protein conserved in bacteria (DUF2057); InterPro: IPR018635 The proteins in this entry are functionally uncharacterised.
Probab=34.88 E-value=35 Score=24.34 Aligned_cols=51 Identities=22% Similarity=0.327 Sum_probs=39.8
Q ss_pred CCCcCCceeEEEeeccccCc--------chHHHHhhhhcCCcccccccCCceeeeccccc
Q psy12841 28 PDVFSTDVHIMIWESYTYAS--------AFADTFKAFTRHPVWDLKTFTGLTVCFKNLVL 79 (88)
Q Consensus 28 ~~~F~~Dv~Iv~Wdt~~Y~d--------~F~~tw~aFt~~~~~~L~~~~gKrVCFk~a~f 79 (88)
...|..+.-|+-.|... .+ .=...-++|.+.|.+.|.|=.|+.|=++-..+
T Consensus 53 ~~~~~S~p~i~~f~~~~-~~~~l~~p~~~~~~~a~~F~~~P~~~l~d~~g~~i~~~~~~L 111 (189)
T PF09829_consen 53 HEKVKSDPYIVTFDASD-QDLTLSLPKIRSEQQAKAFAKNPQFTLTDSNGNPIPFKQDKL 111 (189)
T ss_pred eeEEEeCCEEEEEEcCC-cEEEEEcCCCCCHHHHHHHHhCCcEEEEeCCCCEEEEEeeee
Confidence 35588888998888844 32 11456677999999999999999999987665
No 24
>PRK04517 hypothetical protein; Provisional
Probab=33.82 E-value=49 Score=24.79 Aligned_cols=55 Identities=18% Similarity=0.236 Sum_probs=40.6
Q ss_pred cCCCCCCcCCceeEEEeecc---------ccCcchHHHHhhhhcCCcccccccCCceeeecccccc
Q psy12841 24 NASHPDVFSTDVHIMIWESY---------TYASAFADTFKAFTRHPVWDLKTFTGLTVCFKNLVLP 80 (88)
Q Consensus 24 N~S~~~~F~~Dv~Iv~Wdt~---------~Y~d~F~~tw~aFt~~~~~~L~~~~gKrVCFk~a~f~ 80 (88)
.|+....|..|..|+-.|+. .+.+ ..-=++|.+.|.+.|.|=.||.|=++.-+++
T Consensus 73 ~~~~~~~~~S~p~IvtF~a~~~~~~l~~P~~~~--~~~a~~f~~~p~~~L~d~~g~~I~~~qd~L~ 136 (216)
T PRK04517 73 QGNDRIIVESDVIIATFDAANTELTFDMPKYRD--ARQAEKAIKTMQWQLVDEQGKAVEVRQDKLI 136 (216)
T ss_pred cCCCceEEECCCEEEEEecCCcEEEEECCCCCC--HHHHHHHHhCCcEEEEcCCCCEEEEEEEEec
Confidence 34444669999999988872 2322 2344778899999999999999999876654
No 25
>cd04122 Rab14 Rab14 subfamily. Rab14 GTPases are localized to biosynthetic compartments, including the rough ER, the Golgi complex, and the trans-Golgi network, and to endosomal compartments, including early endosomal vacuoles and associated vesicles. Rab14 is believed to function in both the biosynthetic and recycling pathways between the Golgi and endosomal compartments. Rab14 has also been identified on GLUT4 vesicles, and has been suggested to help regulate GLUT4 translocation. In addition, Rab14 is believed to play a role in the regulation of 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 GT
Probab=33.75 E-value=41 Score=21.97 Aligned_cols=23 Identities=13% Similarity=0.514 Sum_probs=14.5
Q ss_pred ceeEEEeeccccCcchHHHHhhhh
Q psy12841 34 DVHIMIWESYTYASAFADTFKAFT 57 (88)
Q Consensus 34 Dv~Iv~Wdt~~Y~d~F~~tw~aFt 57 (88)
++++.+|||.+ .+.|...|+.+-
T Consensus 50 ~~~l~i~Dt~G-~~~~~~~~~~~~ 72 (166)
T cd04122 50 KIKLQIWDTAG-QERFRAVTRSYY 72 (166)
T ss_pred EEEEEEEECCC-cHHHHHHHHHHh
Confidence 56788999955 234555555543
No 26
>KOG1087|consensus
Probab=33.35 E-value=15 Score=31.38 Aligned_cols=14 Identities=36% Similarity=0.641 Sum_probs=9.8
Q ss_pred cccccchhhhhhhhHh
Q psy12841 2 VSAVNMYHHFCDFFNL 17 (88)
Q Consensus 2 da~vNMYHHFCDF~NL 17 (88)
|+|+|| ++||.+|.
T Consensus 18 DWa~Nl--eIcD~IN~ 31 (470)
T KOG1087|consen 18 DWALNL--EICDLINS 31 (470)
T ss_pred cHHHHH--HHHHHHhc
Confidence 566776 77887773
No 27
>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=32.29 E-value=47 Score=20.97 Aligned_cols=27 Identities=7% Similarity=0.255 Sum_probs=18.1
Q ss_pred CceeEEEeeccccCcchHHHHhhhhcCC
Q psy12841 33 TDVHIMIWESYTYASAFADTFKAFTRHP 60 (88)
Q Consensus 33 ~Dv~Iv~Wdt~~Y~d~F~~tw~aFt~~~ 60 (88)
.++++.+|||.+.. .|...++.+-+..
T Consensus 47 ~~~~l~i~Dt~G~~-~~~~~~~~~~~~~ 73 (168)
T cd04119 47 KEVRVNFFDLSGHP-EYLEVRNEFYKDT 73 (168)
T ss_pred eEEEEEEEECCccH-HHHHHHHHHhccC
Confidence 46788899996653 4666777665443
No 28
>cd04169 RF3 RF3 subfamily. Peptide chain release factor 3 (RF3) is a protein involved in the termination step of translation in bacteria. Termination occurs when class I release factors (RF1 or RF2) recognize the stop codon at the A-site of the ribosome and activate the release of the nascent polypeptide. The class II release factor RF3 then initiates the release of the class I RF from the ribosome. RF3 binds to the RF/ribosome complex in the inactive (GDP-bound) state. GDP/GTP exchange occurs, followed by the release of the class I RF. Subsequent hydrolysis of GTP to GDP triggers the release of RF3 from the ribosome. RF3 also enhances the efficiency of class I RFs at less preferred stop codons and at stop codons in weak contexts.
Probab=32.29 E-value=41 Score=25.44 Aligned_cols=25 Identities=20% Similarity=0.264 Sum_probs=20.5
Q ss_pred CceeEEEeeccccCcchHHHHhhhh
Q psy12841 33 TDVHIMIWESYTYASAFADTFKAFT 57 (88)
Q Consensus 33 ~Dv~Iv~Wdt~~Y~d~F~~tw~aFt 57 (88)
.+..|.+|||.|+.+.-+++|+++.
T Consensus 69 ~~~~i~liDTPG~~df~~~~~~~l~ 93 (267)
T cd04169 69 RDCVINLLDTPGHEDFSEDTYRTLT 93 (267)
T ss_pred CCEEEEEEECCCchHHHHHHHHHHH
Confidence 4788999999998887778888864
No 29
>cd01863 Rab18 Rab18 subfamily. Mammalian Rab18 is implicated in endocytic transport and is expressed most highly in polarized epithelial cells. However, trypanosomal Rab, TbRAB18, is upregulated in the BSF (Blood Stream Form) stage and localized predominantly to elements of the Golgi complex. In human and mouse cells, Rab18 has been identified in lipid droplets, organelles that store neutral lipids. 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 mos
Probab=32.03 E-value=45 Score=21.34 Aligned_cols=24 Identities=21% Similarity=0.495 Sum_probs=15.6
Q ss_pred ceeEEEeeccccCcchHHHHhhhhc
Q psy12841 34 DVHIMIWESYTYASAFADTFKAFTR 58 (88)
Q Consensus 34 Dv~Iv~Wdt~~Y~d~F~~tw~aFt~ 58 (88)
.+++.+|||.+- +.|...++++-+
T Consensus 48 ~~~~~l~D~~g~-~~~~~~~~~~~~ 71 (161)
T cd01863 48 KVKLAIWDTAGQ-ERFRTLTSSYYR 71 (161)
T ss_pred EEEEEEEECCCc-hhhhhhhHHHhC
Confidence 478899999663 345555665543
No 30
>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=31.25 E-value=47 Score=21.81 Aligned_cols=27 Identities=7% Similarity=0.333 Sum_probs=17.6
Q ss_pred CceeEEEeeccccCcchHHHHhhhhcCC
Q psy12841 33 TDVHIMIWESYTYASAFADTFKAFTRHP 60 (88)
Q Consensus 33 ~Dv~Iv~Wdt~~Y~d~F~~tw~aFt~~~ 60 (88)
..++|-+|||.+- +.|...|+.+-++-
T Consensus 47 ~~~~~~i~Dt~G~-~~~~~~~~~~~~~~ 73 (161)
T cd04124 47 KTILVDFWDTAGQ-ERFQTMHASYYHKA 73 (161)
T ss_pred EEEEEEEEeCCCc-hhhhhhhHHHhCCC
Confidence 3567888999664 35666777655443
No 31
>PTZ00133 ADP-ribosylation factor; Provisional
Probab=30.43 E-value=60 Score=22.25 Aligned_cols=26 Identities=4% Similarity=0.355 Sum_probs=18.2
Q ss_pred CceeEEEeeccccCcchHHHHhhhhcC
Q psy12841 33 TDVHIMIWESYTYASAFADTFKAFTRH 59 (88)
Q Consensus 33 ~Dv~Iv~Wdt~~Y~d~F~~tw~aFt~~ 59 (88)
.++.+.+|||.+- +.|...|+.+-+.
T Consensus 59 ~~~~~~l~D~~G~-~~~~~~~~~~~~~ 84 (182)
T PTZ00133 59 KNLKFTMWDVGGQ-DKLRPLWRHYYQN 84 (182)
T ss_pred CCEEEEEEECCCC-HhHHHHHHHHhcC
Confidence 4688999999663 3567777776443
No 32
>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=29.90 E-value=54 Score=23.03 Aligned_cols=25 Identities=12% Similarity=0.248 Sum_probs=17.5
Q ss_pred ceeEEEeeccccCcchHHHHhhhhcC
Q psy12841 34 DVHIMIWESYTYASAFADTFKAFTRH 59 (88)
Q Consensus 34 Dv~Iv~Wdt~~Y~d~F~~tw~aFt~~ 59 (88)
.+.+.+|||.+- +.|...|+.|-+.
T Consensus 49 ~~~~~i~Dt~G~-~~~~~l~~~~~~~ 73 (215)
T cd04109 49 NVTLQVWDIGGQ-SIGGKMLDKYIYG 73 (215)
T ss_pred EEEEEEEECCCc-HHHHHHHHHHhhc
Confidence 577889999663 4567777777443
No 33
>TIGR00231 small_GTP small GTP-binding protein domain. This model recognizes a large number of small GTP-binding proteins and related domains in larger proteins. Note that the alpha chains of heterotrimeric G proteins are larger proteins in which the NKXD motif is separated from the GxxxxGK[ST] motif (P-loop) by a long insert and are not easily detected by this model.
Probab=29.62 E-value=51 Score=19.82 Aligned_cols=25 Identities=4% Similarity=0.092 Sum_probs=16.1
Q ss_pred eeEEEeeccccCcchHHHHhhhhcCC
Q psy12841 35 VHIMIWESYTYASAFADTFKAFTRHP 60 (88)
Q Consensus 35 v~Iv~Wdt~~Y~d~F~~tw~aFt~~~ 60 (88)
.++.+|||.+. ..|...|+.+.+.-
T Consensus 50 ~~~~~~D~~G~-~~~~~~~~~~~~~~ 74 (161)
T TIGR00231 50 YKFNLLDTAGQ-EDYRAIRRLYYRAV 74 (161)
T ss_pred EEEEEEECCCc-ccchHHHHHHHhhh
Confidence 67889999773 34555666555443
No 34
>COG3221 PhnD ABC-type phosphate/phosphonate transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=29.62 E-value=26 Score=27.68 Aligned_cols=31 Identities=19% Similarity=0.288 Sum_probs=23.1
Q ss_pred cccCcchHHHHhhhhcCCcccccccCCceeeeccc
Q psy12841 43 YTYASAFADTFKAFTRHPVWDLKTFTGLTVCFKNL 77 (88)
Q Consensus 43 ~~Y~d~F~~tw~aFt~~~~~~L~~~~gKrVCFk~a 77 (88)
.+|.+.|- |=.+.|+-.|+|.+|||++|-+.
T Consensus 122 ~~Y~S~~i----~~~ds~i~sl~dlkgk~~af~d~ 152 (299)
T COG3221 122 PGYYSVII----VRADSPIKSLEDLKGKRFAFGDP 152 (299)
T ss_pred cceeEEEE----EeCCCCcchHHHhcCCeEeccCC
Confidence 34555442 34678899999999999999764
No 35
>PF09730 BicD: Microtubule-associated protein Bicaudal-D; InterPro: IPR018477 BicD proteins consist of three coiled-coiled domains and are involved in dynein-mediated minus end-directed transport from the Golgi apparatus to the endoplasmic reticulum (ER) []. Glycogen synthase kinase-3beta (GSK-3beta) is required for the binding of BICD to dynein but not to dynactin, acting to maintain the anchoring of microtubules to the centromere []. It appears that amino-acid residues 437-617 of BicD and the kinase activity of GSK-3 are necessary for the formation of a complex between BicD and GSK-3beta in intact cells [].; GO: 0006810 transport, 0005794 Golgi apparatus
Probab=29.17 E-value=18 Score=32.44 Aligned_cols=9 Identities=44% Similarity=1.184 Sum_probs=7.6
Q ss_pred ccchhhhhh
Q psy12841 5 VNMYHHFCD 13 (88)
Q Consensus 5 vNMYHHFCD 13 (88)
-|+|||.|=
T Consensus 457 AqLYHHVC~ 465 (717)
T PF09730_consen 457 AQLYHHVCM 465 (717)
T ss_pred HHHHHHHHH
Confidence 379999995
No 36
>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=29.00 E-value=64 Score=21.47 Aligned_cols=22 Identities=5% Similarity=0.208 Sum_probs=13.2
Q ss_pred ceeEEEeeccccCcchHHHHhhh
Q psy12841 34 DVHIMIWESYTYASAFADTFKAF 56 (88)
Q Consensus 34 Dv~Iv~Wdt~~Y~d~F~~tw~aF 56 (88)
.+.+.+|||.+- +.|...|+.+
T Consensus 48 ~~~l~i~Dt~G~-~~~~~~~~~~ 69 (187)
T cd04132 48 IIELALWDTAGQ-EEYDRLRPLS 69 (187)
T ss_pred EEEEEEEECCCc-hhHHHHHHHh
Confidence 567889999552 2344455444
No 37
>PLN00223 ADP-ribosylation factor; Provisional
Probab=28.19 E-value=61 Score=22.29 Aligned_cols=25 Identities=4% Similarity=0.365 Sum_probs=18.1
Q ss_pred ceeEEEeeccccCcchHHHHhhhhcC
Q psy12841 34 DVHIMIWESYTYASAFADTFKAFTRH 59 (88)
Q Consensus 34 Dv~Iv~Wdt~~Y~d~F~~tw~aFt~~ 59 (88)
++.+.+|||.+- +.|...|+.+-++
T Consensus 60 ~~~~~i~D~~Gq-~~~~~~~~~~~~~ 84 (181)
T PLN00223 60 NISFTVWDVGGQ-DKIRPLWRHYFQN 84 (181)
T ss_pred CEEEEEEECCCC-HHHHHHHHHHhcc
Confidence 577889999663 4677888876443
No 38
>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=27.87 E-value=71 Score=21.71 Aligned_cols=26 Identities=15% Similarity=0.395 Sum_probs=18.5
Q ss_pred CceeEEEeeccccCcchHHHHhhhhcC
Q psy12841 33 TDVHIMIWESYTYASAFADTFKAFTRH 59 (88)
Q Consensus 33 ~Dv~Iv~Wdt~~Y~d~F~~tw~aFt~~ 59 (88)
..+.+.+|||.+.. .|...|+.+-+.
T Consensus 50 ~~~~l~l~Dt~G~~-~~~~~~~~~~~~ 75 (183)
T cd04152 50 KGITFHFWDVGGQE-KLRPLWKSYTRC 75 (183)
T ss_pred CceEEEEEECCCcH-hHHHHHHHHhcc
Confidence 35778899997643 467888887543
No 39
>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=27.58 E-value=97 Score=22.76 Aligned_cols=22 Identities=18% Similarity=0.359 Sum_probs=14.1
Q ss_pred ceeEEEeeccccCcchHHHHhhh
Q psy12841 34 DVHIMIWESYTYASAFADTFKAF 56 (88)
Q Consensus 34 Dv~Iv~Wdt~~Y~d~F~~tw~aF 56 (88)
.+++.+|||.+- ..|...|+.+
T Consensus 43 ~~~l~iwDt~G~-e~~~~l~~~~ 64 (220)
T cd04126 43 PYNISIWDTAGR-EQFHGLGSMY 64 (220)
T ss_pred EEEEEEEeCCCc-ccchhhHHHH
Confidence 567889999553 2455566554
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=27.05 E-value=65 Score=21.15 Aligned_cols=26 Identities=23% Similarity=0.542 Sum_probs=16.9
Q ss_pred CceeEEEeeccccCcchHHHHhhhhcC
Q psy12841 33 TDVHIMIWESYTYASAFADTFKAFTRH 59 (88)
Q Consensus 33 ~Dv~Iv~Wdt~~Y~d~F~~tw~aFt~~ 59 (88)
.++++-+|||.+= +-|...|+.+-++
T Consensus 61 ~~~~~~i~Dt~G~-~~~~~~~~~~~~~ 86 (180)
T cd04127 61 QRIHLQLWDTAGQ-ERFRSLTTAFFRD 86 (180)
T ss_pred CEEEEEEEeCCCh-HHHHHHHHHHhCC
Confidence 3577889999652 3466666665544
No 41
>cd01889 SelB_euk SelB subfamily. SelB is an elongation factor needed for the co-translational incorporation of selenocysteine. Selenocysteine is coded by a UGA stop codon in combination with a specific downstream mRNA hairpin. In bacteria, the C-terminal part of SelB recognizes this hairpin, while the N-terminal part binds GTP and tRNA in analogy with elongation factor Tu (EF-Tu). It specifically recognizes the selenocysteine charged tRNAsec, which has a UCA anticodon, in an EF-Tu like manner. This allows insertion of selenocysteine at in-frame UGA stop codons. In E. coli SelB binds GTP, selenocysteyl-tRNAsec and a stem-loop structure immediately downstream of the UGA codon (the SECIS sequence). The absence of active SelB prevents the participation of selenocysteyl-tRNAsec in translation. Archaeal and animal mechanisms of selenocysteine incorporation are more complex. Although the SECIS elements have different secondary structures and conserved elements between archaea and euk
Probab=26.84 E-value=52 Score=22.48 Aligned_cols=23 Identities=13% Similarity=0.096 Sum_probs=17.4
Q ss_pred ceeEEEeeccccCcchHHHHhhh
Q psy12841 34 DVHIMIWESYTYASAFADTFKAF 56 (88)
Q Consensus 34 Dv~Iv~Wdt~~Y~d~F~~tw~aF 56 (88)
..++.+|||-|+.+..+..+++-
T Consensus 67 ~~~~~i~DtpG~~~~~~~~~~~~ 89 (192)
T cd01889 67 NLQITLVDCPGHASLIRTIIGGA 89 (192)
T ss_pred CceEEEEECCCcHHHHHHHHHHH
Confidence 67888999988877667666653
No 42
>smart00094 TR_FER Transferrin.
Probab=26.73 E-value=26 Score=28.03 Aligned_cols=19 Identities=11% Similarity=0.457 Sum_probs=15.9
Q ss_pred CCcccccccCCceeeeccc
Q psy12841 59 HPVWDLKTFTGLTVCFKNL 77 (88)
Q Consensus 59 ~~~~~L~~~~gKrVCFk~a 77 (88)
-++..|.+.+|||+||-+.
T Consensus 96 S~i~sl~dLkGKksChtg~ 114 (332)
T smart00094 96 SAIFTWNQLRGKKSCHTGV 114 (332)
T ss_pred CCCCCHHHhCCCceecCCC
Confidence 3678899999999999764
No 43
>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=26.63 E-value=65 Score=20.47 Aligned_cols=22 Identities=9% Similarity=0.163 Sum_probs=13.5
Q ss_pred ceeEEEeeccccCcchHHHHhhh
Q psy12841 34 DVHIMIWESYTYASAFADTFKAF 56 (88)
Q Consensus 34 Dv~Iv~Wdt~~Y~d~F~~tw~aF 56 (88)
.+.+.+|||.|- +.|...|+.+
T Consensus 48 ~~~l~i~Dt~G~-~~~~~~~~~~ 69 (163)
T cd04136 48 QCMLEILDTAGT-EQFTAMRDLY 69 (163)
T ss_pred EEEEEEEECCCc-cccchHHHHH
Confidence 356678999653 2355566554
No 44
>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=26.61 E-value=71 Score=21.47 Aligned_cols=23 Identities=9% Similarity=0.372 Sum_probs=16.2
Q ss_pred CceeEEEeeccccCcchHHHHhhh
Q psy12841 33 TDVHIMIWESYTYASAFADTFKAF 56 (88)
Q Consensus 33 ~Dv~Iv~Wdt~~Y~d~F~~tw~aF 56 (88)
+++.+.+|||.+-. -|...|+.+
T Consensus 51 ~~~~~~l~Dt~G~~-~~~~~~~~~ 73 (168)
T cd04149 51 KNVKFNVWDVGGQD-KIRPLWRHY 73 (168)
T ss_pred CCEEEEEEECCCCH-HHHHHHHHH
Confidence 46889999996543 356677665
No 45
>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=26.17 E-value=85 Score=21.14 Aligned_cols=26 Identities=4% Similarity=0.335 Sum_probs=17.9
Q ss_pred CceeEEEeeccccCcchHHHHhhhhcC
Q psy12841 33 TDVHIMIWESYTYASAFADTFKAFTRH 59 (88)
Q Consensus 33 ~Dv~Iv~Wdt~~Y~d~F~~tw~aFt~~ 59 (88)
.++.+.+|||.+- +.|...|+.+-+.
T Consensus 55 ~~~~l~l~D~~G~-~~~~~~~~~~~~~ 80 (175)
T smart00177 55 KNISFTVWDVGGQ-DKIRPLWRHYYTN 80 (175)
T ss_pred CCEEEEEEECCCC-hhhHHHHHHHhCC
Confidence 3578899999664 3466778776443
No 46
>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=26.01 E-value=60 Score=21.23 Aligned_cols=26 Identities=19% Similarity=0.431 Sum_probs=16.4
Q ss_pred ceeEEEeeccccCcchHHHHhhhhcCC
Q psy12841 34 DVHIMIWESYTYASAFADTFKAFTRHP 60 (88)
Q Consensus 34 Dv~Iv~Wdt~~Y~d~F~~tw~aFt~~~ 60 (88)
.+.+.+|||.+- +.|...|.++-+.-
T Consensus 49 ~~~~~l~Dt~g~-~~~~~~~~~~~~~~ 74 (165)
T cd01865 49 RVKLQIWDTAGQ-ERYRTITTAYYRGA 74 (165)
T ss_pred EEEEEEEECCCh-HHHHHHHHHHccCC
Confidence 477899999653 33555666655443
No 47
>cd01885 EF2 EF2 (for archaea and eukarya). Translocation requires hydrolysis of a molecule of GTP and is mediated by EF-G in bacteria and by eEF2 in eukaryotes. The eukaryotic elongation factor eEF2 is a GTPase involved in the translocation of the peptidyl-tRNA from the A site to the P site on the ribosome. The 95-kDa protein is highly conserved, with 60% amino acid sequence identity between the human and yeast proteins. Two major mechanisms are known to regulate protein elongation and both involve eEF2. First, eEF2 can be modulated by reversible phosphorylation. Increased levels of phosphorylated eEF2 reduce elongation rates presumably because phosphorylated eEF2 fails to bind the ribosomes. Treatment of mammalian cells with agents that raise the cytoplasmic Ca2+ and cAMP levels reduce elongation rates by activating the kinase responsible for phosphorylating eEF2. In contrast, treatment of cells with insulin increases elongation rates by promoting eEF2 dephosphorylation. Seco
Probab=25.66 E-value=75 Score=23.57 Aligned_cols=27 Identities=11% Similarity=-0.026 Sum_probs=21.3
Q ss_pred ceeEEEeeccccCcchHHHHhhhhcCC
Q psy12841 34 DVHIMIWESYTYASAFADTFKAFTRHP 60 (88)
Q Consensus 34 Dv~Iv~Wdt~~Y~d~F~~tw~aFt~~~ 60 (88)
+.+|.+|||.|..+.-+++..++..=.
T Consensus 72 ~~~i~iiDTPG~~~f~~~~~~~l~~aD 98 (222)
T cd01885 72 EYLINLIDSPGHVDFSSEVTAALRLCD 98 (222)
T ss_pred ceEEEEECCCCccccHHHHHHHHHhcC
Confidence 688999999998887778887775443
No 48
>COG3466 ISA1214 Putative transposon-encoded protein [Function unknown]
Probab=25.39 E-value=30 Score=22.02 Aligned_cols=10 Identities=30% Similarity=0.494 Sum_probs=9.1
Q ss_pred cccCCceeee
Q psy12841 65 KTFTGLTVCF 74 (88)
Q Consensus 65 ~~~~gKrVCF 74 (88)
|+|-|||||.
T Consensus 38 K~yiG~rv~v 47 (52)
T COG3466 38 KRYIGKRVYV 47 (52)
T ss_pred hHHcCcEEEE
Confidence 8999999995
No 49
>cd04108 Rab36_Rab34 Rab34/Rab36 subfamily. Rab34, found primarily in the Golgi, interacts with its effector, Rab-interacting lysosomal protein (RILP). This enables its participation in microtubular dynenin-dynactin-mediated repositioning of lysosomes from the cell periphery to the Golgi. A Rab34 (Rah) isoform that lacks the consensus GTP-binding region has been identified in mice. This isoform is associated with membrane ruffles and promotes macropinosome formation. Rab36 has been mapped to human chromosome 22q11.2, a region that is homozygously deleted in malignant rhabdoid tumors (MRTs). However, experimental assessments do not implicate Rab36 as a tumor suppressor that would enable tumor formation through a loss-of-function mechanism. 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 re
Probab=24.78 E-value=83 Score=21.17 Aligned_cols=10 Identities=10% Similarity=0.654 Sum_probs=7.6
Q ss_pred eeEEEeeccc
Q psy12841 35 VHIMIWESYT 44 (88)
Q Consensus 35 v~Iv~Wdt~~ 44 (88)
+++.+|||.+
T Consensus 49 ~~l~i~Dt~G 58 (170)
T cd04108 49 FSLQLWDTAG 58 (170)
T ss_pred EEEEEEeCCC
Confidence 4678899965
No 50
>cd04151 Arl1 Arl1 subfamily. Arl1 (Arf-like 1) localizes to the Golgi complex, where it is believed to recruit effector proteins to the trans-Golgi network. Like most members of the Arf family, Arl1 is myristoylated at its N-terminal helix and mutation of the myristoylation site disrupts Golgi targeting. In humans, the Golgi-localized proteins golgin-97 and golgin-245 have been identified as Arl1 effectors. Golgins are large coiled-coil proteins found in the Golgi, and these golgins contain a C-terminal GRIP domain, which is the site of Arl1 binding. Additional Arl1 effectors include the GARP (Golgi-associated retrograde protein)/VFT (Vps53) vesicle-tethering complex and Arfaptin 2. Arl1 is not required for exocytosis, but appears necessary for trafficking from the endosomes to the Golgi. In Drosophila zygotes, mutation of Arl1 is lethal, and in the host-bloodstream form of Trypanosoma brucei, Arl1 is essential for viability.
Probab=24.43 E-value=83 Score=20.31 Aligned_cols=26 Identities=4% Similarity=0.339 Sum_probs=17.5
Q ss_pred CceeEEEeeccccCcchHHHHhhhhcC
Q psy12841 33 TDVHIMIWESYTYASAFADTFKAFTRH 59 (88)
Q Consensus 33 ~Dv~Iv~Wdt~~Y~d~F~~tw~aFt~~ 59 (88)
.++.+.+|||.+-. .|...|+.+-+.
T Consensus 41 ~~~~~~i~Dt~G~~-~~~~~~~~~~~~ 66 (158)
T cd04151 41 KNLKFQVWDLGGQT-SIRPYWRCYYSN 66 (158)
T ss_pred CCEEEEEEECCCCH-HHHHHHHHHhcC
Confidence 46788999996643 366777765443
No 51
>PLN03118 Rab family protein; Provisional
Probab=24.36 E-value=80 Score=21.94 Aligned_cols=25 Identities=16% Similarity=0.461 Sum_probs=16.3
Q ss_pred ceeEEEeeccccCcchHHHHhhhhcC
Q psy12841 34 DVHIMIWESYTYASAFADTFKAFTRH 59 (88)
Q Consensus 34 Dv~Iv~Wdt~~Y~d~F~~tw~aFt~~ 59 (88)
++++.+|||.+- +.|...|+.+-+.
T Consensus 61 ~~~l~l~Dt~G~-~~~~~~~~~~~~~ 85 (211)
T PLN03118 61 RLKLTIWDTAGQ-ERFRTLTSSYYRN 85 (211)
T ss_pred EEEEEEEECCCc-hhhHHHHHHHHhc
Confidence 467889999664 3456666665443
No 52
>TIGR00503 prfC peptide chain release factor 3. This translation releasing factor, RF-3 (prfC) was originally described as stop codon-independent, in contrast to peptide chain release factor 1 (RF-1, prfA) and RF-2 (prfB). RF-1 and RF-2 are closely related to each other, while RF-3 is similar to elongation factors EF-Tu and EF-G; RF-1 is active at UAA and UAG and RF-2 is active at UAA and UGA. More recently, RF-3 was shown to be active primarily at UGA stop codons in E. coli. All bacteria and organelles have RF-1. The Mycoplasmas and organelles, which translate UGA as Trp rather than as a stop codon, lack RF-2. RF-3, in contrast, seems to be rare among bacteria and is found so far only in Escherichia coli and some other gamma subdivision Proteobacteria, in Synechocystis PCC6803, and in Staphylococcus aureus.
Probab=24.30 E-value=64 Score=27.21 Aligned_cols=27 Identities=15% Similarity=0.203 Sum_probs=21.9
Q ss_pred CceeEEEeeccccCcchHHHHhhhhcC
Q psy12841 33 TDVHIMIWESYTYASAFADTFKAFTRH 59 (88)
Q Consensus 33 ~Dv~Iv~Wdt~~Y~d~F~~tw~aFt~~ 59 (88)
.+.+|.+|||-|+.+.-+++|++...-
T Consensus 78 ~~~~inliDTPG~~df~~~~~~~l~~a 104 (527)
T TIGR00503 78 RDCLVNLLDTPGHEDFSEDTYRTLTAV 104 (527)
T ss_pred CCeEEEEEECCChhhHHHHHHHHHHhC
Confidence 378899999998888778899987543
No 53
>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=24.26 E-value=65 Score=20.73 Aligned_cols=13 Identities=0% Similarity=-0.077 Sum_probs=10.2
Q ss_pred ceeEEEeeccccC
Q psy12841 34 DVHIMIWESYTYA 46 (88)
Q Consensus 34 Dv~Iv~Wdt~~Y~ 46 (88)
++.+.+|||.|..
T Consensus 46 ~~~~~i~Dt~G~~ 58 (168)
T cd01897 46 YLRWQVIDTPGLL 58 (168)
T ss_pred ceEEEEEECCCcC
Confidence 5788999997653
No 54
>cd04110 Rab35 Rab35 subfamily. Rab35 is one of several Rab proteins to be found to participate in the regulation of osteoclast cells in rats. In addition, Rab35 has been identified as a protein that interacts with nucleophosmin-anaplastic lymphoma kinase (NPM-ALK) in human cells. Overexpression of NPM-ALK is a key oncogenic event in some anaplastic large-cell lymphomas; since Rab35 interacts with N|PM-ALK, it may provide a target for cancer treatments. 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
Probab=23.95 E-value=1.5e+02 Score=20.49 Aligned_cols=25 Identities=20% Similarity=0.470 Sum_probs=16.2
Q ss_pred eeEEEeeccccCcchHHHHhhhhcCC
Q psy12841 35 VHIMIWESYTYASAFADTFKAFTRHP 60 (88)
Q Consensus 35 v~Iv~Wdt~~Y~d~F~~tw~aFt~~~ 60 (88)
+.+.+|||.+ ...|+..|+.+-++.
T Consensus 55 ~~l~l~D~~G-~~~~~~~~~~~~~~a 79 (199)
T cd04110 55 VKLQIWDTAG-QERFRTITSTYYRGT 79 (199)
T ss_pred EEEEEEeCCC-chhHHHHHHHHhCCC
Confidence 5678999955 234667776655543
No 55
>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=23.41 E-value=94 Score=21.35 Aligned_cols=27 Identities=19% Similarity=0.400 Sum_probs=17.6
Q ss_pred CceeEEEeeccccCcchHHHHhhhhcCC
Q psy12841 33 TDVHIMIWESYTYASAFADTFKAFTRHP 60 (88)
Q Consensus 33 ~Dv~Iv~Wdt~~Y~d~F~~tw~aFt~~~ 60 (88)
..+.+.+|||.+- +.|...|+.+-++-
T Consensus 48 ~~~~l~l~Dt~G~-~~~~~~~~~~~~~a 74 (201)
T cd04107 48 TVVRLQLWDIAGQ-ERFGGMTRVYYRGA 74 (201)
T ss_pred CEEEEEEEECCCc-hhhhhhHHHHhCCC
Confidence 4677889999653 34666776655443
No 56
>cd04157 Arl6 Arl6 subfamily. Arl6 (Arf-like 6) forms a subfamily of the Arf family of small GTPases. Arl6 expression is limited to the brain and kidney in adult mice, but it is expressed in the neural plate and somites during embryogenesis, suggesting a possible role for Arl6 in early development. Arl6 is also believed to have a role in cilia or flagella function. Several proteins have been identified that bind Arl6, including Arl6 interacting protein (Arl6ip), and SEC61beta, a subunit of the heterotrimeric conducting channel SEC61p. Based on Arl6 binding to these effectors, Arl6 is also proposed to play a role in protein transport, membrane trafficking, or cell signaling during hematopoietic maturation. At least three specific homozygous Arl6 mutations in humans have been found to cause Bardet-Biedl syndrome, a disorder characterized by obesity, retinopathy, polydactyly, renal and cardiac malformations, learning disabilities, and hypogenitalism. Older literature suggests that A
Probab=23.40 E-value=1e+02 Score=19.55 Aligned_cols=26 Identities=0% Similarity=0.220 Sum_probs=17.2
Q ss_pred CceeEEEeeccccCcchHHHHhhhhcC
Q psy12841 33 TDVHIMIWESYTYASAFADTFKAFTRH 59 (88)
Q Consensus 33 ~Dv~Iv~Wdt~~Y~d~F~~tw~aFt~~ 59 (88)
.++.+.+|||.+.. .|...|+.+-++
T Consensus 43 ~~~~~~l~Dt~G~~-~~~~~~~~~~~~ 68 (162)
T cd04157 43 GNLSFTAFDMSGQG-KYRGLWEHYYKN 68 (162)
T ss_pred CCEEEEEEECCCCH-hhHHHHHHHHcc
Confidence 46778899996644 366677765443
No 57
>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=22.09 E-value=94 Score=20.08 Aligned_cols=24 Identities=17% Similarity=0.490 Sum_probs=15.9
Q ss_pred ceeEEEeeccccCcchHHHHhhhhc
Q psy12841 34 DVHIMIWESYTYASAFADTFKAFTR 58 (88)
Q Consensus 34 Dv~Iv~Wdt~~Y~d~F~~tw~aFt~ 58 (88)
.+++-+|||.|- +.|...|+.+-+
T Consensus 50 ~~~~~i~D~~G~-~~~~~~~~~~~~ 73 (166)
T cd01869 50 TIKLQIWDTAGQ-ERFRTITSSYYR 73 (166)
T ss_pred EEEEEEEECCCc-HhHHHHHHHHhC
Confidence 457888999663 346667766544
No 58
>cd00878 Arf_Arl Arf (ADP-ribosylation factor)/Arl (Arf-like) small GTPases. Arf proteins are activators 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. Members of the Arf family are regulators of vesicle formation in intracellular traffic that interact reversibly with membranes of the secretory and endocytic compartments in a GTP-dependent manner. They depart from other small GTP-binding proteins by a unique structural device, interswitch toggle, that implements front-back communication from N-terminus to the nucleotide binding site. Arf-like (Arl) proteins are close relatives of the Arf, but only Arl1 has been shown to function in membrane traffic like the Arf proteins. Arl2 has an unrelated function in the folding of native tubulin, and Arl4 may function in the nucleus. Most other Arf family proteins are so far relatively poorly characterized. Thu
Probab=21.97 E-value=1.1e+02 Score=19.55 Aligned_cols=25 Identities=12% Similarity=0.355 Sum_probs=16.9
Q ss_pred ceeEEEeeccccCcchHHHHhhhhcC
Q psy12841 34 DVHIMIWESYTYASAFADTFKAFTRH 59 (88)
Q Consensus 34 Dv~Iv~Wdt~~Y~d~F~~tw~aFt~~ 59 (88)
++.+.+|||.+.. .|...|+.+.+.
T Consensus 42 ~~~~~i~D~~G~~-~~~~~~~~~~~~ 66 (158)
T cd00878 42 NVSFTVWDVGGQD-KIRPLWKHYYEN 66 (158)
T ss_pred CEEEEEEECCCCh-hhHHHHHHHhcc
Confidence 5778899996643 456677766443
No 59
>cd01888 eIF2_gamma eIF2-gamma (gamma subunit of initiation factor 2). eIF2 is a heterotrimeric translation initiation factor that consists of alpha, beta, and gamma subunits. The GTP-bound gamma subunit also binds initiator methionyl-tRNA and delivers it to the 40S ribosomal subunit. Following hydrolysis of GTP to GDP, eIF2:GDP is released from the ribosome. The gamma subunit has no intrinsic GTPase activity, but is stimulated by the GTPase activating protein (GAP) eIF5, and GDP/GTP exchange is stimulated by the guanine nucleotide exchange factor (GEF) eIF2B. eIF2B is a heteropentamer, and the epsilon chain binds eIF2. Both eIF5 and eIF2B-epsilon are known to bind strongly to eIF2-beta, but have also been shown to bind directly to eIF2-gamma. It is possible that eIF2-beta serves simply as a high-affinity docking site for eIF5 and eIF2B-epsilon, or that eIF2-beta serves a regulatory role. eIF2-gamma is found only in eukaryotes and archaea. It is closely related to SelB, the sel
Probab=21.79 E-value=65 Score=22.62 Aligned_cols=23 Identities=9% Similarity=0.029 Sum_probs=17.5
Q ss_pred eeEEEeeccccCcchHHHHhhhh
Q psy12841 35 VHIMIWESYTYASAFADTFKAFT 57 (88)
Q Consensus 35 v~Iv~Wdt~~Y~d~F~~tw~aFt 57 (88)
.+|.+|||-|+.++-++++.+..
T Consensus 83 ~~i~~iDtPG~~~~~~~~~~~~~ 105 (203)
T cd01888 83 RHVSFVDCPGHEILMATMLSGAA 105 (203)
T ss_pred cEEEEEECCChHHHHHHHHHhhh
Confidence 68899999888776666666653
No 60
>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=21.32 E-value=87 Score=21.33 Aligned_cols=23 Identities=22% Similarity=0.518 Sum_probs=13.8
Q ss_pred ceeEEEeeccccCcchHHHHhhhh
Q psy12841 34 DVHIMIWESYTYASAFADTFKAFT 57 (88)
Q Consensus 34 Dv~Iv~Wdt~~Y~d~F~~tw~aFt 57 (88)
.+++.+|||.+ .+.|...|+.+-
T Consensus 49 ~~~~~i~Dt~G-~~~~~~~~~~~~ 71 (191)
T cd04112 49 KVKLQIWDTAG-QERFRSVTHAYY 71 (191)
T ss_pred EEEEEEEeCCC-cHHHHHhhHHHc
Confidence 35788999955 234555555543
No 61
>PF12911 OppC_N: N-terminal TM domain of oligopeptide transport permease C
Probab=21.21 E-value=55 Score=18.76 Aligned_cols=16 Identities=25% Similarity=0.563 Sum_probs=13.3
Q ss_pred cchHHHHhhhhcCCcc
Q psy12841 47 SAFADTFKAFTRHPVW 62 (88)
Q Consensus 47 d~F~~tw~aFt~~~~~ 62 (88)
+.+++.|+-|.+|+..
T Consensus 3 s~~~~~~~~f~~nk~a 18 (56)
T PF12911_consen 3 SPWKDAWRRFRRNKLA 18 (56)
T ss_pred CHHHHHHHHHHhCchH
Confidence 5789999999998753
No 62
>cd01870 RhoA_like RhoA-like subfamily. The RhoA subfamily consists of RhoA, RhoB, and RhoC. RhoA promotes the formation of stress fibers and focal adhesions, regulating cell shape, attachment, and motility. RhoA can bind to multiple effector proteins, thereby triggering different downstream responses. In many cell types, RhoA mediates local assembly of the contractile ring, which is necessary for cytokinesis. RhoA is vital for muscle contraction; in vascular smooth muscle cells, RhoA plays a key role in cell contraction, differentiation, migration, and proliferation. RhoA activities appear to be elaborately regulated in a time- and space-dependent manner to control cytoskeletal changes. 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. RhoA and RhoC are observed only in geranyl
Probab=21.20 E-value=65 Score=20.95 Aligned_cols=12 Identities=17% Similarity=0.689 Sum_probs=9.3
Q ss_pred CceeEEEeeccc
Q psy12841 33 TDVHIMIWESYT 44 (88)
Q Consensus 33 ~Dv~Iv~Wdt~~ 44 (88)
.++++.+|||.+
T Consensus 47 ~~~~l~i~Dt~G 58 (175)
T cd01870 47 KQVELALWDTAG 58 (175)
T ss_pred EEEEEEEEeCCC
Confidence 457889999954
No 63
>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=21.06 E-value=95 Score=22.30 Aligned_cols=24 Identities=21% Similarity=0.526 Sum_probs=15.6
Q ss_pred ceeEEEeeccccCcchHHHHhhhhc
Q psy12841 34 DVHIMIWESYTYASAFADTFKAFTR 58 (88)
Q Consensus 34 Dv~Iv~Wdt~~Y~d~F~~tw~aFt~ 58 (88)
.+++-+|||.|- +.|...|+.+-+
T Consensus 48 ~v~l~iwDtaGq-e~~~~l~~~y~~ 71 (202)
T cd04120 48 KIRLQIWDTAGQ-ERFNSITSAYYR 71 (202)
T ss_pred EEEEEEEeCCCc-hhhHHHHHHHhc
Confidence 477789999553 346666665543
No 64
>smart00175 RAB Rab subfamily of small GTPases. Rab GTPases are implicated in vesicle trafficking.
Probab=20.95 E-value=93 Score=19.67 Aligned_cols=24 Identities=21% Similarity=0.517 Sum_probs=15.5
Q ss_pred ceeEEEeeccccCcchHHHHhhhhc
Q psy12841 34 DVHIMIWESYTYASAFADTFKAFTR 58 (88)
Q Consensus 34 Dv~Iv~Wdt~~Y~d~F~~tw~aFt~ 58 (88)
+++|.+|||.+ .+.|...++++-+
T Consensus 48 ~~~~~l~D~~G-~~~~~~~~~~~~~ 71 (164)
T smart00175 48 RVKLQIWDTAG-QERFRSITSSYYR 71 (164)
T ss_pred EEEEEEEECCC-hHHHHHHHHHHhC
Confidence 36788899965 3345566666654
No 65
>smart00062 PBPb Bacterial periplasmic substrate-binding proteins. bacterial proteins, eukaryotic ones are in PBPe
Probab=20.90 E-value=54 Score=20.38 Aligned_cols=19 Identities=21% Similarity=0.372 Sum_probs=15.0
Q ss_pred cCCcccccccCCceeeecc
Q psy12841 58 RHPVWDLKTFTGLTVCFKN 76 (88)
Q Consensus 58 ~~~~~~L~~~~gKrVCFk~ 76 (88)
+.|+.+++|++||+|+.-.
T Consensus 95 ~~~~~~~~dL~g~~i~~~~ 113 (219)
T smart00062 95 DSPIKSLEDLKGKKVAVVA 113 (219)
T ss_pred CCCCCChHHhCCCEEEEec
Confidence 3457788999999999753
No 66
>cd00154 Rab Rab family. Rab GTPases form the largest family within the Ras superfamily. There are at least 60 Rab genes in the human genome, and a number of Rab GTPases are conserved from yeast to humans. Rab GTPases are small, monomeric proteins that function as molecular switches to regulate vesicle trafficking pathways. The different Rab GTPases are localized to the cytosolic face of specific intracellular membranes, where they regulate distinct steps in membrane traffic pathways. In the GTP-bound form, Rab GTPases recruit specific sets of effector proteins onto membranes. Through their effectors, Rab GTPases regulate vesicle formation, actin- and tubulin-dependent vesicle movement, and membrane fusion. 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 di
Probab=20.60 E-value=98 Score=18.90 Aligned_cols=26 Identities=19% Similarity=0.434 Sum_probs=17.5
Q ss_pred CceeEEEeeccccCcchHHHHhhhhcC
Q psy12841 33 TDVHIMIWESYTYASAFADTFKAFTRH 59 (88)
Q Consensus 33 ~Dv~Iv~Wdt~~Y~d~F~~tw~aFt~~ 59 (88)
..+++.+||+.+.. .|...|+++-++
T Consensus 47 ~~~~~~l~D~~g~~-~~~~~~~~~~~~ 72 (159)
T cd00154 47 KTVKLQIWDTAGQE-RFRSITPSYYRG 72 (159)
T ss_pred EEEEEEEEecCChH-HHHHHHHHHhcC
Confidence 45778899996653 455677776654
No 67
>cd04176 Rap2 Rap2 subgroup. The Rap2 subgroup is part of the Rap subfamily of the Ras family. It consists of Rap2a, Rap2b, and Rap2c. Both isoform 3 of the human mitogen-activated protein kinase kinase kinase kinase 4 (MAP4K4) and Traf2- and Nck-interacting kinase (TNIK) are putative effectors of Rap2 in mediating the activation of c-Jun N-terminal kinase (JNK) to regulate the actin cytoskeleton. In human platelets, Rap2 was shown to interact with the cytoskeleton by binding the actin filaments. In embryonic Xenopus development, Rap2 is necessary for the Wnt/beta-catenin signaling pathway. The Rap2 interacting protein 9 (RPIP9) is highly expressed in human breast carcinomas and correlates with a poor prognosis, suggesting a role for Rap2 in breast cancer oncogenesis. Rap2b, but not Rap2a, Rap2c, Rap1a, or Rap1b, is expressed in human red blood cells, where it is believed to be involved in vesiculation. A number of additional effector proteins for Rap2 have been identified, incl
Probab=20.40 E-value=88 Score=20.07 Aligned_cols=22 Identities=14% Similarity=0.190 Sum_probs=12.8
Q ss_pred ceeEEEeeccccCcchHHHHhhh
Q psy12841 34 DVHIMIWESYTYASAFADTFKAF 56 (88)
Q Consensus 34 Dv~Iv~Wdt~~Y~d~F~~tw~aF 56 (88)
.+.+-+|||.+ .+.|...|..+
T Consensus 48 ~~~l~i~Dt~G-~~~~~~~~~~~ 69 (163)
T cd04176 48 PSVLEILDTAG-TEQFASMRDLY 69 (163)
T ss_pred EEEEEEEECCC-cccccchHHHH
Confidence 34566899955 23355555553
No 68
>cd04175 Rap1 Rap1 subgroup. The Rap1 subgroup is part of the Rap subfamily of the Ras family. It can be further divided into the Rap1a and Rap1b isoforms. In humans, Rap1a and Rap1b share 95% sequence homology, but are products of two different genes located on chromosomes 1 and 12, respectively. Rap1a is sometimes called smg p21 or Krev1 in the older literature. Rap1 proteins are believed to perform different cellular functions, depending on the isoform, its subcellular localization, and the effector proteins it binds. 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 the microsomal membrane of pancreatic acini, as well as in the endocytic compartment of skeletal muscle cells and fibroblasts. High expression of Rap1 has been observed in the n
Probab=20.38 E-value=96 Score=20.00 Aligned_cols=22 Identities=9% Similarity=0.163 Sum_probs=13.2
Q ss_pred ceeEEEeeccccCcchHHHHhhh
Q psy12841 34 DVHIMIWESYTYASAFADTFKAF 56 (88)
Q Consensus 34 Dv~Iv~Wdt~~Y~d~F~~tw~aF 56 (88)
.+.+.+|||.+- +.|...|+.+
T Consensus 48 ~~~l~i~Dt~G~-~~~~~~~~~~ 69 (164)
T cd04175 48 QCMLEILDTAGT-EQFTAMRDLY 69 (164)
T ss_pred EEEEEEEECCCc-ccchhHHHHH
Confidence 456678999653 2355555553
No 69
>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=20.38 E-value=86 Score=19.63 Aligned_cols=24 Identities=8% Similarity=0.303 Sum_probs=15.3
Q ss_pred CceeEEEeeccccCcchHHHHhhhh
Q psy12841 33 TDVHIMIWESYTYASAFADTFKAFT 57 (88)
Q Consensus 33 ~Dv~Iv~Wdt~~Y~d~F~~tw~aFt 57 (88)
..+++.+|||.+- +.|...|+.+-
T Consensus 47 ~~~~~~~~D~~g~-~~~~~~~~~~~ 70 (162)
T cd04123 47 KRIDLAIWDTAGQ-ERYHALGPIYY 70 (162)
T ss_pred EEEEEEEEECCch-HHHHHhhHHHh
Confidence 3467889999662 23556666653
No 70
>PF12974 Phosphonate-bd: ABC transporter, phosphonate, periplasmic substrate-binding protein ; PDB: 3N5L_B 3QUJ_C 3P7I_A 3QK6_A 3S4U_A.
Probab=20.20 E-value=40 Score=23.85 Aligned_cols=21 Identities=24% Similarity=0.420 Sum_probs=14.4
Q ss_pred cCCcccccccCCceeeecccc
Q psy12841 58 RHPVWDLKTFTGLTVCFKNLV 78 (88)
Q Consensus 58 ~~~~~~L~~~~gKrVCFk~a~ 78 (88)
+.++-+|+|..||||++-+.-
T Consensus 94 ds~i~~l~dL~Gk~v~~~~~~ 114 (243)
T PF12974_consen 94 DSPITSLADLKGKRVAFPDPS 114 (243)
T ss_dssp TSS--SHHHHGGSEEEEE-TT
T ss_pred CCCCCChhhcCCCEEEEecCC
Confidence 445668999999999996543
Done!