Query 032387
Match_columns 142
No_of_seqs 139 out of 228
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 13:25:58 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032387.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032387hhsearch_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 9.6E-80 2.1E-84 494.3 12.0 141 1-141 45-189 (189)
2 KOG3320 40S ribosomal protein 100.0 1.9E-75 4.1E-80 467.9 15.0 141 1-141 50-191 (192)
3 PTZ00389 40S ribosomal protein 100.0 2.3E-74 5E-79 461.7 15.7 140 1-141 43-184 (184)
4 PRK06418 transcription elongat 99.7 1.2E-17 2.6E-22 132.4 6.7 87 29-137 79-165 (166)
5 TIGR01618 phage_P_loop phage n 81.3 11 0.00025 30.9 8.1 95 19-119 110-206 (220)
6 COG0195 NusA Transcription elo 80.7 4.7 0.0001 32.9 5.6 61 77-139 121-181 (190)
7 smart00174 RHO Rho (Ras homolo 65.3 23 0.00049 25.6 5.5 45 10-54 71-115 (174)
8 cd00157 Rho Rho (Ras homology) 51.0 58 0.0012 23.2 5.5 45 10-54 73-117 (171)
9 TIGR01952 nusA_arch NusA famil 49.0 42 0.00091 26.1 4.8 57 76-133 77-133 (141)
10 PF01577 Peptidase_S30: Potyvi 47.4 89 0.0019 25.0 6.7 25 83-107 125-155 (245)
11 PF01383 CpcD: CpcD/allophycoc 43.9 24 0.00051 23.4 2.4 21 9-29 24-45 (56)
12 cd04135 Tc10 TC10 subfamily. 42.1 98 0.0021 22.3 5.6 41 11-51 74-114 (174)
13 cd04130 Wrch_1 Wrch-1 subfamil 41.1 96 0.0021 22.6 5.5 44 10-53 73-116 (173)
14 PF00071 Ras: Ras family; Int 40.6 93 0.002 22.0 5.2 42 9-51 72-114 (162)
15 cd01893 Miro1 Miro1 subfamily. 39.9 1.1E+02 0.0024 22.1 5.7 41 11-51 73-113 (166)
16 cd01870 RhoA_like RhoA-like su 39.7 1.1E+02 0.0024 22.0 5.6 43 11-53 75-117 (175)
17 cd04134 Rho3 Rho3 subfamily. 38.8 1.1E+02 0.0024 23.0 5.7 44 11-54 74-117 (189)
18 PF01883 DUF59: Domain of unkn 38.6 68 0.0015 20.9 4.0 40 1-41 27-66 (72)
19 cd00877 Ran Ran (Ras-related n 37.2 1.2E+02 0.0026 22.3 5.5 44 10-54 74-117 (166)
20 cd01874 Cdc42 Cdc42 subfamily. 36.2 1.3E+02 0.0028 22.5 5.6 44 10-53 74-117 (175)
21 PF02374 ArsA_ATPase: Anion-tr 33.3 76 0.0017 26.9 4.4 31 19-49 255-285 (305)
22 cd01875 RhoG RhoG subfamily. 32.6 1.6E+02 0.0034 22.3 5.7 45 10-54 76-120 (191)
23 cd04172 Rnd3_RhoE_Rho8 Rnd3/Rh 32.6 1.5E+02 0.0033 22.6 5.7 44 10-53 78-121 (182)
24 PF06858 NOG1: Nucleolar GTP-b 31.6 71 0.0015 21.7 3.2 24 26-49 32-55 (58)
25 PF13479 AAA_24: AAA domain 31.1 63 0.0014 25.5 3.4 62 21-88 105-169 (213)
26 cd04173 Rnd2_Rho7 Rnd2/Rho7 su 31.1 1.5E+02 0.0034 23.8 5.7 44 10-53 74-117 (222)
27 smart00175 RAB Rab subfamily o 31.0 1.9E+02 0.0041 20.2 5.7 40 10-50 74-114 (164)
28 PF08534 Redoxin: Redoxin; In 29.8 1.2E+02 0.0026 21.6 4.4 40 8-48 28-67 (146)
29 cd02970 PRX_like2 Peroxiredoxi 29.4 1.2E+02 0.0027 21.2 4.4 42 7-49 22-63 (149)
30 cd04132 Rho4_like Rho4-like su 28.6 2.1E+02 0.0045 21.0 5.6 44 10-53 74-117 (187)
31 cd04129 Rho2 Rho2 subfamily. 28.6 2E+02 0.0044 21.4 5.6 41 11-51 75-115 (187)
32 PRK08406 transcription elongat 27.8 1.8E+02 0.0039 22.3 5.3 58 75-133 75-132 (140)
33 cd01873 RhoBTB RhoBTB subfamil 26.9 2.1E+02 0.0046 22.2 5.6 46 9-54 88-133 (195)
34 cd01871 Rac1_like Rac1-like su 26.7 2.3E+02 0.0049 21.1 5.6 44 10-53 74-117 (174)
35 cd04133 Rop_like Rop subfamily 26.2 2.3E+02 0.0049 21.6 5.6 44 10-53 74-117 (176)
36 cd04124 RabL2 RabL2 subfamily. 26.0 2.5E+02 0.0053 20.2 5.6 40 11-51 75-114 (161)
37 cd04121 Rab40 Rab40 subfamily. 25.2 2.3E+02 0.005 21.9 5.5 44 9-53 79-122 (189)
38 cd08971 AcNei2_N N-terminal do 25.2 1.2E+02 0.0025 22.2 3.7 60 30-107 9-68 (114)
39 cd04131 Rnd Rnd subfamily. Th 24.9 2.5E+02 0.0054 21.2 5.6 44 10-53 74-117 (178)
40 cd04910 ACT_AK-Ectoine_1 ACT d 24.1 1.9E+02 0.0041 20.0 4.4 31 8-43 38-68 (71)
41 cd00936 WEPRS_RNA WEPRS_RNA bi 22.5 64 0.0014 20.4 1.6 18 116-133 30-47 (50)
42 COG4496 Uncharacterized protei 22.1 28 0.00061 26.2 -0.1 32 63-94 4-49 (100)
43 cd01869 Rab1_Ypt1 Rab1/Ypt1 su 20.9 3.2E+02 0.0069 19.4 5.5 41 10-51 76-117 (166)
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=9.6e-80 Score=494.30 Aligned_cols=141 Identities=63% Similarity=0.988 Sum_probs=121.3
Q ss_pred CeeeecCCeeEEEEEecchhHHHHHHHHHHHHHHHHhhcCCCeEEEEeeeeecCCCCCC----CcccccCCcchhHHHHh
Q 032387 1 MQIDVPGNRKAVVIHIPYRLRKAYRKIHTKLVRELEKKFSGKDVILIATRRILRPPKKG----SAVQRPRSRTLTSVHEA 76 (142)
Q Consensus 1 kei~v~~~kkaivifVP~~~lk~f~kiq~rLv~ELEKKfsg~~Vv~iaqRrIl~kp~~~----~~qkrPRSRTLTaVhda 76 (142)
||||||+|+||||||||||||++|||||.||++||||||||+||+|||||||||+|+++ .+|+|||||||||||||
T Consensus 45 KEi~v~~~kKAivIfVP~~~lk~f~KIq~rLv~ELEKKfsgk~Vv~iAqRrIl~kp~r~~~~~~~qkrPRSRTLTaVhda 124 (189)
T PF01251_consen 45 KEIEVGGGKKAIVIFVPVPQLKAFQKIQVRLVRELEKKFSGKHVVFIAQRRILPKPTRKSRQKQKQKRPRSRTLTAVHDA 124 (189)
T ss_dssp EEEEECTCEEEEEEEE-CCCCHHHHHHCHHHHHHHHHCTTTCEEEEEE------SS-SSS---TTS---CCCSHHHHHHH
T ss_pred EEEEECCCcEEEEEEEcHHHHHHHHHHHHHHHHHHHhhcCCCeEEEeccceEcCCCCcCccccccccCcCCcchHHHHHH
Confidence 69999999999999999999999999999999999999999999999999999999887 48999999999999999
Q ss_pred hhhcccccceeeeeeEEEeeCCcEEEEEEeCccccccchhhhhHHHHHHHHhhCCcEEEECCCCC
Q 032387 77 MLEDVVLPAEIVGKRIRYRLDGSKIMKVFLDPKERNNTEYKLDTFAAVYRKLSGKDVVFDFPVTE 141 (142)
Q Consensus 77 iLeDLv~PseIvGKRir~~~DGskl~KV~LD~~~~~~ve~Kl~tfs~VYkkLTgKdv~FeFp~~~ 141 (142)
||||||||+|||||||||++|||+++|||||++|||++|||+|||++|||+||||||+||||+++
T Consensus 125 ILeDLV~PseIVGKRir~rlDGskl~KV~LD~k~~~~ve~Kl~tfs~VYkkLTgK~v~FeFp~~~ 189 (189)
T PF01251_consen 125 ILEDLVYPSEIVGKRIRVRLDGSKLIKVHLDKKDQNNVEHKLDTFSAVYKKLTGKDVVFEFPEQE 189 (189)
T ss_dssp HHHHHTTTS-ECEEEEEE-TTS-EEEEEEEECCCCHHHHCCHHHHHHHHHHHCS-EEEEEEE---
T ss_pred HHHhhccHHHhheeeEEEecCCCEEEEEEEChHHcccHHHHHHHHHHHHHHHcCCceEEEcCCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999864
No 2
>KOG3320 consensus 40S ribosomal protein S7 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.9e-75 Score=467.86 Aligned_cols=141 Identities=62% Similarity=0.964 Sum_probs=138.7
Q ss_pred CeeeecCCeeEEEEEecchhHHHHHHHHHHHHHHHHhhcCCCeEEEEeeeeecCCCCCCCc-ccccCCcchhHHHHhhhh
Q 032387 1 MQIDVPGNRKAVVIHIPYRLRKAYRKIHTKLVRELEKKFSGKDVILIATRRILRPPKKGSA-VQRPRSRTLTSVHEAMLE 79 (142)
Q Consensus 1 kei~v~~~kkaivifVP~~~lk~f~kiq~rLv~ELEKKfsg~~Vv~iaqRrIl~kp~~~~~-qkrPRSRTLTaVhdaiLe 79 (142)
+|||||||+||||||||+|+|++|||||.+|+|||||||||+||+|||+|||||+|++++. ||||||||||||||||||
T Consensus 50 ~eiev~Gg~Kaivi~VP~p~lk~fqki~~~LvreleKKF~gk~Vifia~Rrilpkp~rks~~qKRprsrtltaVhdaiLe 129 (192)
T KOG3320|consen 50 KEIEVGGGRKAIVIFVPVPQLKAFQKIQVRLVRELEKKFSGKHVIFIAQRRILPKPTRKSRTQKRPRSRTLTAVHDAILE 129 (192)
T ss_pred EEEEecCCcEEEEEEechHHHHHHHHHHHHHHHHHHHhcCCceEEEEEeeeeccCCCCCcccccCCccchHHHHHHHHHH
Confidence 5899999999999999999999999999999999999999999999999999999999997 899999999999999999
Q ss_pred cccccceeeeeeEEEeeCCcEEEEEEeCccccccchhhhhHHHHHHHHhhCCcEEEECCCCC
Q 032387 80 DVVLPAEIVGKRIRYRLDGSKIMKVFLDPKERNNTEYKLDTFAAVYRKLSGKDVVFDFPVTE 141 (142)
Q Consensus 80 DLv~PseIvGKRir~~~DGskl~KV~LD~~~~~~ve~Kl~tfs~VYkkLTgKdv~FeFp~~~ 141 (142)
|+|||+|||||||||++||++++|||||++|+||+|||+|+|++||++||||||+||||+.+
T Consensus 130 d~vfP~eIvGkR~rv~ldg~ki~kV~LD~~~~n~~e~K~e~f~~vy~kLtGKdv~fEfp~~~ 191 (192)
T KOG3320|consen 130 DLVFPAEIVGKRTRVKLDGSKLVKVHLDKKQQNNVEHKVETFSAVYKKLTGKDVVFEFPEFT 191 (192)
T ss_pred hccchhhhcceeEEEEecCcEEEEEEechhhccchHHhHHHHHHHHHHhcCCceEEecCccc
Confidence 99999999999999999999999999999999999999999999999999999999999864
No 3
>PTZ00389 40S ribosomal protein S7; Provisional
Probab=100.00 E-value=2.3e-74 Score=461.67 Aligned_cols=140 Identities=59% Similarity=0.957 Sum_probs=136.9
Q ss_pred CeeeecCC-eeEEEEEecchhHHHHHHHHHHHHHHHHhhcCCCeEEEEeeeeecCCCCCCCc-ccccCCcchhHHHHhhh
Q 032387 1 MQIDVPGN-RKAVVIHIPYRLRKAYRKIHTKLVRELEKKFSGKDVILIATRRILRPPKKGSA-VQRPRSRTLTSVHEAML 78 (142)
Q Consensus 1 kei~v~~~-kkaivifVP~~~lk~f~kiq~rLv~ELEKKfsg~~Vv~iaqRrIl~kp~~~~~-qkrPRSRTLTaVhdaiL 78 (142)
|||||++| |||||||||||||++|||||.||++|||||| |+||+|||||||||+|+++++ |+|||||||||||||||
T Consensus 43 kei~v~~~~kkaivIfVP~~~lk~~~kiq~rLv~ELEKK~-g~~Vv~ia~RrIl~kp~r~~~~q~rPrSRTLTaVhdaiL 121 (184)
T PTZ00389 43 KEVTVGKDKKKAVVVFVPYRMLMIYRKIQRKLIPELEKKL-KKHVVIVAQRTILKKPVKNYKLKTRPRSRTLTAVHEAIL 121 (184)
T ss_pred EEEEecCCCcEEEEEEecHHHHHHHHHHHHHHHHHHHHHh-CCeEEEEEEEEEcCCCCcCccccCCCCccchHHHHHHHH
Confidence 69999887 9999999999999999999999999999999 999999999999999999986 99999999999999999
Q ss_pred hcccccceeeeeeEEEeeCCcEEEEEEeCccccccchhhhhHHHHHHHHhhCCcEEEECCCCC
Q 032387 79 EDVVLPAEIVGKRIRYRLDGSKIMKVFLDPKERNNTEYKLDTFAAVYRKLSGKDVVFDFPVTE 141 (142)
Q Consensus 79 eDLv~PseIvGKRir~~~DGskl~KV~LD~~~~~~ve~Kl~tfs~VYkkLTgKdv~FeFp~~~ 141 (142)
||||||+|||||||||++|||+++||+||++|++++|||+|+|++||++|||+||.||||+++
T Consensus 122 eDLvyPaeIvGkRir~~~DGsk~~KV~Ld~~d~~~ve~Kletf~~VykkLTgkdV~fefp~~~ 184 (184)
T PTZ00389 122 EDLVYPSEIVGKRTRVRVDGSKLLKVFLDPKDRKNVEEKLDAFSAVYKKLTGRDVVFEFPWDP 184 (184)
T ss_pred HHhccchheeeeEEEEecCCcEEEEEEeCHHHhcccchhHHHHHHHHHHHhCCCeEEEecCCC
Confidence 999999999999999999999999999999999999999999999999999999999999864
No 4
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=99.71 E-value=1.2e-17 Score=132.39 Aligned_cols=87 Identities=18% Similarity=0.391 Sum_probs=76.1
Q ss_pred HHHHHHHHhhcCCCeEEEEeeeeecCCCCCCCcccccCCcchhHHHHhhhhcccccceeeeeeEEEeeCCcEEEEEEeCc
Q 032387 29 TKLVRELEKKFSGKDVILIATRRILRPPKKGSAVQRPRSRTLTSVHEAMLEDVVLPAEIVGKRIRYRLDGSKIMKVFLDP 108 (142)
Q Consensus 29 ~rLv~ELEKKfsg~~Vv~iaqRrIl~kp~~~~~qkrPRSRTLTaVhdaiLeDLv~PseIvGKRir~~~DGskl~KV~LD~ 108 (142)
...++.|++++ ||+|=+|- .|-+ -+.+|+||+||++|+|+|++++.||+..+||++|+
T Consensus 79 G~~ik~l~~~l-gk~VevVE-----------------~s~d----~~~fl~Nl~~PA~V~gV~i~~~~dG~~~~kV~Vd~ 136 (166)
T PRK06418 79 GKIAKALSRKL-GKKVRVVE-----------------KTND----IKKLAVQLLSPARVLGVNTVWLPDGTVQYVIRVSR 136 (166)
T ss_pred chHHHHHHHHh-CCcEEEEE-----------------cCCC----HHHHHHhcCCCcEEEEEEEEEeCCCcEEEEEEECH
Confidence 45667777777 77776663 2222 46789999999999999999999999999999999
Q ss_pred cccccchhhhhHHHHHHHHhhCCcEEEEC
Q 032387 109 KERNNTEYKLDTFAAVYRKLSGKDVVFDF 137 (142)
Q Consensus 109 ~~~~~ve~Kl~tfs~VYkkLTgKdv~FeF 137 (142)
+|++++++|+++|++||++|||++|.|+|
T Consensus 137 ~Dk~~l~~k~e~~~~v~~kltgk~v~~~f 165 (166)
T PRK06418 137 RDRRRLPAKPELLESILSKITGTEVKIRV 165 (166)
T ss_pred HHhhcccccHHHHHHHHHHHHCCcEEEEe
Confidence 99999999999999999999999999998
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=81.29 E-value=11 Score=30.92 Aligned_cols=95 Identities=22% Similarity=0.264 Sum_probs=58.5
Q ss_pred hhHHHHHHHHHHHHHHHHh-hcCCCeEEEEeeeeecCCCCCCCcccccCCcchhHHHHhhhhcccccceeeeeeEEEee-
Q 032387 19 RLRKAYRKIHTKLVRELEK-KFSGKDVILIATRRILRPPKKGSAVQRPRSRTLTSVHEAMLEDVVLPAEIVGKRIRYRL- 96 (142)
Q Consensus 19 ~~lk~f~kiq~rLv~ELEK-Kfsg~~Vv~iaqRrIl~kp~~~~~qkrPRSRTLTaVhdaiLeDLv~PseIvGKRir~~~- 96 (142)
+.+..|.+.+.+++.=|.. +-.|++|+|+|-+.+-..+ - .--.+.+|=....++...+-+.--+++|| |+.+..
T Consensus 110 ~~~~~yg~~~~~fl~~l~~L~~~g~nII~tAhe~~~~~~-d--e~G~~~~r~~P~i~~K~~n~l~G~~DvV~-rl~i~~~ 185 (220)
T TIGR01618 110 PELQHYQKLDLWFLDLLTVLKESNKNIYATAWELTNQSS-G--ESGQIYNRYQPDIREKVLNAFLGLTDVVG-RIVLNGE 185 (220)
T ss_pred cccccHHHHHHHHHHHHHHHHhCCCcEEEEEeecccccc-C--CCCCCcceechhhhhhHHHhhcccccEEE-EEEEccC
Confidence 3567888887665543321 2259999999988642111 1 11123445566677888888888999999 666655
Q ss_pred CCcEEEEEEeCccccccchhhhh
Q 032387 97 DGSKIMKVFLDPKERNNTEYKLD 119 (142)
Q Consensus 97 DGskl~KV~LD~~~~~~ve~Kl~ 119 (142)
+|.+.+ .+++.+.....++||
T Consensus 186 ~g~R~~--~~~~~~~~~AKNrld 206 (220)
T TIGR01618 186 TGERGF--ILDPSKGNYAKNRLD 206 (220)
T ss_pred CCceEE--EECCCCCcccccccc
Confidence 477665 455555444444443
No 6
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=80.69 E-value=4.7 Score=32.87 Aligned_cols=61 Identities=18% Similarity=0.279 Sum_probs=53.2
Q ss_pred hhhcccccceeeeeeEEEeeCCcEEEEEEeCccccccchhhhhHHHHHHHHhhCCcEEEECCC
Q 032387 77 MLEDVVLPAEIVGKRIRYRLDGSKIMKVFLDPKERNNTEYKLDTFAAVYRKLSGKDVVFDFPV 139 (142)
Q Consensus 77 iLeDLv~PseIvGKRir~~~DGskl~KV~LD~~~~~~ve~Kl~tfs~VYkkLTgKdv~FeFp~ 139 (142)
.+-++++|+++++-.+... ||. .+.|.+.+.|...+-.|-..-...-++|||..+..++..
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 4567888999999888877 776 899999999999999999999999999999999988753
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=65.30 E-value=23 Score=25.60 Aligned_cols=45 Identities=18% Similarity=0.292 Sum_probs=36.0
Q ss_pred eEEEEEecchhHHHHHHHHHHHHHHHHhhcCCCeEEEEeeeeecC
Q 032387 10 KAVVIHIPYRLRKAYRKIHTKLVRELEKKFSGKDVILIATRRILR 54 (142)
Q Consensus 10 kaivifVP~~~lk~f~kiq~rLv~ELEKKfsg~~Vv~iaqRrIl~ 54 (142)
-++|+.+-.....+|..+...+..++.+..++.++++++...=++
T Consensus 71 d~~ilv~d~~~~~s~~~~~~~~~~~i~~~~~~~piilv~nK~Dl~ 115 (174)
T smart00174 71 DVFLICFSVDSPASFENVKEKWYPEVKHFCPNTPIILVGTKLDLR 115 (174)
T ss_pred CEEEEEEECCCHHHHHHHHHHHHHHHHhhCCCCCEEEEecChhhh
Confidence 466666677888999999888888888888899999998865443
No 8
>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=51.01 E-value=58 Score=23.16 Aligned_cols=45 Identities=20% Similarity=0.341 Sum_probs=35.8
Q ss_pred eEEEEEecchhHHHHHHHHHHHHHHHHhhcCCCeEEEEeeeeecC
Q 032387 10 KAVVIHIPYRLRKAYRKIHTKLVRELEKKFSGKDVILIATRRILR 54 (142)
Q Consensus 10 kaivifVP~~~lk~f~kiq~rLv~ELEKKfsg~~Vv~iaqRrIl~ 54 (142)
-++++.+......+|......+..++....++..+++++...=++
T Consensus 73 ~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~p~ivv~nK~Dl~ 117 (171)
T cd00157 73 DVFLICFSVDSPSSFENVKTKWIPEIRHYCPNVPIILVGTKIDLR 117 (171)
T ss_pred CEEEEEEECCCHHHHHHHHHHHHHHHHhhCCCCCEEEEEccHHhh
Confidence 477777777788999888888888888887889999998855433
No 9
>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=48.98 E-value=42 Score=26.09 Aligned_cols=57 Identities=16% Similarity=0.244 Sum_probs=39.4
Q ss_pred hhhhcccccceeeeeeEEEeeCCcEEEEEEeCccccccchhhhhHHHHHHHHhhCCcE
Q 032387 76 AMLEDVVLPAEIVGKRIRYRLDGSKIMKVFLDPKERNNTEYKLDTFAAVYRKLSGKDV 133 (142)
Q Consensus 76 aiLeDLv~PseIvGKRir~~~DGskl~KV~LD~~~~~~ve~Kl~tfs~VYkkLTgKdv 133 (142)
..+..+++|+++.+-.+.- .||++...|.+++.|....=-|=--=...-++|||...
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 4566799999999886644 68889999999988876544443333344556666543
No 10
>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=47.38 E-value=89 Score=25.04 Aligned_cols=25 Identities=40% Similarity=0.545 Sum_probs=20.1
Q ss_pred ccceeeeeeE------EEeeCCcEEEEEEeC
Q 032387 83 LPAEIVGKRI------RYRLDGSKIMKVFLD 107 (142)
Q Consensus 83 ~PseIvGKRi------r~~~DGskl~KV~LD 107 (142)
.|-||+|||- .++.+|+.+.+|.|-
T Consensus 125 ~~vEiIgKrk~~~~~~~~~~~~~~~~kv~~~ 155 (245)
T PF01577_consen 125 KPVEIIGKRKKRTRARYKRRGGKRYLKVETK 155 (245)
T ss_pred CeEEEEecCCceEEEEEEEECCEEEEEEECC
Confidence 5899999975 345688899999974
No 11
>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=43.89 E-value=24 Score=23.36 Aligned_cols=21 Identities=19% Similarity=0.403 Sum_probs=15.0
Q ss_pred eeEEEEEecchhH-HHHHHHHH
Q 032387 9 RKAVVIHIPYRLR-KAYRKIHT 29 (142)
Q Consensus 9 kkaivifVP~~~l-k~f~kiq~ 29 (142)
+..-..+|||.+| ..+|.||.
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 4455667999999 55677764
No 12
>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=42.10 E-value=98 Score=22.25 Aligned_cols=41 Identities=15% Similarity=0.235 Sum_probs=31.0
Q ss_pred EEEEEecchhHHHHHHHHHHHHHHHHhhcCCCeEEEEeeee
Q 032387 11 AVVIHIPYRLRKAYRKIHTKLVRELEKKFSGKDVILIATRR 51 (142)
Q Consensus 11 aivifVP~~~lk~f~kiq~rLv~ELEKKfsg~~Vv~iaqRr 51 (142)
++++.+-.....+|+.+...+.++|.+..++.++++++...
T Consensus 74 ~~ilv~~~~~~~s~~~~~~~~~~~l~~~~~~~piivv~nK~ 114 (174)
T cd04135 74 VFLICFSVVNPASFQNVKEEWVPELKEYAPNVPYLLVGTQI 114 (174)
T ss_pred EEEEEEECCCHHHHHHHHHHHHHHHHhhCCCCCEEEEeEch
Confidence 34444455667899999888889998777889999998754
No 13
>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=41.09 E-value=96 Score=22.63 Aligned_cols=44 Identities=18% Similarity=0.300 Sum_probs=33.2
Q ss_pred eEEEEEecchhHHHHHHHHHHHHHHHHhhcCCCeEEEEeeeeec
Q 032387 10 KAVVIHIPYRLRKAYRKIHTKLVRELEKKFSGKDVILIATRRIL 53 (142)
Q Consensus 10 kaivifVP~~~lk~f~kiq~rLv~ELEKKfsg~~Vv~iaqRrIl 53 (142)
-++|+.+.+....+|+.+...+..++.+..++..+++++...=+
T Consensus 73 ~~~i~v~d~~~~~sf~~~~~~~~~~~~~~~~~~piilv~nK~Dl 116 (173)
T cd04130 73 DVFLLCFSVVNPSSFQNISEKWIPEIRKHNPKAPIILVGTQADL 116 (173)
T ss_pred cEEEEEEECCCHHHHHHHHHHHHHHHHhhCCCCCEEEEeeChhh
Confidence 35555556677889998877778888877778899999886544
No 14
>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=40.56 E-value=93 Score=22.01 Aligned_cols=42 Identities=14% Similarity=0.336 Sum_probs=34.2
Q ss_pred eeEEEEEecchhHHHHHHHHHHHHHHHHhhcC-CCeEEEEeeee
Q 032387 9 RKAVVIHIPYRLRKAYRKIHTKLVRELEKKFS-GKDVILIATRR 51 (142)
Q Consensus 9 kkaivifVP~~~lk~f~kiq~rLv~ELEKKfs-g~~Vv~iaqRr 51 (142)
-.|+++..-+....+|+.++ .+..++.+..+ +.++++++...
T Consensus 72 ~~~~ii~fd~~~~~S~~~~~-~~~~~i~~~~~~~~~iivvg~K~ 114 (162)
T PF00071_consen 72 SDAIIIVFDVTDEESFENLK-KWLEEIQKYKPEDIPIIVVGNKS 114 (162)
T ss_dssp ESEEEEEEETTBHHHHHTHH-HHHHHHHHHSTTTSEEEEEEETT
T ss_pred cccccccccccccccccccc-cccccccccccccccceeeeccc
Confidence 34777777889999999999 78888988887 68889988754
No 15
>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=39.91 E-value=1.1e+02 Score=22.12 Aligned_cols=41 Identities=12% Similarity=0.185 Sum_probs=30.4
Q ss_pred EEEEEecchhHHHHHHHHHHHHHHHHhhcCCCeEEEEeeee
Q 032387 11 AVVIHIPYRLRKAYRKIHTKLVRELEKKFSGKDVILIATRR 51 (142)
Q Consensus 11 aivifVP~~~lk~f~kiq~rLv~ELEKKfsg~~Vv~iaqRr 51 (142)
++++.+......+|..+...+..+++....+.++++++...
T Consensus 73 ~~ilv~d~~~~~s~~~~~~~~~~~i~~~~~~~pviiv~nK~ 113 (166)
T cd01893 73 VICLVYSVDRPSTLERIRTKWLPLIRRLGVKVPIILVGNKS 113 (166)
T ss_pred EEEEEEECCCHHHHHHHHHHHHHHHHHhCCCCCEEEEEEch
Confidence 45555667778889988777777777655678999998754
No 16
>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=39.70 E-value=1.1e+02 Score=22.00 Aligned_cols=43 Identities=14% Similarity=0.258 Sum_probs=32.1
Q ss_pred EEEEEecchhHHHHHHHHHHHHHHHHhhcCCCeEEEEeeeeec
Q 032387 11 AVVIHIPYRLRKAYRKIHTKLVRELEKKFSGKDVILIATRRIL 53 (142)
Q Consensus 11 aivifVP~~~lk~f~kiq~rLv~ELEKKfsg~~Vv~iaqRrIl 53 (142)
++++...+....+|..+...+..++.+..++.++++++...=+
T Consensus 75 ~~i~v~~~~~~~s~~~~~~~~~~~~~~~~~~~piilv~nK~Dl 117 (175)
T cd01870 75 VILMCFSIDSPDSLENIPEKWTPEVKHFCPNVPIILVGNKKDL 117 (175)
T ss_pred EEEEEEECCCHHHHHHHHHHHHHHHHhhCCCCCEEEEeeChhc
Confidence 4555556777788888877788888877678899999875544
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=38.79 E-value=1.1e+02 Score=22.98 Aligned_cols=44 Identities=16% Similarity=0.354 Sum_probs=33.0
Q ss_pred EEEEEecchhHHHHHHHHHHHHHHHHhhcCCCeEEEEeeeeecC
Q 032387 11 AVVIHIPYRLRKAYRKIHTKLVRELEKKFSGKDVILIATRRILR 54 (142)
Q Consensus 11 aivifVP~~~lk~f~kiq~rLv~ELEKKfsg~~Vv~iaqRrIl~ 54 (142)
++|+..-+....+|+.+....+.++....++.+++++|...=|+
T Consensus 74 ~~ilv~dv~~~~sf~~~~~~~~~~i~~~~~~~piilvgNK~Dl~ 117 (189)
T cd04134 74 VIMLCFSVDSPDSLENVESKWLGEIREHCPGVKLVLVALKCDLR 117 (189)
T ss_pred EEEEEEECCCHHHHHHHHHHHHHHHHHhCCCCCEEEEEEChhhc
Confidence 55555556778899988766678887777788999999865554
No 18
>PF01883 DUF59: Domain of unknown function DUF59; InterPro: IPR002744 This family includes prokaryotic proteins of unknown function. The family also includes PhaH (O84984 from SWISSPROT) from Pseudomonas putida. PhaH forms a complex with PhaF (O84982 from SWISSPROT), PhaG (O84983 from SWISSPROT) and PhaI (O84985 from SWISSPROT), which hydroxylates phenylacetic acid to 2-hydroxyphenylacetic acid []. So members of this family may all be components of ring hydroxylating complexes.; PDB: 3LNO_C 3CQ3_A 3CQ2_D 2CU6_B 3CQ1_A 3UX3_B 3UX2_A 1WCJ_A 1UWD_A.
Probab=38.63 E-value=68 Score=20.92 Aligned_cols=40 Identities=18% Similarity=0.369 Sum_probs=31.0
Q ss_pred CeeeecCCeeEEEEEecchhHHHHHHHHHHHHHHHHhhcCC
Q 032387 1 MQIDVPGNRKAVVIHIPYRLRKAYRKIHTKLVRELEKKFSG 41 (142)
Q Consensus 1 kei~v~~~kkaivifVP~~~lk~f~kiq~rLv~ELEKKfsg 41 (142)
++|++.+|+=.+.+.+|+|....+..++..+...|. .+.|
T Consensus 27 ~~i~i~~~~V~v~l~l~~~~~~~~~~l~~~i~~~l~-~l~g 66 (72)
T PF01883_consen 27 RDISIEGGKVSVSLELPTPACPAAEPLREEIREALK-ALPG 66 (72)
T ss_dssp EEEEECTCEEEEEE--SSTTHTTHHHHHHHHHHHHH-TSTT
T ss_pred eEEEEECCEEEEEEEECCCCchHHHHHHHHHHHHHH-hCCC
Confidence 368899988889999999999888888888877776 5555
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=37.19 E-value=1.2e+02 Score=22.25 Aligned_cols=44 Identities=14% Similarity=0.302 Sum_probs=34.2
Q ss_pred eEEEEEecchhHHHHHHHHHHHHHHHHhhcCCCeEEEEeeeeecC
Q 032387 10 KAVVIHIPYRLRKAYRKIHTKLVRELEKKFSGKDVILIATRRILR 54 (142)
Q Consensus 10 kaivifVP~~~lk~f~kiq~rLv~ELEKKfsg~~Vv~iaqRrIl~ 54 (142)
-|+|+.+-.....+|+.++. .+.++.+...+.+++++|...=++
T Consensus 74 d~~i~v~d~~~~~s~~~~~~-~~~~i~~~~~~~piiiv~nK~Dl~ 117 (166)
T cd00877 74 QCAIIMFDVTSRVTYKNVPN-WHRDLVRVCGNIPIVLCGNKVDIK 117 (166)
T ss_pred CEEEEEEECCCHHHHHHHHH-HHHHHHHhCCCCcEEEEEEchhcc
Confidence 46777778888899998864 678888777789999998865443
No 20
>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=36.16 E-value=1.3e+02 Score=22.47 Aligned_cols=44 Identities=14% Similarity=0.255 Sum_probs=32.0
Q ss_pred eEEEEEecchhHHHHHHHHHHHHHHHHhhcCCCeEEEEeeeeec
Q 032387 10 KAVVIHIPYRLRKAYRKIHTKLVRELEKKFSGKDVILIATRRIL 53 (142)
Q Consensus 10 kaivifVP~~~lk~f~kiq~rLv~ELEKKfsg~~Vv~iaqRrIl 53 (142)
.++|+.+=+....+|..+...+..|+++.-++.++++++...=+
T Consensus 74 ~~~ilv~d~~~~~s~~~~~~~w~~~i~~~~~~~piilvgnK~Dl 117 (175)
T cd01874 74 DVFLVCFSVVSPSSFENVKEKWVPEITHHCPKTPFLLVGTQIDL 117 (175)
T ss_pred CEEEEEEECCCHHHHHHHHHHHHHHHHHhCCCCCEEEEEECHhh
Confidence 35555555677789999877677888776667899999885433
No 21
>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=33.35 E-value=76 Score=26.93 Aligned_cols=31 Identities=26% Similarity=0.350 Sum_probs=26.9
Q ss_pred hhHHHHHHHHHHHHHHHHhhcCCCeEEEEee
Q 032387 19 RLRKAYRKIHTKLVRELEKKFSGKDVILIAT 49 (142)
Q Consensus 19 ~~lk~f~kiq~rLv~ELEKKfsg~~Vv~iaq 49 (142)
+.+.+.++.|.+.+.++++.|+|.+|+-+-.
T Consensus 255 ~~~~~r~~~Q~~~l~~i~~~f~~~~v~~vp~ 285 (305)
T PF02374_consen 255 PFCAARRKEQQKYLAEIEESFPDLPVVKVPL 285 (305)
T ss_dssp HHHHHHHHHHHHHHHHHHHHTTTSEEEEEE-
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCEEEecC
Confidence 4578999999999999999999999887754
No 22
>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=32.64 E-value=1.6e+02 Score=22.33 Aligned_cols=45 Identities=18% Similarity=0.332 Sum_probs=34.3
Q ss_pred eEEEEEecchhHHHHHHHHHHHHHHHHhhcCCCeEEEEeeeeecC
Q 032387 10 KAVVIHIPYRLRKAYRKIHTKLVRELEKKFSGKDVILIATRRILR 54 (142)
Q Consensus 10 kaivifVP~~~lk~f~kiq~rLv~ELEKKfsg~~Vv~iaqRrIl~ 54 (142)
.++|+..-+....+|..++..+..++....++-+++++|...=|+
T Consensus 76 ~~~ilvydit~~~Sf~~~~~~w~~~i~~~~~~~piilvgNK~DL~ 120 (191)
T cd01875 76 NVFIICFSIASPSSYENVRHKWHPEVCHHCPNVPILLVGTKKDLR 120 (191)
T ss_pred CEEEEEEECCCHHHHHHHHHHHHHHHHhhCCCCCEEEEEeChhhh
Confidence 356666667778899999876677777666788999999877664
No 23
>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=32.60 E-value=1.5e+02 Score=22.63 Aligned_cols=44 Identities=16% Similarity=0.234 Sum_probs=34.1
Q ss_pred eEEEEEecchhHHHHHHHHHHHHHHHHhhcCCCeEEEEeeeeec
Q 032387 10 KAVVIHIPYRLRKAYRKIHTKLVRELEKKFSGKDVILIATRRIL 53 (142)
Q Consensus 10 kaivifVP~~~lk~f~kiq~rLv~ELEKKfsg~~Vv~iaqRrIl 53 (142)
-++++..-+....+|..+..+++.++..-.++.++++||...=|
T Consensus 78 d~~ilvyDit~~~Sf~~~~~~w~~~i~~~~~~~piilVgNK~DL 121 (182)
T cd04172 78 DAVLICFDISRPETLDSVLKKWKGEIQEFCPNTKMLLVGCKSDL 121 (182)
T ss_pred CEEEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCEEEEeEChhh
Confidence 46666666788899999877788888776677889999876544
No 24
>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=31.63 E-value=71 Score=21.74 Aligned_cols=24 Identities=25% Similarity=0.447 Sum_probs=19.7
Q ss_pred HHHHHHHHHHHhhcCCCeEEEEee
Q 032387 26 KIHTKLVRELEKKFSGKDVILIAT 49 (142)
Q Consensus 26 kiq~rLv~ELEKKfsg~~Vv~iaq 49 (142)
.-|..|-.|+..-|++++++.+..
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 559999999999999999988864
No 25
>PF13479 AAA_24: AAA domain
Probab=31.12 E-value=63 Score=25.48 Aligned_cols=62 Identities=19% Similarity=0.307 Sum_probs=34.6
Q ss_pred HHHHHHHHHHHHHHHHhh--cCCCeEEEEeeeeecCCCCCC-CcccccCCcchhHHHHhhhhcccccceee
Q 032387 21 RKAYRKIHTKLVRELEKK--FSGKDVILIATRRILRPPKKG-SAVQRPRSRTLTSVHEAMLEDVVLPAEIV 88 (142)
Q Consensus 21 lk~f~kiq~rLv~ELEKK--fsg~~Vv~iaqRrIl~kp~~~-~~qkrPRSRTLTaVhdaiLeDLv~PseIv 88 (142)
++.|..++..+.+-+.+- ..|+||||+|.-..---+..+ ..+.+|. .+....+-+.+-+++|
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 667777776655555542 249999999976654332111 1222222 2334445566666777
No 26
>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=31.08 E-value=1.5e+02 Score=23.80 Aligned_cols=44 Identities=16% Similarity=0.192 Sum_probs=35.2
Q ss_pred eEEEEEecchhHHHHHHHHHHHHHHHHhhcCCCeEEEEeeeeec
Q 032387 10 KAVVIHIPYRLRKAYRKIHTKLVRELEKKFSGKDVILIATRRIL 53 (142)
Q Consensus 10 kaivifVP~~~lk~f~kiq~rLv~ELEKKfsg~~Vv~iaqRrIl 53 (142)
-++++.+-+....+|..+...+..|+....++-++++|+...=|
T Consensus 74 d~illvfdis~~~Sf~~i~~~w~~~~~~~~~~~piiLVgnK~DL 117 (222)
T cd04173 74 DAVLICFDISRPETLDSVLKKWQGETQEFCPNAKVVLVGCKLDM 117 (222)
T ss_pred CEEEEEEECCCHHHHHHHHHHHHHHHHhhCCCCCEEEEEECccc
Confidence 47777777888899999987777888777788899999875444
No 27
>smart00175 RAB Rab subfamily of small GTPases. Rab GTPases are implicated in vesicle trafficking.
Probab=31.01 E-value=1.9e+02 Score=20.24 Aligned_cols=40 Identities=10% Similarity=0.290 Sum_probs=29.9
Q ss_pred eEEEEEecchhHHHHHHHHHHHHHHHHhhc-CCCeEEEEeee
Q 032387 10 KAVVIHIPYRLRKAYRKIHTKLVRELEKKF-SGKDVILIATR 50 (142)
Q Consensus 10 kaivifVP~~~lk~f~kiq~rLv~ELEKKf-sg~~Vv~iaqR 50 (142)
-++|+.+......+|..+.. +..++++-- ++.++++++..
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 36777777888889988876 666776644 57899999873
No 28
>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=29.75 E-value=1.2e+02 Score=21.62 Aligned_cols=40 Identities=23% Similarity=0.265 Sum_probs=26.3
Q ss_pred CeeEEEEEecchhHHHHHHHHHHHHHHHHhhcCCCeEEEEe
Q 032387 8 NRKAVVIHIPYRLRKAYRKIHTKLVRELEKKFSGKDVILIA 48 (142)
Q Consensus 8 ~kkaivifVP~~~lk~f~kiq~rLv~ELEKKfsg~~Vv~ia 48 (142)
||..+|.|.+-.--..+++-.. .+.+|-+++.++.|.+++
T Consensus 28 gk~~vv~f~~~~~Cp~C~~~~p-~l~~l~~~~~~~~v~~v~ 67 (146)
T PF08534_consen 28 GKPVVVNFWASAWCPPCRKELP-YLNELQEKYKDKGVDVVG 67 (146)
T ss_dssp TSEEEEEEESTTTSHHHHHHHH-HHHHHHHHHHTTTCEEEE
T ss_pred CCeEEEEEEccCCCCcchhhhh-hHHhhhhhhccCceEEEE
Confidence 7888999988745555555333 788887776555444443
No 29
>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=29.38 E-value=1.2e+02 Score=21.16 Aligned_cols=42 Identities=19% Similarity=0.135 Sum_probs=24.5
Q ss_pred CCeeEEEEEecchhHHHHHHHHHHHHHHHHhhcCCCeEEEEee
Q 032387 7 GNRKAVVIHIPYRLRKAYRKIHTKLVRELEKKFSGKDVILIAT 49 (142)
Q Consensus 7 ~~kkaivifVP~~~lk~f~kiq~rLv~ELEKKfsg~~Vv~iaq 49 (142)
++++.+|+|++-.--..++. +..-+.++-.+|.+..+.+||-
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 35778899988665555554 3444455666664444545443
No 30
>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=28.65 E-value=2.1e+02 Score=20.98 Aligned_cols=44 Identities=14% Similarity=0.243 Sum_probs=32.1
Q ss_pred eEEEEEecchhHHHHHHHHHHHHHHHHhhcCCCeEEEEeeeeec
Q 032387 10 KAVVIHIPYRLRKAYRKIHTKLVRELEKKFSGKDVILIATRRIL 53 (142)
Q Consensus 10 kaivifVP~~~lk~f~kiq~rLv~ELEKKfsg~~Vv~iaqRrIl 53 (142)
-++++.+......+|..+...+..++..--++.++++++...=+
T Consensus 74 d~ii~v~d~~~~~s~~~~~~~~~~~~~~~~~~~piilv~nK~Dl 117 (187)
T cd04132 74 DVLLICYAVDNPTSLDNVEDKWFPEVNHFCPGTPIMLVGLKTDL 117 (187)
T ss_pred CEEEEEEECCCHHHHHHHHHHHHHHHHHhCCCCCEEEEEeChhh
Confidence 46777778888899998876666677654457788998876544
No 31
>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=28.63 E-value=2e+02 Score=21.43 Aligned_cols=41 Identities=17% Similarity=0.354 Sum_probs=31.0
Q ss_pred EEEEEecchhHHHHHHHHHHHHHHHHhhcCCCeEEEEeeee
Q 032387 11 AVVIHIPYRLRKAYRKIHTKLVRELEKKFSGKDVILIATRR 51 (142)
Q Consensus 11 aivifVP~~~lk~f~kiq~rLv~ELEKKfsg~~Vv~iaqRr 51 (142)
++++..-+....+|+.+...+..++.+..+..++++|+..-
T Consensus 75 ~~llv~~i~~~~s~~~~~~~~~~~i~~~~~~~piilvgnK~ 115 (187)
T cd04129 75 VILIGFAVDTPDSLENVRTKWIEEVRRYCPNVPVILVGLKK 115 (187)
T ss_pred EEEEEEECCCHHHHHHHHHHHHHHHHHhCCCCCEEEEeeCh
Confidence 44544556777899999887888887777788899998753
No 32
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=27.81 E-value=1.8e+02 Score=22.29 Aligned_cols=58 Identities=17% Similarity=0.303 Sum_probs=39.8
Q ss_pred HhhhhcccccceeeeeeEEEeeCCcEEEEEEeCccccccchhhhhHHHHHHHHhhCCcE
Q 032387 75 EAMLEDVVLPAEIVGKRIRYRLDGSKIMKVFLDPKERNNTEYKLDTFAAVYRKLSGKDV 133 (142)
Q Consensus 75 daiLeDLv~PseIvGKRir~~~DGskl~KV~LD~~~~~~ve~Kl~tfs~VYkkLTgKdv 133 (142)
...+.+++.|+++.+-.+. .-++++.+.|.+++.|...+=.|=-.=.....+|+|+..
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 4568899999999887664 345678999999988776554443333444566666654
No 33
>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=26.86 E-value=2.1e+02 Score=22.16 Aligned_cols=46 Identities=20% Similarity=0.247 Sum_probs=34.2
Q ss_pred eeEEEEEecchhHHHHHHHHHHHHHHHHhhcCCCeEEEEeeeeecC
Q 032387 9 RKAVVIHIPYRLRKAYRKIHTKLVRELEKKFSGKDVILIATRRILR 54 (142)
Q Consensus 9 kkaivifVP~~~lk~f~kiq~rLv~ELEKKfsg~~Vv~iaqRrIl~ 54 (142)
-.++++..-+....+|..+...++.++....++.+++++|...=|+
T Consensus 88 ad~iilv~d~t~~~Sf~~~~~~w~~~i~~~~~~~piilvgNK~DL~ 133 (195)
T cd01873 88 SDVVLLCFSIASPNSLRNVKTMWYPEIRHFCPRVPVILVGCKLDLR 133 (195)
T ss_pred CCEEEEEEECCChhHHHHHHHHHHHHHHHhCCCCCEEEEEEchhcc
Confidence 3456777777888999988766677887666677899998865554
No 34
>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=26.69 E-value=2.3e+02 Score=21.09 Aligned_cols=44 Identities=16% Similarity=0.287 Sum_probs=32.7
Q ss_pred eEEEEEecchhHHHHHHHHHHHHHHHHhhcCCCeEEEEeeeeec
Q 032387 10 KAVVIHIPYRLRKAYRKIHTKLVRELEKKFSGKDVILIATRRIL 53 (142)
Q Consensus 10 kaivifVP~~~lk~f~kiq~rLv~ELEKKfsg~~Vv~iaqRrIl 53 (142)
-|+|+.+-+....+|+.+...+..++...-++.++++++...=|
T Consensus 74 d~~ilv~d~~~~~sf~~~~~~~~~~~~~~~~~~piilvgnK~Dl 117 (174)
T cd01871 74 DVFLICFSLVSPASFENVRAKWYPEVRHHCPNTPIILVGTKLDL 117 (174)
T ss_pred CEEEEEEECCCHHHHHHHHHHHHHHHHHhCCCCCEEEEeeChhh
Confidence 46666677777899999876667777766667889999885444
No 35
>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=26.25 E-value=2.3e+02 Score=21.60 Aligned_cols=44 Identities=23% Similarity=0.329 Sum_probs=31.6
Q ss_pred eEEEEEecchhHHHHHHHHHHHHHHHHhhcCCCeEEEEeeeeec
Q 032387 10 KAVVIHIPYRLRKAYRKIHTKLVRELEKKFSGKDVILIATRRIL 53 (142)
Q Consensus 10 kaivifVP~~~lk~f~kiq~rLv~ELEKKfsg~~Vv~iaqRrIl 53 (142)
-++|+..=+....+|..+...+++++.+.-++-+++++|...=|
T Consensus 74 ~~~ilvyd~~~~~Sf~~~~~~w~~~i~~~~~~~piilvgnK~Dl 117 (176)
T cd04133 74 DVFVLAFSLISRASYENVLKKWVPELRHYAPNVPIVLVGTKLDL 117 (176)
T ss_pred cEEEEEEEcCCHHHHHHHHHHHHHHHHHhCCCCCEEEEEeChhh
Confidence 35566666777899999876677888655566788888875444
No 36
>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=26.04 E-value=2.5e+02 Score=20.23 Aligned_cols=40 Identities=15% Similarity=0.249 Sum_probs=29.2
Q ss_pred EEEEEecchhHHHHHHHHHHHHHHHHhhcCCCeEEEEeeee
Q 032387 11 AVVIHIPYRLRKAYRKIHTKLVRELEKKFSGKDVILIATRR 51 (142)
Q Consensus 11 aivifVP~~~lk~f~kiq~rLv~ELEKKfsg~~Vv~iaqRr 51 (142)
++++.+....-.+|+.++. ++.++.+..++.++++++...
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 557776666788999998753
No 37
>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=25.24 E-value=2.3e+02 Score=21.89 Aligned_cols=44 Identities=18% Similarity=0.374 Sum_probs=34.0
Q ss_pred eeEEEEEecchhHHHHHHHHHHHHHHHHhhcCCCeEEEEeeeeec
Q 032387 9 RKAVVIHIPYRLRKAYRKIHTKLVRELEKKFSGKDVILIATRRIL 53 (142)
Q Consensus 9 kkaivifVP~~~lk~f~kiq~rLv~ELEKKfsg~~Vv~iaqRrIl 53 (142)
-.++|+.+-+....+|..+. ..+.|+.+-.++-.+++||...=|
T Consensus 79 ad~illVfD~t~~~Sf~~~~-~w~~~i~~~~~~~piilVGNK~DL 122 (189)
T cd04121 79 AQGIILVYDITNRWSFDGID-RWIKEIDEHAPGVPKILVGNRLHL 122 (189)
T ss_pred CCEEEEEEECcCHHHHHHHH-HHHHHHHHhCCCCCEEEEEECccc
Confidence 34777777888899999995 578888777788889999874433
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=25.17 E-value=1.2e+02 Score=22.19 Aligned_cols=60 Identities=25% Similarity=0.365 Sum_probs=35.4
Q ss_pred HHHHHHHhhcCCCeEEEEeeeeecCCCCCCCcccccCCcchhHHHHhhhhcccccceeeeeeEEEeeCCcEEEEEEeC
Q 032387 30 KLVRELEKKFSGKDVILIATRRILRPPKKGSAVQRPRSRTLTSVHEAMLEDVVLPAEIVGKRIRYRLDGSKIMKVFLD 107 (142)
Q Consensus 30 rLv~ELEKKfsg~~Vv~iaqRrIl~kp~~~~~qkrPRSRTLTaVhdaiLeDLv~PseIvGKRir~~~DGskl~KV~LD 107 (142)
.+.+.|++.+.|+.|.-+--++ ++ .-+..-..|| +--.+=.||.+-+.+|+...+-+||-
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--LATADLAGRT------------VEEVVARGKHLLIRFDGGLTLHTHLR 68 (114)
T ss_pred HHHHHHHHHhCCCEEEEEEecC----ch--hhhhhcCCCE------------EEEEEEeeeEEEEEcCCCCEEEEeCC
Confidence 4667899999999886553211 10 0011122222 33345589999999875557777764
No 39
>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=24.90 E-value=2.5e+02 Score=21.20 Aligned_cols=44 Identities=18% Similarity=0.245 Sum_probs=32.5
Q ss_pred eEEEEEecchhHHHHHHHHHHHHHHHHhhcCCCeEEEEeeeeec
Q 032387 10 KAVVIHIPYRLRKAYRKIHTKLVRELEKKFSGKDVILIATRRIL 53 (142)
Q Consensus 10 kaivifVP~~~lk~f~kiq~rLv~ELEKKfsg~~Vv~iaqRrIl 53 (142)
-++|+..-+....+|..+...+..++..-.++-++++||...=|
T Consensus 74 ~~~ilvfdit~~~Sf~~~~~~w~~~i~~~~~~~~iilVgnK~DL 117 (178)
T cd04131 74 DAVLICFDISRPETLDSVLKKWRGEIQEFCPNTKVLLVGCKTDL 117 (178)
T ss_pred CEEEEEEECCChhhHHHHHHHHHHHHHHHCCCCCEEEEEEChhh
Confidence 35666666778899998766677888766667788999876544
No 40
>cd04910 ACT_AK-Ectoine_1 ACT domains located C-terminal to the catalytic domain of the aspartokinase of the ectoine (1,4,5,6-tetrahydro-2-methyl pyrimidine-4-carboxylate) biosynthetic pathway. This CD includes the first of two ACT domains located C-terminal to the catalytic domain of the aspartokinase of the ectoine (1,4,5,6-tetrahydro-2-methyl pyrimidine-4-carboxylate) biosynthetic pathway found in Methylomicrobium alcaliphilum, Vibrio cholerae, and various other halotolerant or halophilic bacteria. Bacteria exposed to hyperosmotic stress accumulate organic solutes called 'compatible solutes' of which ectoine, a heterocyclic amino acid, is one. Apart from its osmotic function, ectoine also exhibits a protective effect on proteins, nucleic acids and membranes against a variety of stress factors. de novo synthesis of ectoine starts with the phosphorylation of L-aspartate and shares its first two enzymatic steps with the biosynthesis of amino acids of the aspartate family: aspartokinase
Probab=24.08 E-value=1.9e+02 Score=19.99 Aligned_cols=31 Identities=19% Similarity=0.340 Sum_probs=22.7
Q ss_pred CeeEEEEEecchhHHHHHHHHHHHHHHHHhhcCCCe
Q 032387 8 NRKAVVIHIPYRLRKAYRKIHTKLVRELEKKFSGKD 43 (142)
Q Consensus 8 ~kkaivifVP~~~lk~f~kiq~rLv~ELEKKfsg~~ 43 (142)
+-..|-+|++.+ .|-..|+++|||+.|++-.
T Consensus 38 nANtit~yl~~~-----~k~~~r~~~~Le~~~p~a~ 68 (71)
T cd04910 38 NANTITHYLAGS-----LKTIKRLTEDLENRFPNAE 68 (71)
T ss_pred CCCeEEEEEEcC-----HHHHHHHHHHHHHhCccCc
Confidence 344677777765 3557889999999998643
No 41
>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=22.50 E-value=64 Score=20.37 Aligned_cols=18 Identities=33% Similarity=0.492 Sum_probs=14.7
Q ss_pred hhhhHHHHHHHHhhCCcE
Q 032387 116 YKLDTFAAVYRKLSGKDV 133 (142)
Q Consensus 116 ~Kl~tfs~VYkkLTgKdv 133 (142)
.+|-....-|+.+||+|.
T Consensus 30 ~~Ll~lK~~~k~~tg~~~ 47 (50)
T cd00936 30 KKLLALKADYKEATGQDY 47 (50)
T ss_pred HHHHHHHHHHHHhcCCCC
Confidence 466677888999999985
No 42
>COG4496 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.10 E-value=28 Score=26.18 Aligned_cols=32 Identities=25% Similarity=0.511 Sum_probs=25.0
Q ss_pred cccCCcchhHHHHhhh------------hccccccee--eeeeEEE
Q 032387 63 QRPRSRTLTSVHEAML------------EDVVLPAEI--VGKRIRY 94 (142)
Q Consensus 63 krPRSRTLTaVhdaiL------------eDLv~PseI--vGKRir~ 94 (142)
.+||+.+|.+..|||| +||+-|.|| ...|++|
T Consensus 4 ~klr~~~Ld~l~dailtL~n~eecy~FfdDlcTinEiqslaqRlqV 49 (100)
T COG4496 4 EKLRGAALDELFDAILTLENLEECYAFFDDLCTINEIQSLAQRLQV 49 (100)
T ss_pred cchhhHHHHHHHHHHHHhccHHHHHHHHHhhcCHHHHHHHHHHHHH
Confidence 3688999999999885 799999998 4445443
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=20.92 E-value=3.2e+02 Score=19.43 Aligned_cols=41 Identities=7% Similarity=0.303 Sum_probs=29.2
Q ss_pred eEEEEEecchhHHHHHHHHHHHHHHHHhhc-CCCeEEEEeeee
Q 032387 10 KAVVIHIPYRLRKAYRKIHTKLVRELEKKF-SGKDVILIATRR 51 (142)
Q Consensus 10 kaivifVP~~~lk~f~kiq~rLv~ELEKKf-sg~~Vv~iaqRr 51 (142)
.|+++.+-.....+|..+.. +..++.+.. ++..+++++...
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 46777777777889988866 566665543 467888888754
Done!