Query 032455
Match_columns 140
No_of_seqs 112 out of 224
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 14:19:05 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032455.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032455hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01251 Ribosomal_S7e: Riboso 100.0 3.5E-78 7.5E-83 484.2 11.4 139 1-139 47-189 (189)
2 KOG3320 40S ribosomal protein 100.0 4.3E-74 9.3E-79 459.1 14.4 139 1-139 52-191 (192)
3 PTZ00389 40S ribosomal protein 100.0 6.3E-73 1.4E-77 452.4 15.0 138 1-139 45-184 (184)
4 PRK06418 transcription elongat 99.7 1.4E-17 3E-22 131.7 6.6 64 72-135 102-165 (166)
5 TIGR01618 phage_P_loop phage n 81.9 11 0.00023 31.0 8.1 93 17-117 110-206 (220)
6 COG0195 NusA Transcription elo 78.6 6.1 0.00013 32.1 5.6 61 75-137 121-181 (190)
7 smart00174 RHO Rho (Ras homolo 65.9 22 0.00048 25.6 5.5 45 8-52 71-115 (174)
8 PF01577 Peptidase_S30: Potyvi 56.8 18 0.0004 28.9 4.1 41 65-105 102-155 (245)
9 cd00157 Rho Rho (Ras homology) 50.8 59 0.0013 23.1 5.6 45 8-52 73-117 (171)
10 TIGR01952 nusA_arch NusA famil 48.9 43 0.00094 26.0 4.9 57 74-131 77-133 (141)
11 PF00071 Ras: Ras family; Int 44.3 82 0.0018 22.2 5.5 43 7-50 72-115 (162)
12 PF01383 CpcD: CpcD/allophycoc 43.7 21 0.00045 23.6 2.1 21 7-27 24-45 (56)
13 cd04135 Tc10 TC10 subfamily. 43.6 91 0.002 22.4 5.7 41 9-49 74-114 (174)
14 cd04130 Wrch_1 Wrch-1 subfamil 41.4 96 0.0021 22.6 5.6 43 9-51 74-116 (173)
15 cd01870 RhoA_like RhoA-like su 41.2 1E+02 0.0022 22.1 5.6 43 9-51 75-117 (175)
16 cd01893 Miro1 Miro1 subfamily. 40.6 1.1E+02 0.0023 22.1 5.7 41 9-49 73-113 (166)
17 cd04134 Rho3 Rho3 subfamily. 40.6 1E+02 0.0022 23.1 5.7 44 9-52 74-117 (189)
18 cd01874 Cdc42 Cdc42 subfamily. 37.4 1.2E+02 0.0026 22.6 5.7 43 9-51 75-117 (175)
19 cd00877 Ran Ran (Ras-related n 36.6 1.2E+02 0.0027 22.1 5.5 43 8-51 74-116 (166)
20 cd01875 RhoG RhoG subfamily. 34.4 1.4E+02 0.0031 22.5 5.7 45 8-52 76-120 (191)
21 PF06858 NOG1: Nucleolar GTP-b 34.0 59 0.0013 22.0 3.1 24 24-47 32-55 (58)
22 cd04172 Rnd3_RhoE_Rho8 Rnd3/Rh 33.9 1.4E+02 0.0031 22.7 5.7 44 8-51 78-121 (182)
23 cd04173 Rnd2_Rho7 Rnd2/Rho7 su 32.3 1.5E+02 0.0032 23.9 5.7 44 8-51 74-117 (222)
24 PF02374 ArsA_ATPase: Anion-tr 32.3 80 0.0017 26.8 4.4 32 17-48 255-286 (305)
25 smart00175 RAB Rab subfamily o 31.6 1.8E+02 0.0039 20.3 5.7 40 8-48 74-114 (164)
26 cd04132 Rho4_like Rho4-like su 30.2 1.9E+02 0.0041 21.1 5.7 44 8-51 74-117 (187)
27 cd04129 Rho2 Rho2 subfamily. 30.1 1.9E+02 0.004 21.6 5.7 41 9-49 75-115 (187)
28 cd01873 RhoBTB RhoBTB subfamil 28.9 1.9E+02 0.004 22.4 5.6 45 8-52 89-133 (195)
29 cd01871 Rac1_like Rac1-like su 28.1 2.1E+02 0.0045 21.2 5.6 44 8-51 74-117 (174)
30 cd02970 PRX_like2 Peroxiredoxi 28.0 1.2E+02 0.0027 21.1 4.2 42 5-47 22-63 (149)
31 cd04133 Rop_like Rop subfamily 27.5 2.1E+02 0.0046 21.7 5.6 43 9-51 75-117 (176)
32 PF08534 Redoxin: Redoxin; In 27.4 1.3E+02 0.0028 21.3 4.2 39 6-45 28-66 (146)
33 cd04121 Rab40 Rab40 subfamily. 27.0 2.1E+02 0.0045 22.1 5.6 43 8-51 80-122 (189)
34 cd04124 RabL2 RabL2 subfamily. 26.7 2.4E+02 0.0052 20.3 5.6 40 9-49 75-114 (161)
35 PF13479 AAA_24: AAA domain 26.5 1.2E+02 0.0026 23.8 4.2 62 19-86 105-169 (213)
36 cd04131 Rnd Rnd subfamily. Th 26.3 2.3E+02 0.0049 21.4 5.6 44 8-51 74-117 (178)
37 PRK08406 transcription elongat 26.1 2.1E+02 0.0046 21.9 5.4 58 73-131 75-132 (140)
38 cd08971 AcNei2_N N-terminal do 25.7 1.2E+02 0.0027 22.0 3.9 60 28-105 9-68 (114)
39 TIGR02110 PQQ_syn_pqqF coenzym 24.3 1.7E+02 0.0036 28.2 5.4 46 2-51 610-668 (696)
40 COG4496 Uncharacterized protei 24.3 24 0.00051 26.5 -0.2 26 61-86 4-41 (100)
41 cd03018 PRX_AhpE_like Peroxire 23.3 1.1E+02 0.0024 21.7 3.2 39 7-46 29-67 (149)
42 PRK10470 ribosome hibernation 22.5 32 0.0007 23.8 0.2 35 102-136 10-44 (95)
43 cd01869 Rab1_Ypt1 Rab1/Ypt1 su 21.7 3E+02 0.0066 19.5 5.6 41 8-49 76-117 (166)
44 cd00936 WEPRS_RNA WEPRS_RNA bi 20.9 68 0.0015 20.2 1.5 18 114-131 30-47 (50)
45 PF00408 PGM_PMM_IV: Phosphogl 20.8 1.3E+02 0.0028 19.8 3.0 35 87-121 35-70 (73)
46 cd04126 Rab20 Rab20 subfamily. 20.6 3.2E+02 0.0068 21.9 5.6 46 8-53 69-114 (220)
47 PF14085 DUF4265: Domain of un 20.1 1.1E+02 0.0023 22.5 2.6 61 76-138 28-96 (117)
48 PRK14962 DNA polymerase III su 20.0 1E+02 0.0022 28.0 3.0 37 100-136 410-449 (472)
No 1
>PF01251 Ribosomal_S7e: Ribosomal protein S7e; InterPro: IPR000554 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic ribosomal proteins can be grouped on the basis of sequence similarities []. One of these families consists of Xenopus S8, and mammalian, insect and yeast S7. These proteins have about 200 amino acids.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2XZN_3 2XZM_3 3U5G_H 3U5C_H.
Probab=100.00 E-value=3.5e-78 Score=484.20 Aligned_cols=139 Identities=64% Similarity=1.026 Sum_probs=119.0
Q ss_pred CeecCCeeEEEEEeehhhHHHHHHHHHHHHHHHhhhcCCCeEEEEeeecccCCCCCC----CcccccCCcchhHHHHHhh
Q 032455 1 MDVSGNRKAIVVYVPYRLRKAYRKIHSRLVRELEKKFSGKDVVLIATRRIVRPPKKG----SAVQRPRSRTLTAVHDAML 76 (140)
Q Consensus 1 i~v~~~kkaivIfVP~~~lk~f~kiq~rLv~ELEKKfsg~~Vv~iaqRrIl~kp~~k----~~q~rPRsRTLTaVhdaiL 76 (140)
||||+|+||||||||||||++|||||.||++||||||||+||+|||||||||+|+++ .+|+|||||||||||||||
T Consensus 47 i~v~~~kKAivIfVP~~~lk~f~KIq~rLv~ELEKKfsgk~Vv~iAqRrIl~kp~r~~~~~~~qkrPRSRTLTaVhdaIL 126 (189)
T PF01251_consen 47 IEVGGGKKAIVIFVPVPQLKAFQKIQVRLVRELEKKFSGKHVVFIAQRRILPKPTRKSRQKQKQKRPRSRTLTAVHDAIL 126 (189)
T ss_dssp EEECTCEEEEEEEE-CCCCHHHHHHCHHHHHHHHHCTTTCEEEEEE------SS-SSS---TTS---CCCSHHHHHHHHH
T ss_pred EEECCCcEEEEEEEcHHHHHHHHHHHHHHHHHHHhhcCCCeEEEeccceEcCCCCcCccccccccCcCCcchHHHHHHHH
Confidence 689999999999999999999999999999999999999999999999999999887 4799999999999999999
Q ss_pred hcccccceeeeeeEEEeeCCceEEEEEeCccccccchhhhhhHHHHHhhhhCCcEEEECCCCC
Q 032455 77 EDVVYPAEIVGKRVRYRLDGSKIIKIFLDPKERNNTEYKLESFSGVYRKLTGKDVVFDYPITD 139 (140)
Q Consensus 77 eDLV~PseIVGKRir~~~DGskl~KV~LD~~~~~~ve~Kl~tfs~VYkkLtgkdv~FeFp~~~ 139 (140)
||||||+|||||||||++|||+++|||||++|||++|||+|||++|||+||||||+||||+++
T Consensus 127 eDLV~PseIVGKRir~rlDGskl~KV~LD~k~~~~ve~Kl~tfs~VYkkLTgK~v~FeFp~~~ 189 (189)
T PF01251_consen 127 EDLVYPSEIVGKRIRVRLDGSKLIKVHLDKKDQNNVEHKLDTFSAVYKKLTGKDVVFEFPEQE 189 (189)
T ss_dssp HHHTTTS-ECEEEEEE-TTS-EEEEEEEECCCCHHHHCCHHHHHHHHHHHCS-EEEEEEE---
T ss_pred HhhccHHHhheeeEEEecCCCEEEEEEEChHHcccHHHHHHHHHHHHHHHcCCceEEEcCCCC
Confidence 999999999999999999999999999999999999999999999999999999999999863
No 2
>KOG3320 consensus 40S ribosomal protein S7 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=4.3e-74 Score=459.05 Aligned_cols=139 Identities=63% Similarity=1.000 Sum_probs=136.7
Q ss_pred CeecCCeeEEEEEeehhhHHHHHHHHHHHHHHHhhhcCCCeEEEEeeecccCCCCCCCc-ccccCCcchhHHHHHhhhcc
Q 032455 1 MDVSGNRKAIVVYVPYRLRKAYRKIHSRLVRELEKKFSGKDVVLIATRRIVRPPKKGSA-VQRPRSRTLTAVHDAMLEDV 79 (140)
Q Consensus 1 i~v~~~kkaivIfVP~~~lk~f~kiq~rLv~ELEKKfsg~~Vv~iaqRrIl~kp~~k~~-q~rPRsRTLTaVhdaiLeDL 79 (140)
||||||+||||||||+|+|++|||||.+|++||||||||+||+|||+|||||+|++++. |||||||||||||||||||+
T Consensus 52 iev~Gg~Kaivi~VP~p~lk~fqki~~~LvreleKKF~gk~Vifia~Rrilpkp~rks~~qKRprsrtltaVhdaiLed~ 131 (192)
T KOG3320|consen 52 IEVGGGRKAIVIFVPVPQLKAFQKIQVRLVRELEKKFSGKHVIFIAQRRILPKPTRKSRTQKRPRSRTLTAVHDAILEDL 131 (192)
T ss_pred EEecCCcEEEEEEechHHHHHHHHHHHHHHHHHHHhcCCceEEEEEeeeeccCCCCCcccccCCccchHHHHHHHHHHhc
Confidence 68999999999999999999999999999999999999999999999999999999997 89999999999999999999
Q ss_pred cccceeeeeeEEEeeCCceEEEEEeCccccccchhhhhhHHHHHhhhhCCcEEEECCCCC
Q 032455 80 VYPAEIVGKRVRYRLDGSKIIKIFLDPKERNNTEYKLESFSGVYRKLTGKDVVFDYPITD 139 (140)
Q Consensus 80 V~PseIVGKRir~~~DGskl~KV~LD~~~~~~ve~Kl~tfs~VYkkLtgkdv~FeFp~~~ 139 (140)
|||+|||||||||++||++++|||||++|+||+|||+|+|++||++||||||+||||+.+
T Consensus 132 vfP~eIvGkR~rv~ldg~ki~kV~LD~~~~n~~e~K~e~f~~vy~kLtGKdv~fEfp~~~ 191 (192)
T KOG3320|consen 132 VFPAEIVGKRTRVKLDGSKLVKVHLDKKQQNNVEHKVETFSAVYKKLTGKDVVFEFPEFT 191 (192)
T ss_pred cchhhhcceeEEEEecCcEEEEEEechhhccchHHhHHHHHHHHHHhcCCceEEecCccc
Confidence 999999999999999999999999999999999999999999999999999999999865
No 3
>PTZ00389 40S ribosomal protein S7; Provisional
Probab=100.00 E-value=6.3e-73 Score=452.37 Aligned_cols=138 Identities=59% Similarity=0.993 Sum_probs=134.5
Q ss_pred CeecCC-eeEEEEEeehhhHHHHHHHHHHHHHHHhhhcCCCeEEEEeeecccCCCCCCCc-ccccCCcchhHHHHHhhhc
Q 032455 1 MDVSGN-RKAIVVYVPYRLRKAYRKIHSRLVRELEKKFSGKDVVLIATRRIVRPPKKGSA-VQRPRSRTLTAVHDAMLED 78 (140)
Q Consensus 1 i~v~~~-kkaivIfVP~~~lk~f~kiq~rLv~ELEKKfsg~~Vv~iaqRrIl~kp~~k~~-q~rPRsRTLTaVhdaiLeD 78 (140)
|||++| |||||||||||||++|||||.||++|||||| |+||+|||||||||+|+++++ |+|||||||||||||||||
T Consensus 45 i~v~~~~kkaivIfVP~~~lk~~~kiq~rLv~ELEKK~-g~~Vv~ia~RrIl~kp~r~~~~q~rPrSRTLTaVhdaiLeD 123 (184)
T PTZ00389 45 VTVGKDKKKAVVVFVPYRMLMIYRKIQRKLIPELEKKL-KKHVVIVAQRTILKKPVKNYKLKTRPRSRTLTAVHEAILED 123 (184)
T ss_pred EEecCCCcEEEEEEecHHHHHHHHHHHHHHHHHHHHHh-CCeEEEEEEEEEcCCCCcCccccCCCCccchHHHHHHHHHH
Confidence 588777 9999999999999999999999999999999 999999999999999999886 9999999999999999999
Q ss_pred ccccceeeeeeEEEeeCCceEEEEEeCccccccchhhhhhHHHHHhhhhCCcEEEECCCCC
Q 032455 79 VVYPAEIVGKRVRYRLDGSKIIKIFLDPKERNNTEYKLESFSGVYRKLTGKDVVFDYPITD 139 (140)
Q Consensus 79 LV~PseIVGKRir~~~DGskl~KV~LD~~~~~~ve~Kl~tfs~VYkkLtgkdv~FeFp~~~ 139 (140)
||||+|||||||||++|||+++||+||++|++++|||+|+|++||++|||+||+||||+++
T Consensus 124 LvyPaeIvGkRir~~~DGsk~~KV~Ld~~d~~~ve~Kletf~~VykkLTgkdV~fefp~~~ 184 (184)
T PTZ00389 124 LVYPSEIVGKRTRVRVDGSKLLKVFLDPKDRKNVEEKLDAFSAVYKKLTGRDVVFEFPWDP 184 (184)
T ss_pred hccchheeeeEEEEecCCcEEEEEEeCHHHhcccchhHHHHHHHHHHHhCCCeEEEecCCC
Confidence 9999999999999999999999999999999999999999999999999999999999864
No 4
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=99.71 E-value=1.4e-17 Score=131.71 Aligned_cols=64 Identities=20% Similarity=0.320 Sum_probs=62.4
Q ss_pred HHHhhhcccccceeeeeeEEEeeCCceEEEEEeCccccccchhhhhhHHHHHhhhhCCcEEEEC
Q 032455 72 HDAMLEDVVYPAEIVGKRVRYRLDGSKIIKIFLDPKERNNTEYKLESFSGVYRKLTGKDVVFDY 135 (140)
Q Consensus 72 hdaiLeDLV~PseIVGKRir~~~DGskl~KV~LD~~~~~~ve~Kl~tfs~VYkkLtgkdv~FeF 135 (140)
-+.+|+||+||++|+|+|++++.||+..+||++|++|++++++|+++|++||++|||++|.|+|
T Consensus 102 ~~~fl~Nl~~PA~V~gV~i~~~~dG~~~~kV~Vd~~Dk~~l~~k~e~~~~v~~kltgk~v~~~f 165 (166)
T PRK06418 102 IKKLAVQLLSPARVLGVNTVWLPDGTVQYVIRVSRRDRRRLPAKPELLESILSKITGTEVKIRV 165 (166)
T ss_pred HHHHHHhcCCCcEEEEEEEEEeCCCcEEEEEEECHHHhhcccccHHHHHHHHHHHHCCcEEEEe
Confidence 4678999999999999999999999999999999999999999999999999999999999999
No 5
>TIGR01618 phage_P_loop phage nucleotide-binding protein. This model represents an uncharacterized family of proteins from a number of phage of Gram-positive bacteria. This protein contains a P-loop motif, G/A-X-X-G-X-G-K-T near its amino end. The function of this protein is unknown.
Probab=81.90 E-value=11 Score=31.02 Aligned_cols=93 Identities=19% Similarity=0.286 Sum_probs=59.3
Q ss_pred hhHHHHHHHHHHHH---HHHhhhcCCCeEEEEeeecccCCCCCCCcccccCCcchhHHHHHhhhcccccceeeeeeEEEe
Q 032455 17 RLRKAYRKIHSRLV---RELEKKFSGKDVVLIATRRIVRPPKKGSAVQRPRSRTLTAVHDAMLEDVVYPAEIVGKRVRYR 93 (140)
Q Consensus 17 ~~lk~f~kiq~rLv---~ELEKKfsg~~Vv~iaqRrIl~kp~~k~~q~rPRsRTLTaVhdaiLeDLV~PseIVGKRir~~ 93 (140)
+.+..|.+.+.+++ ..| +- .|++|+++|-+.+-..+ - ..-.+.+|=....++...+.+.--+++|| |+.+.
T Consensus 110 ~~~~~yg~~~~~fl~~l~~L-~~-~g~nII~tAhe~~~~~~-d--e~G~~~~r~~P~i~~K~~n~l~G~~DvV~-rl~i~ 183 (220)
T TIGR01618 110 PELQHYQKLDLWFLDLLTVL-KE-SNKNIYATAWELTNQSS-G--ESGQIYNRYQPDIREKVLNAFLGLTDVVG-RIVLN 183 (220)
T ss_pred cccccHHHHHHHHHHHHHHH-Hh-CCCcEEEEEeecccccc-C--CCCCCcceechhhhhhHHHhhcccccEEE-EEEEc
Confidence 35677888876655 455 22 59999999998542111 1 11224455566777888888888999999 66655
Q ss_pred e-CCceEEEEEeCccccccchhhhh
Q 032455 94 L-DGSKIIKIFLDPKERNNTEYKLE 117 (140)
Q Consensus 94 ~-DGskl~KV~LD~~~~~~ve~Kl~ 117 (140)
. +|.+.+ .+++.+.....++||
T Consensus 184 ~~~g~R~~--~~~~~~~~~AKNrld 206 (220)
T TIGR01618 184 GETGERGF--ILDPSKGNYAKNRLD 206 (220)
T ss_pred cCCCceEE--EECCCCCcccccccc
Confidence 4 466655 466666555555554
No 6
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=78.60 E-value=6.1 Score=32.12 Aligned_cols=61 Identities=16% Similarity=0.257 Sum_probs=52.5
Q ss_pred hhhcccccceeeeeeEEEeeCCceEEEEEeCccccccchhhhhhHHHHHhhhhCCcEEEECCC
Q 032455 75 MLEDVVYPAEIVGKRVRYRLDGSKIIKIFLDPKERNNTEYKLESFSGVYRKLTGKDVVFDYPI 137 (140)
Q Consensus 75 iLeDLV~PseIVGKRir~~~DGskl~KV~LD~~~~~~ve~Kl~tfs~VYkkLtgkdv~FeFp~ 137 (140)
.+-++++|+++++-.+... ||. .+.|.+.+.|...+--|-..-...-++|||..+..++..
T Consensus 121 fI~nal~Pa~v~~V~~~~~-d~~-~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~~~ 181 (190)
T COG0195 121 FIKNALAPAEVLSVNIKED-DGH-VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIETIS 181 (190)
T ss_pred HHHHhcCcceEeEEEEEeC-CCc-EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEehh
Confidence 4667888999999888877 776 889999999999888888888899999999999988753
No 7
>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=65.91 E-value=22 Score=25.62 Aligned_cols=45 Identities=9% Similarity=0.267 Sum_probs=35.8
Q ss_pred eEEEEEeehhhHHHHHHHHHHHHHHHhhhcCCCeEEEEeeecccC
Q 032455 8 KAIVVYVPYRLRKAYRKIHSRLVRELEKKFSGKDVVLIATRRIVR 52 (140)
Q Consensus 8 kaivIfVP~~~lk~f~kiq~rLv~ELEKKfsg~~Vv~iaqRrIl~ 52 (140)
-++|+.+-.....+|..+...+..++.+..++.++++++...=++
T Consensus 71 d~~ilv~d~~~~~s~~~~~~~~~~~i~~~~~~~piilv~nK~Dl~ 115 (174)
T smart00174 71 DVFLICFSVDSPASFENVKEKWYPEVKHFCPNTPIILVGTKLDLR 115 (174)
T ss_pred CEEEEEEECCCHHHHHHHHHHHHHHHHhhCCCCCEEEEecChhhh
Confidence 466666677788999999877888888878899999998865443
No 8
>PF01577 Peptidase_S30: Potyvirus P1 protease; InterPro: IPR002540 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. The potyviridae are a family of positive strand RNA viruses, members of which include Zucchini yellow mosaic virus, and Turnip mosaic virus (strain Japanese) which cause considerable losses of crops worldwide. This entry represents a C-terminal region from various plant potyvirus P1 proteins (found at the N terminus of the polyprotein). The C terminus of P1 is a serine peptidase belonging to MEROPS peptidase family S30 (clan PA(S)). It is the protease responsible for autocatalytic cleavage between P1 and the helper component protease, which is a cysteine peptidase belonging to MEROPS peptidase family C6 IPR001456 from INTERPRO [, ]. The P1 protein may be involved in virus-host interactions [].; GO: 0004197 cysteine-type endopeptidase activity, 0006508 proteolysis
Probab=56.83 E-value=18 Score=28.93 Aligned_cols=41 Identities=29% Similarity=0.537 Sum_probs=27.6
Q ss_pred CcchhHHHHHhhhccc-------ccceeeeeeE---E---EeeCCceEEEEEeC
Q 032455 65 SRTLTAVHDAMLEDVV-------YPAEIVGKRV---R---YRLDGSKIIKIFLD 105 (140)
Q Consensus 65 sRTLTaVhdaiLeDLV-------~PseIVGKRi---r---~~~DGskl~KV~LD 105 (140)
.-++++--+.++.+|+ .|-||+|||- + ++.+|+...+|.|-
T Consensus 102 ~~~~~~~~~~l~~~v~~i~~~~~~~vEiIgKrk~~~~~~~~~~~~~~~~kv~~~ 155 (245)
T PF01577_consen 102 KVKMSDTFDNLIRQVLKIAKKKGKPVEIIGKRKKRTRARYKRRGGKRYLKVETK 155 (245)
T ss_pred ccccchhHHHHHHHHHHHHHhcCCeEEEEecCCceEEEEEEEECCEEEEEEECC
Confidence 3344432445555544 3999999974 2 66789999999974
No 9
>cd00157 Rho Rho (Ras homology) family. Members of the Rho family include RhoA, Cdc42, Rac, Rnd, Wrch1, RhoBTB, and Rop. There are 22 human Rho family members identified currently. These proteins are all involved in the reorganization of the actin cytoskeleton in response to external stimuli. They also have roles in cell transformation by Ras in cytokinesis, in focal adhesion formation and in the stimulation of stress-activated kinase. These various functions are controlled through distinct effector proteins and mediated through a GTP-binding/GTPase cycle involving three classes of regulating proteins: GAPs (GTPase-activating proteins), GEFs (guanine nucleotide exchange factors), and GDIs (guanine nucleotide dissociation inhibitors). 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 protein
Probab=50.83 E-value=59 Score=23.05 Aligned_cols=45 Identities=9% Similarity=0.307 Sum_probs=35.5
Q ss_pred eEEEEEeehhhHHHHHHHHHHHHHHHhhhcCCCeEEEEeeecccC
Q 032455 8 KAIVVYVPYRLRKAYRKIHSRLVRELEKKFSGKDVVLIATRRIVR 52 (140)
Q Consensus 8 kaivIfVP~~~lk~f~kiq~rLv~ELEKKfsg~~Vv~iaqRrIl~ 52 (140)
.++++.+......+|......+..++....++.++++++...=++
T Consensus 73 ~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~p~ivv~nK~Dl~ 117 (171)
T cd00157 73 DVFLICFSVDSPSSFENVKTKWIPEIRHYCPNVPIILVGTKIDLR 117 (171)
T ss_pred CEEEEEEECCCHHHHHHHHHHHHHHHHhhCCCCCEEEEEccHHhh
Confidence 367777777788889888877888888877789999998865443
No 10
>TIGR01952 nusA_arch NusA family KH domain protein, archaeal. This model represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains (pfam00013) and is most closely related to the central region bacterial NusA, a transcription termination factor named for its iteraction with phage lambda protein N in E. coli. The proteins required for antitermination by N include NusA, NusB, nusE (ribosomal protein S10), and nusG. This system, on the whole, appears not to be present in the Archaea.
Probab=48.89 E-value=43 Score=25.96 Aligned_cols=57 Identities=16% Similarity=0.219 Sum_probs=37.8
Q ss_pred HhhhcccccceeeeeeEEEeeCCceEEEEEeCccccccchhhhhhHHHHHhhhhCCcE
Q 032455 74 AMLEDVVYPAEIVGKRVRYRLDGSKIIKIFLDPKERNNTEYKLESFSGVYRKLTGKDV 131 (140)
Q Consensus 74 aiLeDLV~PseIVGKRir~~~DGskl~KV~LD~~~~~~ve~Kl~tfs~VYkkLtgkdv 131 (140)
..+..+++|+++.+-.+.- .||++...|.+++.|...+=-|=--=...-++|||...
T Consensus 77 ~fI~N~l~PA~V~~V~i~~-~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~ 133 (141)
T TIGR01952 77 EFVANKLAPAEVKNVTVSE-FNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHH 133 (141)
T ss_pred HHHHHcCCCceEEEEEEEc-CCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCcc
Confidence 4566789999999886644 68889999999988865433332222233455665543
No 11
>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=44.33 E-value=82 Score=22.23 Aligned_cols=43 Identities=9% Similarity=0.288 Sum_probs=34.6
Q ss_pred eeEEEEEeehhhHHHHHHHHHHHHHHHhhhcC-CCeEEEEeeecc
Q 032455 7 RKAIVVYVPYRLRKAYRKIHSRLVRELEKKFS-GKDVVLIATRRI 50 (140)
Q Consensus 7 kkaivIfVP~~~lk~f~kiq~rLv~ELEKKfs-g~~Vv~iaqRrI 50 (140)
-.++++..-+....+|+.++ .+..++++... +.++++++...=
T Consensus 72 ~~~~ii~fd~~~~~S~~~~~-~~~~~i~~~~~~~~~iivvg~K~D 115 (162)
T PF00071_consen 72 SDAIIIVFDVTDEESFENLK-KWLEEIQKYKPEDIPIIVVGNKSD 115 (162)
T ss_dssp ESEEEEEEETTBHHHHHTHH-HHHHHHHHHSTTTSEEEEEEETTT
T ss_pred cccccccccccccccccccc-cccccccccccccccceeeecccc
Confidence 34777777889999999999 77788988887 688888887643
No 12
>PF01383 CpcD: CpcD/allophycocyanin linker domain; InterPro: IPR008213 Ferredoxin-NADP(+) oxydoreductase (FNR) (EC=1.18.1.2) transfers electrons from ferredoxin (or flavodoxin) to NADP(+) to generate NADPH. In eucaryotes, the nuclear-encoded, chloroplast-targeted enzyme contains two domains: an FAD-binding domain (see PDOC51384 from PROSITEDOC) and an NADP(+)-binding domain. With the exception of Gloeobacter violaceus PCC 7421, the predicted sequences of all cyanobacterial petH genes, encoding FNR, correspond to a protein containing three domains. Two domains at the C terminus correspond to the FAD- and NADP(+)-binding domains of higher plants FNR protein, which compose the catalytic domains of the enzyme. The N-terminal domain is similar to phycobilisome (PBS)-associated linker proteins from numerous cyanobacteria [, , ] and is associated with: - CpcD, the phycocyanin (PC)-associated, rod-capping, linker polypeptide of PBS. The similarity spans nearly the entire sequence of this linker class. - CpcC, the PC-associated rod linker polypeptide. The similarity is confined only to the C terminus of this linker class. - ApcC, the allophycocyanin (APC)-associated, core linker polypeptide. The similarity only correspond to about half of the molecule. The CpcD-like domain has an elongated shape and consists of a three-stranded beta-sheet, two alpha-helices, one of which has only about one turn, and the connecting random coil segments [].; GO: 0030089 phycobilisome; PDB: 1B33_O.
Probab=43.66 E-value=21 Score=23.57 Aligned_cols=21 Identities=24% Similarity=0.387 Sum_probs=14.1
Q ss_pred eeEEEEEeehhhHH-HHHHHHH
Q 032455 7 RKAIVVYVPYRLRK-AYRKIHS 27 (140)
Q Consensus 7 kkaivIfVP~~~lk-~f~kiq~ 27 (140)
+..-..+|||.+|. .+|.||.
T Consensus 24 rs~~~~~Vpy~~ls~~~q~I~r 45 (56)
T PF01383_consen 24 RSNQTYVVPYSQLSQEMQRINR 45 (56)
T ss_dssp HHEEEEEEEHHHHHHHHHHHHH
T ss_pred eeeEEEEEcHHHhHHHHHHHHH
Confidence 44556679999994 4566653
No 13
>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=43.63 E-value=91 Score=22.36 Aligned_cols=41 Identities=12% Similarity=0.222 Sum_probs=31.0
Q ss_pred EEEEEeehhhHHHHHHHHHHHHHHHhhhcCCCeEEEEeeec
Q 032455 9 AIVVYVPYRLRKAYRKIHSRLVRELEKKFSGKDVVLIATRR 49 (140)
Q Consensus 9 aivIfVP~~~lk~f~kiq~rLv~ELEKKfsg~~Vv~iaqRr 49 (140)
++++.+-.....+|+.+...+.++|.+..++.++++++...
T Consensus 74 ~~ilv~~~~~~~s~~~~~~~~~~~l~~~~~~~piivv~nK~ 114 (174)
T cd04135 74 VFLICFSVVNPASFQNVKEEWVPELKEYAPNVPYLLVGTQI 114 (174)
T ss_pred EEEEEEECCCHHHHHHHHHHHHHHHHhhCCCCCEEEEeEch
Confidence 34444455667899999888888998777889999998763
No 14
>cd04130 Wrch_1 Wrch-1 subfamily. Wrch-1 (Wnt-1 responsive Cdc42 homolog) is a Rho family GTPase that shares significant sequence and functional similarity with Cdc42. Wrch-1 was first identified in mouse mammary epithelial cells, where its transcription is upregulated in Wnt-1 transformation. Wrch-1 contains N- and C-terminal extensions relative to cdc42, suggesting potential differences in cellular localization and function. The Wrch-1 N-terminal extension contains putative SH3 domain-binding motifs and has been shown to bind the SH3 domain-containing protein Grb2, which increases the level of active Wrch-1 in cells. Unlike Cdc42, which localizes to the cytosol and perinuclear membranes, Wrch-1 localizes extensively with the plasma membrane and endosomes. The membrane association, localization, and biological activity of Wrch-1 indicate an atypical model of regulation distinct from other Rho family GTPases. Most Rho proteins contain a lipid modification site at the C-terminus,
Probab=41.42 E-value=96 Score=22.58 Aligned_cols=43 Identities=12% Similarity=0.276 Sum_probs=32.6
Q ss_pred EEEEEeehhhHHHHHHHHHHHHHHHhhhcCCCeEEEEeeeccc
Q 032455 9 AIVVYVPYRLRKAYRKIHSRLVRELEKKFSGKDVVLIATRRIV 51 (140)
Q Consensus 9 aivIfVP~~~lk~f~kiq~rLv~ELEKKfsg~~Vv~iaqRrIl 51 (140)
++|+.+.+..-.+|+.+...++.++.+..++..+++++...=+
T Consensus 74 ~~i~v~d~~~~~sf~~~~~~~~~~~~~~~~~~piilv~nK~Dl 116 (173)
T cd04130 74 VFLLCFSVVNPSSFQNISEKWIPEIRKHNPKAPIILVGTQADL 116 (173)
T ss_pred EEEEEEECCCHHHHHHHHHHHHHHHHhhCCCCCEEEEeeChhh
Confidence 5555556677789998877778888877778899999887544
No 15
>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=41.23 E-value=1e+02 Score=22.12 Aligned_cols=43 Identities=9% Similarity=0.232 Sum_probs=31.9
Q ss_pred EEEEEeehhhHHHHHHHHHHHHHHHhhhcCCCeEEEEeeeccc
Q 032455 9 AIVVYVPYRLRKAYRKIHSRLVRELEKKFSGKDVVLIATRRIV 51 (140)
Q Consensus 9 aivIfVP~~~lk~f~kiq~rLv~ELEKKfsg~~Vv~iaqRrIl 51 (140)
++++...+....+|..+...+..++.+..++.++++++...=+
T Consensus 75 ~~i~v~~~~~~~s~~~~~~~~~~~~~~~~~~~piilv~nK~Dl 117 (175)
T cd01870 75 VILMCFSIDSPDSLENIPEKWTPEVKHFCPNVPIILVGNKKDL 117 (175)
T ss_pred EEEEEEECCCHHHHHHHHHHHHHHHHhhCCCCCEEEEeeChhc
Confidence 4555556777788888877778888776678899999876444
No 16
>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=40.61 E-value=1.1e+02 Score=22.13 Aligned_cols=41 Identities=7% Similarity=0.169 Sum_probs=30.0
Q ss_pred EEEEEeehhhHHHHHHHHHHHHHHHhhhcCCCeEEEEeeec
Q 032455 9 AIVVYVPYRLRKAYRKIHSRLVRELEKKFSGKDVVLIATRR 49 (140)
Q Consensus 9 aivIfVP~~~lk~f~kiq~rLv~ELEKKfsg~~Vv~iaqRr 49 (140)
++++.+......+|..+...+..+++....+.++++++...
T Consensus 73 ~~ilv~d~~~~~s~~~~~~~~~~~i~~~~~~~pviiv~nK~ 113 (166)
T cd01893 73 VICLVYSVDRPSTLERIRTKWLPLIRRLGVKVPIILVGNKS 113 (166)
T ss_pred EEEEEEECCCHHHHHHHHHHHHHHHHHhCCCCCEEEEEEch
Confidence 45555567778889888777777777655578999998753
No 17
>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=40.55 E-value=1e+02 Score=23.13 Aligned_cols=44 Identities=18% Similarity=0.339 Sum_probs=32.9
Q ss_pred EEEEEeehhhHHHHHHHHHHHHHHHhhhcCCCeEEEEeeecccC
Q 032455 9 AIVVYVPYRLRKAYRKIHSRLVRELEKKFSGKDVVLIATRRIVR 52 (140)
Q Consensus 9 aivIfVP~~~lk~f~kiq~rLv~ELEKKfsg~~Vv~iaqRrIl~ 52 (140)
++|+..-+....+|+.+....+.++....++.+++++|...=|+
T Consensus 74 ~~ilv~dv~~~~sf~~~~~~~~~~i~~~~~~~piilvgNK~Dl~ 117 (189)
T cd04134 74 VIMLCFSVDSPDSLENVESKWLGEIREHCPGVKLVLVALKCDLR 117 (189)
T ss_pred EEEEEEECCCHHHHHHHHHHHHHHHHHhCCCCCEEEEEEChhhc
Confidence 45555556778899988766678887766788999999975554
No 18
>cd01874 Cdc42 Cdc42 subfamily. Cdc42 is an essential GTPase that belongs to the Rho family of Ras-like GTPases. These proteins act as molecular switches by responding to exogenous and/or endogenous signals and relaying those signals to activate downstream components of a biological pathway. Cdc42 transduces signals to the actin cytoskeleton to initiate and maintain polarized growth and to mitogen-activated protein morphogenesis. In the budding yeast Saccharomyces cerevisiae, Cdc42 plays an important role in multiple actin-dependent morphogenetic events such as bud emergence, mating-projection formation, and pseudohyphal growth. In mammalian cells, Cdc42 regulates a variety of actin-dependent events and induces the JNK/SAPK protein kinase cascade, which leads to the activation of transcription factors within the nucleus. Cdc42 mediates these processes through interactions with a myriad of downstream effectors, whose number and regulation we are just starting to understand. In addi
Probab=37.44 E-value=1.2e+02 Score=22.56 Aligned_cols=43 Identities=12% Similarity=0.239 Sum_probs=31.5
Q ss_pred EEEEEeehhhHHHHHHHHHHHHHHHhhhcCCCeEEEEeeeccc
Q 032455 9 AIVVYVPYRLRKAYRKIHSRLVRELEKKFSGKDVVLIATRRIV 51 (140)
Q Consensus 9 aivIfVP~~~lk~f~kiq~rLv~ELEKKfsg~~Vv~iaqRrIl 51 (140)
++|+.+=+....+|..+...+..|+++.-++.++++++...=+
T Consensus 75 ~~ilv~d~~~~~s~~~~~~~w~~~i~~~~~~~piilvgnK~Dl 117 (175)
T cd01874 75 VFLVCFSVVSPSSFENVKEKWVPEITHHCPKTPFLLVGTQIDL 117 (175)
T ss_pred EEEEEEECCCHHHHHHHHHHHHHHHHHhCCCCCEEEEEECHhh
Confidence 5555555677789999876677888776667899999886433
No 19
>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=36.65 E-value=1.2e+02 Score=22.10 Aligned_cols=43 Identities=14% Similarity=0.284 Sum_probs=33.6
Q ss_pred eEEEEEeehhhHHHHHHHHHHHHHHHhhhcCCCeEEEEeeeccc
Q 032455 8 KAIVVYVPYRLRKAYRKIHSRLVRELEKKFSGKDVVLIATRRIV 51 (140)
Q Consensus 8 kaivIfVP~~~lk~f~kiq~rLv~ELEKKfsg~~Vv~iaqRrIl 51 (140)
-|+|+.+-.....+|+.++. .+.++.+...+.+++++|...=+
T Consensus 74 d~~i~v~d~~~~~s~~~~~~-~~~~i~~~~~~~piiiv~nK~Dl 116 (166)
T cd00877 74 QCAIIMFDVTSRVTYKNVPN-WHRDLVRVCGNIPIVLCGNKVDI 116 (166)
T ss_pred CEEEEEEECCCHHHHHHHHH-HHHHHHHhCCCCcEEEEEEchhc
Confidence 46777778888899998864 67788877668899999886544
No 20
>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=34.37 E-value=1.4e+02 Score=22.49 Aligned_cols=45 Identities=11% Similarity=0.304 Sum_probs=34.1
Q ss_pred eEEEEEeehhhHHHHHHHHHHHHHHHhhhcCCCeEEEEeeecccC
Q 032455 8 KAIVVYVPYRLRKAYRKIHSRLVRELEKKFSGKDVVLIATRRIVR 52 (140)
Q Consensus 8 kaivIfVP~~~lk~f~kiq~rLv~ELEKKfsg~~Vv~iaqRrIl~ 52 (140)
.++|+..-+....+|..++..+..++....++-+++++|...=|+
T Consensus 76 ~~~ilvydit~~~Sf~~~~~~w~~~i~~~~~~~piilvgNK~DL~ 120 (191)
T cd01875 76 NVFIICFSIASPSSYENVRHKWHPEVCHHCPNVPILLVGTKKDLR 120 (191)
T ss_pred CEEEEEEECCCHHHHHHHHHHHHHHHHhhCCCCCEEEEEeChhhh
Confidence 356666666778899999876677777666788999999987664
No 21
>PF06858 NOG1: Nucleolar GTP-binding protein 1 (NOG1); InterPro: IPR010674 This domain represents a conserved region of approximately 60 residues in length within nucleolar GTP-binding protein 1 (NOG1). The NOG1 family includes eukaryotic, bacterial and archaeal proteins. In Saccharomyces cerevisiae, the NOG1 gene has been shown to be essential for cell viability, suggesting that NOG1 may play an important role in nucleolar functions. In particular, NOG1 is believed to be functionally linked to ribosome biogenesis, which occurs in the nucleolus. In eukaryotes, NOG1 mutants were found to disrupt the biogenesis of the 60S ribosomal subunit []. The DRG and OBG proteins as well as the prokaryotic NOG-like proteins are homologous throughout their length to the amino half of eukaryotic NOG1, which contains the GTP binding motifs (IPR006073 from INTERPRO); the N-terminal GTP-binding motif is required for function.; GO: 0005525 GTP binding; PDB: 2E87_A.
Probab=33.95 E-value=59 Score=22.05 Aligned_cols=24 Identities=21% Similarity=0.419 Sum_probs=19.6
Q ss_pred HHHHHHHHHHhhhcCCCeEEEEee
Q 032455 24 KIHSRLVRELEKKFSGKDVVLIAT 47 (140)
Q Consensus 24 kiq~rLv~ELEKKfsg~~Vv~iaq 47 (140)
.-|..|-.|+..-|++++++.+..
T Consensus 32 e~Q~~L~~~ik~~F~~~P~i~V~n 55 (58)
T PF06858_consen 32 EEQLSLFKEIKPLFPNKPVIVVLN 55 (58)
T ss_dssp HHHHHHHHHHHHHTTTS-EEEEE-
T ss_pred HHHHHHHHHHHHHcCCCCEEEEEe
Confidence 459999999999999999988864
No 22
>cd04172 Rnd3_RhoE_Rho8 Rnd3/RhoE/Rho8 subfamily. Rnd3/RhoE/Rho8 is a member of the novel Rho subfamily Rnd, together with Rnd1/Rho6 and Rnd2/Rho7. Rnd3/RhoE is known to bind the serine-threonine kinase ROCK I. Unphosphorylated Rnd3/RhoE associates primarily with membranes, but ROCK I-phosphorylated Rnd3/RhoE localizes in the cytosol. Phosphorylation of Rnd3/RhoE correlates with its activity in disrupting RhoA-induced stress fibers and inhibiting Ras-induced fibroblast transformation. In cells that lack stress fibers, such as macrophages and monocytes, Rnd3/RhoE induces a redistribution of actin, causing morphological changes in the cell. In addition, Rnd3/RhoE has been shown to inhibit cell cycle progression in G1 phase at a point upstream of the pRb family pocket protein checkpoint. Rnd3/RhoE has also been shown to inhibit Ras- and Raf-induced fibroblast transformation. In mammary epithelial tumor cells, Rnd3/RhoE regulates the assembly of the apical junction complex and tight
Probab=33.88 E-value=1.4e+02 Score=22.74 Aligned_cols=44 Identities=7% Similarity=0.196 Sum_probs=33.9
Q ss_pred eEEEEEeehhhHHHHHHHHHHHHHHHhhhcCCCeEEEEeeeccc
Q 032455 8 KAIVVYVPYRLRKAYRKIHSRLVRELEKKFSGKDVVLIATRRIV 51 (140)
Q Consensus 8 kaivIfVP~~~lk~f~kiq~rLv~ELEKKfsg~~Vv~iaqRrIl 51 (140)
.++++..-+....+|..+..+++.++.+-.++.++++||...=|
T Consensus 78 d~~ilvyDit~~~Sf~~~~~~w~~~i~~~~~~~piilVgNK~DL 121 (182)
T cd04172 78 DAVLICFDISRPETLDSVLKKWKGEIQEFCPNTKMLLVGCKSDL 121 (182)
T ss_pred CEEEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCEEEEeEChhh
Confidence 46666666788899999877778888776677889999986544
No 23
>cd04173 Rnd2_Rho7 Rnd2/Rho7 subfamily. Rnd2/Rho7 is a member of the novel Rho subfamily Rnd, together with Rnd1/Rho6 and Rnd3/RhoE/Rho8. Rnd2/Rho7 is transiently expressed in radially migrating cells in the brain while they are within the subventricular zone of the hippocampus and cerebral cortex. These migrating cells typically develop into pyramidal neurons. Cells that exogenously expressed Rnd2/Rho7 failed to migrate to upper layers of the brain, suggesting that Rnd2/Rho7 plays a role in the radial migration and morphological changes of developing pyramidal neurons, and that Rnd2/Rho7 degradation is necessary for proper cellular migration. The Rnd2/Rho7 GEF Rapostlin is found primarily in the brain and together with Rnd2/Rho7 induces dendrite branching. Unlike Rnd1/Rho6 and Rnd3/RhoE/Rho8, which are RhoA antagonists, Rnd2/Rho7 binds the GEF Pragmin and significantly stimulates RhoA activity and Rho-A mediated cell contraction. Rnd2/Rho7 is also found to be expressed in sperma
Probab=32.32 E-value=1.5e+02 Score=23.89 Aligned_cols=44 Identities=11% Similarity=0.172 Sum_probs=35.0
Q ss_pred eEEEEEeehhhHHHHHHHHHHHHHHHhhhcCCCeEEEEeeeccc
Q 032455 8 KAIVVYVPYRLRKAYRKIHSRLVRELEKKFSGKDVVLIATRRIV 51 (140)
Q Consensus 8 kaivIfVP~~~lk~f~kiq~rLv~ELEKKfsg~~Vv~iaqRrIl 51 (140)
-++++.+-+....+|..+...+..|+....++-++++|+...=|
T Consensus 74 d~illvfdis~~~Sf~~i~~~w~~~~~~~~~~~piiLVgnK~DL 117 (222)
T cd04173 74 DAVLICFDISRPETLDSVLKKWQGETQEFCPNAKVVLVGCKLDM 117 (222)
T ss_pred CEEEEEEECCCHHHHHHHHHHHHHHHHhhCCCCCEEEEEECccc
Confidence 46777777888899999987777888777778899999886433
No 24
>PF02374 ArsA_ATPase: Anion-transporting ATPase; PDB: 2WOO_A 3IBG_B 3SJA_A 3H84_B 3SJD_A 3ZS9_A 3A37_A 2WOJ_A 3SJC_B 3A36_B ....
Probab=32.31 E-value=80 Score=26.76 Aligned_cols=32 Identities=25% Similarity=0.316 Sum_probs=26.8
Q ss_pred hhHHHHHHHHHHHHHHHhhhcCCCeEEEEeee
Q 032455 17 RLRKAYRKIHSRLVRELEKKFSGKDVVLIATR 48 (140)
Q Consensus 17 ~~lk~f~kiq~rLv~ELEKKfsg~~Vv~iaqR 48 (140)
+-+.+.++.|.+.+.++++.|+|.+|+-+-..
T Consensus 255 ~~~~~r~~~Q~~~l~~i~~~f~~~~v~~vp~~ 286 (305)
T PF02374_consen 255 PFCAARRKEQQKYLAEIEESFPDLPVVKVPLL 286 (305)
T ss_dssp HHHHHHHHHHHHHHHHHHHHTTTSEEEEEE--
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCEEEecCC
Confidence 45788999999999999999999998877553
No 25
>smart00175 RAB Rab subfamily of small GTPases. Rab GTPases are implicated in vesicle trafficking.
Probab=31.58 E-value=1.8e+02 Score=20.26 Aligned_cols=40 Identities=10% Similarity=0.274 Sum_probs=29.8
Q ss_pred eEEEEEeehhhHHHHHHHHHHHHHHHhhhc-CCCeEEEEeee
Q 032455 8 KAIVVYVPYRLRKAYRKIHSRLVRELEKKF-SGKDVVLIATR 48 (140)
Q Consensus 8 kaivIfVP~~~lk~f~kiq~rLv~ELEKKf-sg~~Vv~iaqR 48 (140)
-++++.+......+|..+.. ++.++++-. ++.++++++..
T Consensus 74 d~~ilv~d~~~~~s~~~~~~-~l~~~~~~~~~~~pivvv~nK 114 (164)
T smart00175 74 VGALLVYDITNRESFENLKN-WLKELREYADPNVVIMLVGNK 114 (164)
T ss_pred CEEEEEEECCCHHHHHHHHH-HHHHHHHhCCCCCeEEEEEEc
Confidence 36777777788889988875 666776544 57889999874
No 26
>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=30.24 E-value=1.9e+02 Score=21.13 Aligned_cols=44 Identities=7% Similarity=0.224 Sum_probs=31.9
Q ss_pred eEEEEEeehhhHHHHHHHHHHHHHHHhhhcCCCeEEEEeeeccc
Q 032455 8 KAIVVYVPYRLRKAYRKIHSRLVRELEKKFSGKDVVLIATRRIV 51 (140)
Q Consensus 8 kaivIfVP~~~lk~f~kiq~rLv~ELEKKfsg~~Vv~iaqRrIl 51 (140)
.++++.+......+|..+...++.++..--++.++++++...=+
T Consensus 74 d~ii~v~d~~~~~s~~~~~~~~~~~~~~~~~~~piilv~nK~Dl 117 (187)
T cd04132 74 DVLLICYAVDNPTSLDNVEDKWFPEVNHFCPGTPIMLVGLKTDL 117 (187)
T ss_pred CEEEEEEECCCHHHHHHHHHHHHHHHHHhCCCCCEEEEEeChhh
Confidence 46777778888899998876666677554456789999886544
No 27
>cd04129 Rho2 Rho2 subfamily. Rho2 is a fungal GTPase that plays a role in cell morphogenesis, control of cell wall integrity, control of growth polarity, and maintenance of growth direction. Rho2 activates the protein kinase C homolog Pck2, and Pck2 controls Mok1, the major (1-3) alpha-D-glucan synthase. Together with Rho1 (RhoA), Rho2 regulates the construction of the cell wall. Unlike Rho1, Rho2 is not an essential protein, but its overexpression is lethal. 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 proper intracellular localization via membrane attachment. As with other Rho family GTPases, the GDP/GTP cycling is regulated by GEFs (guanine nucleotide exchange factors), GAPs (GTPase-activating proteins) and GDIs (guanine nucleotide dissociation inhibitors).
Probab=30.14 E-value=1.9e+02 Score=21.58 Aligned_cols=41 Identities=10% Similarity=0.306 Sum_probs=31.0
Q ss_pred EEEEEeehhhHHHHHHHHHHHHHHHhhhcCCCeEEEEeeec
Q 032455 9 AIVVYVPYRLRKAYRKIHSRLVRELEKKFSGKDVVLIATRR 49 (140)
Q Consensus 9 aivIfVP~~~lk~f~kiq~rLv~ELEKKfsg~~Vv~iaqRr 49 (140)
++++..-+....+|+.+...+..++.+..+..++++|+...
T Consensus 75 ~~llv~~i~~~~s~~~~~~~~~~~i~~~~~~~piilvgnK~ 115 (187)
T cd04129 75 VILIGFAVDTPDSLENVRTKWIEEVRRYCPNVPVILVGLKK 115 (187)
T ss_pred EEEEEEECCCHHHHHHHHHHHHHHHHHhCCCCCEEEEeeCh
Confidence 44544556777899999877788887777778899998863
No 28
>cd01873 RhoBTB RhoBTB subfamily. Members of the RhoBTB subfamily of Rho GTPases are present in vertebrates, Drosophila, and Dictyostelium. RhoBTB proteins are characterized by a modular organization, consisting of a GTPase domain, a proline rich region, a tandem of two BTB (Broad-Complex, Tramtrack, and Bric a brac) domains, and a C-terminal region of unknown function. RhoBTB proteins may act as docking points for multiple components participating in signal transduction cascades. RhoBTB genes appeared upregulated in some cancer cell lines, suggesting a participation of RhoBTB proteins in the pathogenesis of particular tumors. Note that the Dictyostelium RacA GTPase domain is more closely related to Rac proteins than to RhoBTB proteins, where RacA actually belongs. Thus, the Dictyostelium RacA is not included here. Most Rho proteins contain a lipid modification site at the C-terminus; however, RhoBTB is one of few Rho subfamilies that lack this feature.
Probab=28.93 E-value=1.9e+02 Score=22.42 Aligned_cols=45 Identities=11% Similarity=0.211 Sum_probs=33.7
Q ss_pred eEEEEEeehhhHHHHHHHHHHHHHHHhhhcCCCeEEEEeeecccC
Q 032455 8 KAIVVYVPYRLRKAYRKIHSRLVRELEKKFSGKDVVLIATRRIVR 52 (140)
Q Consensus 8 kaivIfVP~~~lk~f~kiq~rLv~ELEKKfsg~~Vv~iaqRrIl~ 52 (140)
.++++..-+....+|..+...++.++.+..++.+++++|...=|+
T Consensus 89 d~iilv~d~t~~~Sf~~~~~~w~~~i~~~~~~~piilvgNK~DL~ 133 (195)
T cd01873 89 DVVLLCFSIASPNSLRNVKTMWYPEIRHFCPRVPVILVGCKLDLR 133 (195)
T ss_pred CEEEEEEECCChhHHHHHHHHHHHHHHHhCCCCCEEEEEEchhcc
Confidence 456777777888999988766677887665677899998875554
No 29
>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=28.13 E-value=2.1e+02 Score=21.23 Aligned_cols=44 Identities=7% Similarity=0.263 Sum_probs=32.5
Q ss_pred eEEEEEeehhhHHHHHHHHHHHHHHHhhhcCCCeEEEEeeeccc
Q 032455 8 KAIVVYVPYRLRKAYRKIHSRLVRELEKKFSGKDVVLIATRRIV 51 (140)
Q Consensus 8 kaivIfVP~~~lk~f~kiq~rLv~ELEKKfsg~~Vv~iaqRrIl 51 (140)
-|+|+.+-+....+|..+...+..++...-++.++++++...=|
T Consensus 74 d~~ilv~d~~~~~sf~~~~~~~~~~~~~~~~~~piilvgnK~Dl 117 (174)
T cd01871 74 DVFLICFSLVSPASFENVRAKWYPEVRHHCPNTPIILVGTKLDL 117 (174)
T ss_pred CEEEEEEECCCHHHHHHHHHHHHHHHHHhCCCCCEEEEeeChhh
Confidence 46666677777889998876667777666567889999886444
No 30
>cd02970 PRX_like2 Peroxiredoxin (PRX)-like 2 family; hypothetical proteins that show sequence similarity to PRXs. Members of this group contain a CXXC motif, similar to TRX. The second cysteine in the motif corresponds to the peroxidatic cysteine of PRX, however, these proteins do not contain the other two residues of the catalytic triad of PRX. PRXs confer a protective antioxidant role in cells through their peroxidase activity in which hydrogen peroxide, peroxynitrate, and organic hydroperoxides are reduced and detoxified using reducing equivalents derived from either thioredoxin, glutathione, trypanothione and AhpF. TRXs alter the redox state of target proteins by catalyzing the reduction of their disulfide bonds via the CXXC motif using reducing equivalents derived from either NADPH or ferredoxins.
Probab=28.04 E-value=1.2e+02 Score=21.12 Aligned_cols=42 Identities=21% Similarity=0.188 Sum_probs=24.3
Q ss_pred CCeeEEEEEeehhhHHHHHHHHHHHHHHHhhhcCCCeEEEEee
Q 032455 5 GNRKAIVVYVPYRLRKAYRKIHSRLVRELEKKFSGKDVVLIAT 47 (140)
Q Consensus 5 ~~kkaivIfVP~~~lk~f~kiq~rLv~ELEKKfsg~~Vv~iaq 47 (140)
++++.+|+|++-.-...++. +..-+.++-.+|.++.+.+++-
T Consensus 22 ~~~~~vl~f~~~~~Cp~C~~-~~~~l~~~~~~~~~~~v~vv~V 63 (149)
T cd02970 22 GEGPVVVVFYRGFGCPFCRE-YLRALSKLLPELDALGVELVAV 63 (149)
T ss_pred cCCCEEEEEECCCCChhHHH-HHHHHHHHHHHHHhcCeEEEEE
Confidence 35678889988655555553 3444455666664444555543
No 31
>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=27.45 E-value=2.1e+02 Score=21.71 Aligned_cols=43 Identities=21% Similarity=0.296 Sum_probs=31.0
Q ss_pred EEEEEeehhhHHHHHHHHHHHHHHHhhhcCCCeEEEEeeeccc
Q 032455 9 AIVVYVPYRLRKAYRKIHSRLVRELEKKFSGKDVVLIATRRIV 51 (140)
Q Consensus 9 aivIfVP~~~lk~f~kiq~rLv~ELEKKfsg~~Vv~iaqRrIl 51 (140)
++|+..=+....+|..+...+++++.+.-++-+++++|...=|
T Consensus 75 ~~ilvyd~~~~~Sf~~~~~~w~~~i~~~~~~~piilvgnK~Dl 117 (176)
T cd04133 75 VFVLAFSLISRASYENVLKKWVPELRHYAPNVPIVLVGTKLDL 117 (176)
T ss_pred EEEEEEEcCCHHHHHHHHHHHHHHHHHhCCCCCEEEEEeChhh
Confidence 5555556777899999866677888655456788888876444
No 32
>PF08534 Redoxin: Redoxin; InterPro: IPR013740 This redoxin domain is found in peroxiredoxin, thioredoxin and glutaredoxin proteins. Peroxiredoxins (Prxs) constitute a family of thiol peroxidases that reduce hydrogen peroxide, peroxinitrite, and hydroperoxides using a strictly conserved cysteine []. Chloroplast thioredoxin systems in plants regulate the enzymes involved in photosynthetic carbon assimilation []. It is thought that redoxins have a large role to play in anti-oxidant defence. Cadmium-sensitive proteins are also regulated via thioredoxin and glutaredoxin thiol redox systems [].; GO: 0016491 oxidoreductase activity; PDB: 2H30_A 1TP9_A 1Y25_A 1XVQ_A 2B1K_A 2G0F_A 2B1L_B 3K8N_A 1Z5Y_E 3OR5_A ....
Probab=27.42 E-value=1.3e+02 Score=21.34 Aligned_cols=39 Identities=21% Similarity=0.331 Sum_probs=25.1
Q ss_pred CeeEEEEEeehhhHHHHHHHHHHHHHHHhhhcCCCeEEEE
Q 032455 6 NRKAIVVYVPYRLRKAYRKIHSRLVRELEKKFSGKDVVLI 45 (140)
Q Consensus 6 ~kkaivIfVP~~~lk~f~kiq~rLv~ELEKKfsg~~Vv~i 45 (140)
||..+|.|.+-.-.-.+++ +.-.+.+|-+++.++.|.++
T Consensus 28 gk~~vv~f~~~~~Cp~C~~-~~p~l~~l~~~~~~~~v~~v 66 (146)
T PF08534_consen 28 GKPVVVNFWASAWCPPCRK-ELPYLNELQEKYKDKGVDVV 66 (146)
T ss_dssp TSEEEEEEESTTTSHHHHH-HHHHHHHHHHHHHTTTCEEE
T ss_pred CCeEEEEEEccCCCCcchh-hhhhHHhhhhhhccCceEEE
Confidence 6888888888734445554 33377888777655544444
No 33
>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=26.99 E-value=2.1e+02 Score=22.09 Aligned_cols=43 Identities=19% Similarity=0.382 Sum_probs=33.4
Q ss_pred eEEEEEeehhhHHHHHHHHHHHHHHHhhhcCCCeEEEEeeeccc
Q 032455 8 KAIVVYVPYRLRKAYRKIHSRLVRELEKKFSGKDVVLIATRRIV 51 (140)
Q Consensus 8 kaivIfVP~~~lk~f~kiq~rLv~ELEKKfsg~~Vv~iaqRrIl 51 (140)
.++|+.+-+....+|..+. ..+.|+.+-.++-.+++||...=|
T Consensus 80 d~illVfD~t~~~Sf~~~~-~w~~~i~~~~~~~piilVGNK~DL 122 (189)
T cd04121 80 QGIILVYDITNRWSFDGID-RWIKEIDEHAPGVPKILVGNRLHL 122 (189)
T ss_pred CEEEEEEECcCHHHHHHHH-HHHHHHHHhCCCCCEEEEEECccc
Confidence 4777777788899999995 567888776788889999975433
No 34
>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=26.75 E-value=2.4e+02 Score=20.26 Aligned_cols=40 Identities=13% Similarity=0.224 Sum_probs=29.2
Q ss_pred EEEEEeehhhHHHHHHHHHHHHHHHhhhcCCCeEEEEeeec
Q 032455 9 AIVVYVPYRLRKAYRKIHSRLVRELEKKFSGKDVVLIATRR 49 (140)
Q Consensus 9 aivIfVP~~~lk~f~kiq~rLv~ELEKKfsg~~Vv~iaqRr 49 (140)
++++.+....-.+|..++. ++.++.+..++.++++++...
T Consensus 75 ~~i~v~d~~~~~s~~~~~~-~~~~i~~~~~~~p~ivv~nK~ 114 (161)
T cd04124 75 ACILVFDVTRKITYKNLSK-WYEELREYRPEIPCIVVANKI 114 (161)
T ss_pred EEEEEEECCCHHHHHHHHH-HHHHHHHhCCCCcEEEEEECc
Confidence 5666667777788888764 557776666788999998863
No 35
>PF13479 AAA_24: AAA domain
Probab=26.46 E-value=1.2e+02 Score=23.81 Aligned_cols=62 Identities=16% Similarity=0.261 Sum_probs=33.5
Q ss_pred HHHHHHHHHHHHHHHhhh--cCCCeEEEEeeecccCCCCC-CCcccccCCcchhHHHHHhhhcccccceee
Q 032455 19 RKAYRKIHSRLVRELEKK--FSGKDVVLIATRRIVRPPKK-GSAVQRPRSRTLTAVHDAMLEDVVYPAEIV 86 (140)
Q Consensus 19 lk~f~kiq~rLv~ELEKK--fsg~~Vv~iaqRrIl~kp~~-k~~q~rPRsRTLTaVhdaiLeDLV~PseIV 86 (140)
++.|..++..+.+-+.+- ..|+||||+|.-..-.-+.. ...+.+|. .+....+-+.+-+++|
T Consensus 105 ~~~yg~~~~~~~~~i~~l~~~~~~~VI~tah~~~~~~~~~~~~~~~~~~------l~~k~~~~l~~~~D~V 169 (213)
T PF13479_consen 105 GKGYGELQQEFMRFIDKLLNALGKNVIFTAHAKEEEDEDGGKYTRYKPK------LGKKVRNELPGWFDVV 169 (213)
T ss_pred cchHHHHHHHHHHHHHHHHHHCCCcEEEEEEEEEEEcCCCCceeEEeec------cChhHHhhhhecccEE
Confidence 566766665555555432 24999999997655433211 11222332 2334445555666777
No 36
>cd04131 Rnd Rnd subfamily. The Rnd subfamily contains Rnd1/Rho6, Rnd2/Rho7, and Rnd3/RhoE/Rho8. These novel Rho family proteins have substantial structural differences compared to other Rho members, including N- and C-terminal extensions relative to other Rhos. Rnd3/RhoE is farnesylated at the C-terminal prenylation site, unlike most other Rho proteins that are geranylgeranylated. In addition, Rnd members are unable to hydrolyze GTP and are resistant to GAP activity. They are believed to exist only in the GTP-bound conformation, and are antagonists of RhoA activity. 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=26.28 E-value=2.3e+02 Score=21.35 Aligned_cols=44 Identities=9% Similarity=0.207 Sum_probs=32.3
Q ss_pred eEEEEEeehhhHHHHHHHHHHHHHHHhhhcCCCeEEEEeeeccc
Q 032455 8 KAIVVYVPYRLRKAYRKIHSRLVRELEKKFSGKDVVLIATRRIV 51 (140)
Q Consensus 8 kaivIfVP~~~lk~f~kiq~rLv~ELEKKfsg~~Vv~iaqRrIl 51 (140)
.++++..-+....+|..+...++.++..-.++-++++||...=|
T Consensus 74 ~~~ilvfdit~~~Sf~~~~~~w~~~i~~~~~~~~iilVgnK~DL 117 (178)
T cd04131 74 DAVLICFDISRPETLDSVLKKWRGEIQEFCPNTKVLLVGCKTDL 117 (178)
T ss_pred CEEEEEEECCChhhHHHHHHHHHHHHHHHCCCCCEEEEEEChhh
Confidence 35666666678899998766677888765567788999886544
No 37
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=26.06 E-value=2.1e+02 Score=21.87 Aligned_cols=58 Identities=12% Similarity=0.267 Sum_probs=37.8
Q ss_pred HHhhhcccccceeeeeeEEEeeCCceEEEEEeCccccccchhhhhhHHHHHhhhhCCcE
Q 032455 73 DAMLEDVVYPAEIVGKRVRYRLDGSKIIKIFLDPKERNNTEYKLESFSGVYRKLTGKDV 131 (140)
Q Consensus 73 daiLeDLV~PseIVGKRir~~~DGskl~KV~LD~~~~~~ve~Kl~tfs~VYkkLtgkdv 131 (140)
...+.+++.|+++.+-.+. .-++++.+.|.+++.|...+=-|=-.=-...++|+|+..
T Consensus 75 ~~fI~n~l~Pa~V~~v~I~-~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~ 132 (140)
T PRK08406 75 EEFIKNIFAPAAVRSVTIK-KKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHF 132 (140)
T ss_pred HHHHHHHcCCCEEEEEEEE-ecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCcc
Confidence 4568889999999888664 335678899999887765543332222234556666543
No 38
>cd08971 AcNei2_N N-terminal domain of the actinomycetal Nei2 and related DNA glycosylases. This family contains the N-terminal domain of the actinomycetal Nei2 and related DNA glycosylases. It belongs to the FpgNei_N, [N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII)] domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. They initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycosylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. This family contains mostly actinom
Probab=25.71 E-value=1.2e+02 Score=22.03 Aligned_cols=60 Identities=25% Similarity=0.377 Sum_probs=35.5
Q ss_pred HHHHHHhhhcCCCeEEEEeeecccCCCCCCCcccccCCcchhHHHHHhhhcccccceeeeeeEEEeeCCceEEEEEeC
Q 032455 28 RLVRELEKKFSGKDVVLIATRRIVRPPKKGSAVQRPRSRTLTAVHDAMLEDVVYPAEIVGKRVRYRLDGSKIIKIFLD 105 (140)
Q Consensus 28 rLv~ELEKKfsg~~Vv~iaqRrIl~kp~~k~~q~rPRsRTLTaVhdaiLeDLV~PseIVGKRir~~~DGskl~KV~LD 105 (140)
.+.+.|++.+.|+.+.-+--++ ++ .-...-..||++ -.+=.||.+-+.+|+...+-+||-
T Consensus 9 ~v~~~L~~~~~G~~I~~v~~~~----~~--~~~~~l~G~~i~------------~v~R~GK~L~~~l~~~~~l~vHLg 68 (114)
T cd08971 9 RAARRLRRALAGRVLTRADLRV----PR--LATADLAGRTVE------------EVVARGKHLLIRFDGGLTLHTHLR 68 (114)
T ss_pred HHHHHHHHHhCCCEEEEEEecC----ch--hhhhhcCCCEEE------------EEEEeeeEEEEEcCCCCEEEEeCC
Confidence 4667899999998886553221 10 011122233333 345689999999875556767764
No 39
>TIGR02110 PQQ_syn_pqqF coenzyme PQQ biosynthesis probable peptidase PqqF. In a subset of species that make coenzyme PQQ (pyrrolo-quinoline-quinone), this probable peptidase is found in the PQQ biosynthesis region and is thought to act as a protease on PqqA (TIGR02107), a probable peptide precursor of the coenzyme. PQQ is required for some glucose dehydrogenases and alcohol dehydrogenases.
Probab=24.34 E-value=1.7e+02 Score=28.25 Aligned_cols=46 Identities=30% Similarity=0.543 Sum_probs=32.6
Q ss_pred eecCCeeEEEEEeehh--h---HHHHH--------HHHHHHHHHHhhhcCCCeEEEEeeeccc
Q 032455 2 DVSGNRKAIVVYVPYR--L---RKAYR--------KIHSRLVRELEKKFSGKDVVLIATRRIV 51 (140)
Q Consensus 2 ~v~~~kkaivIfVP~~--~---lk~f~--------kiq~rLv~ELEKKfsg~~Vv~iaqRrIl 51 (140)
.+.|+-.|+++|.|.| . ..++| ...+||=-|| -. | +|||.+-|++-
T Consensus 610 ~~~~~e~alllf~p~~~~~~~~~aa~rlla~l~~~~f~qrlRve~--ql-G-Y~v~~~~~~~~ 668 (696)
T TIGR02110 610 ACDGGEQALLLFCPLPTADVASEAAWRLLAQLLEPPFFQRLRVEL--QL-G-YVVFCRYRRVA 668 (696)
T ss_pred cCCCCCcEEEEEecCCCCCHHHHHHHHHHHHHhchhHHHHHHHhh--cc-c-eEEEEeeEEcC
Confidence 4567889999999999 3 44554 2345555444 45 6 99999999874
No 40
>COG4496 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.32 E-value=24 Score=26.51 Aligned_cols=26 Identities=31% Similarity=0.475 Sum_probs=21.9
Q ss_pred cccCCcchhHHHHHhh------------hcccccceee
Q 032455 61 QRPRSRTLTAVHDAML------------EDVVYPAEIV 86 (140)
Q Consensus 61 ~rPRsRTLTaVhdaiL------------eDLV~PseIV 86 (140)
.+||+.+|.+..|||| +|||-|.||-
T Consensus 4 ~klr~~~Ld~l~dailtL~n~eecy~FfdDlcTinEiq 41 (100)
T COG4496 4 EKLRGAALDELFDAILTLENLEECYAFFDDLCTINEIQ 41 (100)
T ss_pred cchhhHHHHHHHHHHHHhccHHHHHHHHHhhcCHHHHH
Confidence 3678899999999885 7999999983
No 41
>cd03018 PRX_AhpE_like Peroxiredoxin (PRX) family, AhpE-like subfamily; composed of proteins similar to Mycobacterium tuberculosis AhpE. AhpE is described as a 1-cys PRX because of the absence of a resolving cysteine. The structure and sequence of AhpE, however, show greater similarity to 2-cys PRXs than 1-cys PRXs. PRXs are thiol-specific antioxidant (TSA) proteins that confer a protective role in cells through their peroxidase activity in which hydrogen peroxide, peroxynitrate, and organic hydroperoxides are reduced and detoxified using reducing equivalents derived from either thioredoxin, glutathione, trypanothione and AhpF. The first step of catalysis is the nucleophilic attack by the peroxidatic cysteine on the peroxide leading to the formation of a cysteine sulfenic acid intermediate. The absence of a resolving cysteine suggests that functional AhpE is regenerated by an external reductant. The solution behavior and crystal structure of AhpE show that it forms dimers and octamers.
Probab=23.31 E-value=1.1e+02 Score=21.68 Aligned_cols=39 Identities=13% Similarity=0.305 Sum_probs=19.1
Q ss_pred eeEEEEEeehhhHHHHHHHHHHHHHHHhhhcCCCeEEEEe
Q 032455 7 RKAIVVYVPYRLRKAYRKIHSRLVRELEKKFSGKDVVLIA 46 (140)
Q Consensus 7 kkaivIfVP~~~lk~f~kiq~rLv~ELEKKfsg~~Vv~ia 46 (140)
+..+|+|.|..-...+.+ |..-+.++.++|.++.+.+++
T Consensus 29 k~~vl~f~~~~~c~~C~~-~~~~l~~~~~~~~~~~v~vi~ 67 (149)
T cd03018 29 KPVVLVFFPLAFTPVCTK-ELCALRDSLELFEAAGAEVLG 67 (149)
T ss_pred CeEEEEEeCCCCCccHHH-HHHHHHHHHHHHHhCCCEEEE
Confidence 566777876532333332 333344555555433444444
No 42
>PRK10470 ribosome hibernation promoting factor HPF; Provisional
Probab=22.46 E-value=32 Score=23.85 Aligned_cols=35 Identities=11% Similarity=0.163 Sum_probs=30.7
Q ss_pred EEeCccccccchhhhhhHHHHHhhhhCCcEEEECC
Q 032455 102 IFLDPKERNNTEYKLESFSGVYRKLTGKDVVFDYP 136 (140)
Q Consensus 102 V~LD~~~~~~ve~Kl~tfs~VYkkLtgkdv~FeFp 136 (140)
+.+.++.++.++.|++-+...|...+..+|.++..
T Consensus 10 i~~t~al~~~v~~kl~kL~r~~~~i~~~~V~l~~~ 44 (95)
T PRK10470 10 VEITEALREFVTAKFAKLEQYFDRINQVYVVLKVE 44 (95)
T ss_pred eccCHHHHHHHHHHHHHHHHhcCCCceEEEEEEEe
Confidence 45778899999999999999999999999998864
No 43
>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=21.73 E-value=3e+02 Score=19.49 Aligned_cols=41 Identities=7% Similarity=0.301 Sum_probs=29.1
Q ss_pred eEEEEEeehhhHHHHHHHHHHHHHHHhhhc-CCCeEEEEeeec
Q 032455 8 KAIVVYVPYRLRKAYRKIHSRLVRELEKKF-SGKDVVLIATRR 49 (140)
Q Consensus 8 kaivIfVP~~~lk~f~kiq~rLv~ELEKKf-sg~~Vv~iaqRr 49 (140)
.++++.+-.....+|..+.. +..++++.. ++..+++++...
T Consensus 76 ~~ii~v~d~~~~~s~~~l~~-~~~~~~~~~~~~~~~iiv~nK~ 117 (166)
T cd01869 76 HGIIIVYDVTDQESFNNVKQ-WLQEIDRYASENVNKLLVGNKC 117 (166)
T ss_pred CEEEEEEECcCHHHHHhHHH-HHHHHHHhCCCCCcEEEEEECh
Confidence 46777777777889988876 556665543 467889988764
No 44
>cd00936 WEPRS_RNA WEPRS_RNA binding domain. This short RNA-binding domain is found in several higher eukaryote aminoacyl-tRNA synthetases (aaRSs). It is found in multiple copies in eukaryotic bifunctional glutamyl-prolyl-tRNA synthetases (EPRS) in a region that separates the N-terminal glutamyl-tRNA synthetase (GluRS) from the C-terminal prolyl-tRNA synthetase (ProRS). It is also found at the N-terminus of vertebrate tryptophanyl-tRNA synthetases (TrpRS). This domain consists of a helix-turn-helix structure, which is similar to other RNA-binding proteins. It is involved in both protein-RNA interactions by binding tRNA and protein-protein interactions, which are important for the formation of aaRSs into multienzyme complexes.
Probab=20.89 E-value=68 Score=20.22 Aligned_cols=18 Identities=33% Similarity=0.516 Sum_probs=14.7
Q ss_pred hhhhhHHHHHhhhhCCcE
Q 032455 114 YKLESFSGVYRKLTGKDV 131 (140)
Q Consensus 114 ~Kl~tfs~VYkkLtgkdv 131 (140)
.+|-....=|+.+||+|.
T Consensus 30 ~~Ll~lK~~~k~~tg~~~ 47 (50)
T cd00936 30 KKLLALKADYKEATGQDY 47 (50)
T ss_pred HHHHHHHHHHHHhcCCCC
Confidence 466677888999999985
No 45
>PF00408 PGM_PMM_IV: Phosphoglucomutase/phosphomannomutase, C-terminal domain; InterPro: IPR005843 The alpha-D-phosphohexomutase superfamily is composed of four related enzymes, each of which catalyses a phosphoryl transfer on their sugar substrates: phosphoglucomutase (PGM), phosphoglucomutase/phosphomannomutase (PGM/PMM), phosphoglucosamine mutase (PNGM), and phosphoacetylglucosamine mutase (PAGM) []. PGM (5.4.2.2 from EC) converts D-glucose 1-phosphate into D-glucose 6-phosphate, and participates in both the breakdown and synthesis of glucose []. PGM/PMM (5.4.2.2 from EC; 5.4.2.8 from EC) are primarily bacterial enzymes that use either glucose or mannose as substrate, participating in the biosynthesis of a variety of carbohydrates such as lipopolysaccharides and alginate [, ]. Both PNGM (5.4.2.3 from EC) and PAGM (5.4.2.10 from EC) are involved in the biosynthesis of UDP-N-acetylglucosamine [, ]. Despite differences in substrate specificity, these enzymes share a similar catalytic mechanism, converting 1-phospho-sugars to 6-phospho-sugars via a biphosphorylated 1,6-phospho-sugar. The active enzyme is phosphorylated at a conserved serine residue and binds one magnesium ion; residues around the active site serine are well conserved among family members. The reaction mechanism involves phosphoryl transfer from the phosphoserine to the substrate to create a biophosphorylated sugar, followed by a phosphoryl transfer from the substrate back to the enzyme []. The structures of PGM and PGM/PMM have been determined, and were found to be very similar in topology. These enzymes are both composed of four domains and a large central active site cleft, where each domain contains residues essential for catalysis and/or substrate recognition. Domain I contains the catalytic phosphoserine, domain II contains a metal-binding loop to coordinate the magnesium ion, domain III contains the sugar-binding loop that recognises the two different binding orientations of the 1- and 6-phospho-sugars, and domain IV contains a phosphate-binding site required for orienting the incoming phospho-sugar substrate. This entry represents the C-terminal domain alpha-D-phosphohexomutase enzymes.; GO: 0016868 intramolecular transferase activity, phosphotransferases, 0005975 carbohydrate metabolic process; PDB: 1KFQ_B 1KFI_A 3PDK_B 2F7L_A 1TUO_A 2FKM_X 3C04_A 1K2Y_X 1P5G_X 2H4L_X ....
Probab=20.78 E-value=1.3e+02 Score=19.77 Aligned_cols=35 Identities=20% Similarity=0.382 Sum_probs=24.7
Q ss_pred eeeEEEeeCCc-eEEEEEeCccccccchhhhhhHHH
Q 032455 87 GKRVRYRLDGS-KIIKIFLDPKERNNTEYKLESFSG 121 (140)
Q Consensus 87 GKRir~~~DGs-kl~KV~LD~~~~~~ve~Kl~tfs~ 121 (140)
|-++.+|..|+ .+++|++...++..++.-.+.+..
T Consensus 35 G~~l~vR~SgTEP~iRv~~Ea~~~~~~~~~~~~i~~ 70 (73)
T PF00408_consen 35 GWRLLVRPSGTEPKIRVYVEAPDEEELEEIAEEIAE 70 (73)
T ss_dssp EEEEEEEEESSSSEEEEEEEESSHHHHHHHHHHHHH
T ss_pred ceEEEEECCCCCceEEEEEEeCCHHHHHHHHHHHHH
Confidence 56666777776 679999988877766655555444
No 46
>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=20.55 E-value=3.2e+02 Score=21.87 Aligned_cols=46 Identities=4% Similarity=0.060 Sum_probs=33.8
Q ss_pred eEEEEEeehhhHHHHHHHHHHHHHHHhhhcCCCeEEEEeeecccCC
Q 032455 8 KAIVVYVPYRLRKAYRKIHSRLVRELEKKFSGKDVVLIATRRIVRP 53 (140)
Q Consensus 8 kaivIfVP~~~lk~f~kiq~rLv~ELEKKfsg~~Vv~iaqRrIl~k 53 (140)
-++|+.+-+....+|..+..++...++..-++..+++|+...=|..
T Consensus 69 d~~IlV~Dvt~~~Sf~~l~~~~~~l~~~~~~~~piIlVgNK~DL~~ 114 (220)
T cd04126 69 AAVILTYDVSNVQSLEELEDRFLGLTDTANEDCLFAVVGNKLDLTE 114 (220)
T ss_pred CEEEEEEECCCHHHHHHHHHHHHHHHHhcCCCCcEEEEEECccccc
Confidence 3666666777888999998888777665555678899988755543
No 47
>PF14085 DUF4265: Domain of unknown function (DUF4265)
Probab=20.08 E-value=1.1e+02 Score=22.52 Aligned_cols=61 Identities=21% Similarity=0.377 Sum_probs=37.9
Q ss_pred hhcccc--cceeeeeeEEEee---CCceEEEEEeCcccc---ccchhhhhhHHHHHhhhhCCcEEEECCCC
Q 032455 76 LEDVVY--PAEIVGKRVRYRL---DGSKIIKIFLDPKER---NNTEYKLESFSGVYRKLTGKDVVFDYPIT 138 (140)
Q Consensus 76 LeDLV~--PseIVGKRir~~~---DGskl~KV~LD~~~~---~~ve~Kl~tfs~VYkkLtgkdv~FeFp~~ 138 (140)
+.|+|. +.+ |...-.++ .|...++|+++.... +.+...|+.+..-+....+.-+.++.|..
T Consensus 28 ~gDvV~~~~~~--g~~~~~~~v~~sGnsTiRv~~~~~~~~~~~~v~~~l~~lG~~~E~~~~~~lav~VP~~ 96 (117)
T PF14085_consen 28 LGDVVRAEPDD--GELWFQKVVESSGNSTIRVIFDDPGPDDIEAVREELEALGCTVEGFSERMLAVDVPPS 96 (117)
T ss_pred CCCEEEEEeCC--CeEEEEEEEecCCCEEEEEEEcCCcchhHHHHHHHHHHcCCeEEccCCCEEEEEECCC
Confidence 456555 222 55555555 999999999876655 44555566555555555565666666644
No 48
>PRK14962 DNA polymerase III subunits gamma and tau; Provisional
Probab=20.04 E-value=1e+02 Score=27.97 Aligned_cols=37 Identities=22% Similarity=0.352 Sum_probs=29.0
Q ss_pred EEEEeCccccc---cchhhhhhHHHHHhhhhCCcEEEECC
Q 032455 100 IKIFLDPKERN---NTEYKLESFSGVYRKLTGKDVVFDYP 136 (140)
Q Consensus 100 ~KV~LD~~~~~---~ve~Kl~tfs~VYkkLtgkdv~FeFp 136 (140)
++|-.|+.++= .++.+.+.|..+|+++.|+++.++|-
T Consensus 410 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 449 (472)
T PRK14962 410 VKISFDSSKAMHYELMKEKLPELENLFSRKLGKNVEVELR 449 (472)
T ss_pred EEEEeChHHhHHHHHHHHhHHHHHHHHHHHhCCCeeEEEE
Confidence 55666655543 36679999999999999999999874
Done!