Query 029530
Match_columns 192
No_of_seqs 120 out of 242
Neff 3.8
Searched_HMMs 46136
Date Fri Mar 29 14:23:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029530.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029530hhsearch_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 2.3E-96 5E-101 616.5 13.7 185 6-191 1-189 (189)
2 KOG3320 40S ribosomal protein 100.0 3.4E-92 7.3E-97 588.5 19.3 190 1-191 1-191 (192)
3 PTZ00389 40S ribosomal protein 100.0 3.3E-89 7.3E-94 571.5 20.1 182 8-191 1-184 (184)
4 PRK06418 transcription elongat 99.8 2.2E-18 4.7E-23 142.9 10.9 137 15-187 27-165 (166)
5 TIGR01618 phage_P_loop phage n 83.7 6.1 0.00013 34.2 7.7 93 68-169 110-206 (220)
6 PF01883 DUF59: Domain of unkn 66.3 21 0.00046 24.6 5.3 66 20-90 1-66 (72)
7 TIGR02945 SUF_assoc FeS assemb 58.4 33 0.00071 25.2 5.4 69 19-92 2-71 (99)
8 smart00174 RHO Rho (Ras homolo 50.6 51 0.0011 25.0 5.5 45 59-103 71-115 (174)
9 PF01577 Peptidase_S30: Potyvi 48.4 24 0.00051 29.9 3.6 40 116-156 102-154 (245)
10 PF02154 FliM: Flagellar motor 38.8 2.2E+02 0.0047 23.3 8.5 62 12-74 104-189 (192)
11 cd00157 Rho Rho (Ras homology) 37.8 1.1E+02 0.0024 22.9 5.5 45 59-103 73-117 (171)
12 PF02374 ArsA_ATPase: Anion-tr 33.5 72 0.0016 28.5 4.5 31 68-98 255-285 (305)
13 PF01383 CpcD: CpcD/allophycoc 31.6 59 0.0013 22.6 2.9 21 58-78 24-45 (56)
14 PF08534 Redoxin: Redoxin; In 29.8 1.1E+02 0.0023 23.0 4.3 47 50-97 19-67 (146)
15 TIGR02110 PQQ_syn_pqqF coenzym 29.5 1E+02 0.0022 31.2 5.2 49 50-102 607-668 (696)
16 PF00071 Ras: Ras family; Int 29.0 1.8E+02 0.004 21.6 5.5 43 59-102 73-116 (162)
17 PF03799 FtsQ: Cell division p 28.1 1.4E+02 0.003 21.4 4.5 39 140-184 71-112 (117)
18 cd04135 Tc10 TC10 subfamily. 27.7 2.1E+02 0.0045 21.6 5.7 41 60-100 74-114 (174)
19 cd01870 RhoA_like RhoA-like su 27.5 2.1E+02 0.0045 21.7 5.6 43 60-102 75-117 (175)
20 cd01893 Miro1 Miro1 subfamily. 27.3 2.2E+02 0.0047 21.7 5.7 42 60-101 73-114 (166)
21 cd04130 Wrch_1 Wrch-1 subfamil 27.1 2E+02 0.0044 22.0 5.5 43 60-102 74-116 (173)
22 PF06858 NOG1: Nucleolar GTP-b 26.5 93 0.002 22.2 3.2 25 74-98 31-55 (58)
23 PF13479 AAA_24: AAA domain 26.0 3.3E+02 0.0072 22.5 7.0 90 70-167 105-199 (213)
24 cd04134 Rho3 Rho3 subfamily. 25.6 2.3E+02 0.0049 22.4 5.7 44 60-103 74-117 (189)
25 cd02970 PRX_like2 Peroxiredoxi 25.4 1.3E+02 0.0029 22.1 4.2 42 56-98 22-63 (149)
26 cd00877 Ran Ran (Ras-related n 24.0 2.5E+02 0.0054 21.6 5.5 44 59-103 74-117 (166)
27 cd01874 Cdc42 Cdc42 subfamily. 23.7 2.6E+02 0.0055 22.0 5.7 44 59-102 74-117 (175)
28 TIGR01397 fliM_switch flagella 21.2 5.7E+02 0.012 22.5 9.2 62 12-73 138-222 (320)
29 COG4496 Uncharacterized protei 21.2 29 0.00062 27.4 -0.2 31 112-142 4-48 (100)
30 cd04172 Rnd3_RhoE_Rho8 Rnd3/Rh 21.1 3E+02 0.0065 22.1 5.7 44 59-102 78-121 (182)
31 cd01875 RhoG RhoG subfamily. 21.1 3.1E+02 0.0067 21.8 5.7 45 59-103 76-120 (191)
32 cd04173 Rnd2_Rho7 Rnd2/Rho7 su 20.7 2.9E+02 0.0062 23.4 5.7 44 59-102 74-117 (222)
33 smart00175 RAB Rab subfamily o 20.1 3.6E+02 0.0079 19.8 5.7 40 59-99 74-114 (164)
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=2.3e-96 Score=616.54 Aligned_cols=185 Identities=62% Similarity=0.971 Sum_probs=154.6
Q ss_pred cccccCCCCCCCHHHHHHHHHhHhhhcCChHHHhcCcceeeeeeEEEEecCCeeEEEEEeehhhHHHHHHHHHHHHHHHH
Q 029530 6 KKIQKDKDAEPTEFEETVAQALFDLENTNQELKSDLKDLYINQAIQMDVSGNRKAIVVYVPYRLRKAYRKIHSRLVRELE 85 (192)
Q Consensus 6 ~Ki~k~~~~~p~e~E~~Vaqal~dLe~~~~dLk~~Lr~l~i~~akei~v~~~kKAivIfVP~~~lk~f~Kiq~rLv~ELE 85 (192)
+||+|++|++|||||.+|||||+|||++++|||++|++|+|++||||||++||||||||||||||++|||||.||++|||
T Consensus 1 ~Ki~K~~~~~p~e~E~~Vaqal~dle~~~~dLK~~Lr~L~i~~aKEi~v~~~kKAivIfVP~~~lk~f~KIq~rLv~ELE 80 (189)
T PF01251_consen 1 KKIVKPKGKKPDEFEESVAQALLDLEMNSSDLKAQLRELYITSAKEIEVGGGKKAIVIFVPVPQLKAFQKIQVRLVRELE 80 (189)
T ss_dssp ---SS---SS--CHHHHHHHHHHHHCHCHCHHCCCCCC--ECEEEEEEECTCEEEEEEEE-CCCCHHHHHHCHHHHHHHH
T ss_pred CCccccCCCCCCHHHHHHHHHHHHHHcCcHHHHhhccccEEEEEEEEEECCCcEEEEEEEcHHHHHHHHHHHHHHHHHHH
Confidence 48999999999999999999999999877799999999999999999999999999999999999999999999999999
Q ss_pred hhcCCCeEEEEeeecccCCCCCC----CccccCCCcchhhhhHhhhhcccccceeeceeEEEeeCCceeEEEEecCcccc
Q 029530 86 KKFSGKDVVLIATRRIVRPPKKG----SAVQRPRSRTLTAVHDAMLEDVVYPAEIVGKRVRYRLDGSKIIKVIFLDPKER 161 (192)
Q Consensus 86 KKfsg~~Vv~vAqRrIl~kp~~~----~~q~RPRSRTLTaVheaiLeDlV~P~eIVGKR~r~r~DGsk~~KV~~LD~k~~ 161 (192)
|||||+||||||||||+|+|+++ .+|+|||||||||||||||||||||+|||||||||++|||+++|| |||++||
T Consensus 81 KKfsgk~Vv~iAqRrIl~kp~r~~~~~~~qkrPRSRTLTaVhdaILeDLV~PseIVGKRir~rlDGskl~KV-~LD~k~~ 159 (189)
T PF01251_consen 81 KKFSGKHVVFIAQRRILPKPTRKSRQKQKQKRPRSRTLTAVHDAILEDLVYPSEIVGKRIRVRLDGSKLIKV-HLDKKDQ 159 (189)
T ss_dssp HCTTTCEEEEEE------SS-SSS---TTS---CCCSHHHHHHHHHHHHTTTS-ECEEEEEE-TTS-EEEEE-EEECCCC
T ss_pred hhcCCCeEEEeccceEcCCCCcCccccccccCcCCcchHHHHHHHHHhhccHHHhheeeEEEecCCCEEEEE-EEChHHc
Confidence 99999999999999999999887 479999999999999999999999999999999999999999999 9999999
Q ss_pred cchhhhhhhHHHHHhhhcCCceEEECCCCC
Q 029530 162 NNTEYKLESFSGVYRKLTGKDVVFDYPITD 191 (192)
Q Consensus 162 ~~ve~Kl~tfs~VYkkLTgK~v~FeFp~~~ 191 (192)
+++|||||||++|||+||||||+||||+++
T Consensus 160 ~~ve~Kl~tfs~VYkkLTgK~v~FeFp~~~ 189 (189)
T PF01251_consen 160 NNVEHKLDTFSAVYKKLTGKDVVFEFPEQE 189 (189)
T ss_dssp HHHHCCHHHHHHHHHHHCS-EEEEEEE---
T ss_pred ccHHHHHHHHHHHHHHHcCCceEEEcCCCC
Confidence 999999999999999999999999999864
No 2
>KOG3320 consensus 40S ribosomal protein S7 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.4e-92 Score=588.49 Aligned_cols=190 Identities=59% Similarity=0.929 Sum_probs=187.3
Q ss_pred CCccccccccCCCCCCCHHHHHHHHHhHhhhcCChHHHhcCcceeeeeeEEEEecCCeeEEEEEeehhhHHHHHHHHHHH
Q 029530 1 MFTTKKKIQKDKDAEPTEFEETVAQALFDLENTNQELKSDLKDLYINQAIQMDVSGNRKAIVVYVPYRLRKAYRKIHSRL 80 (192)
Q Consensus 1 m~~~~~Ki~k~~~~~p~e~E~~Vaqal~dLe~~~~dLk~~Lr~l~i~~akei~v~~~kKAivIfVP~~~lk~f~Kiq~rL 80 (192)
||++.+||+|++|..|||||.+|||||+|||++|+|||++|++|||++|+||||+||+||||||||+|+|++|||||.||
T Consensus 1 m~s~~~Ki~k~~~~~ptE~E~~iaqal~~le~~n~~lk~~lr~L~I~~a~eiev~Gg~Kaivi~VP~p~lk~fqki~~~L 80 (192)
T KOG3320|consen 1 MFSSQAKIHKPSGSKPTEFEMQIAQALLDLEMDNSDLKAQLRELNITSAKEIEVGGGRKAIVIFVPVPQLKAFQKIQVRL 80 (192)
T ss_pred CccccccccCCCCCCchHHHHHHHHHHHHHHhcchhhHHHhhhheeeeeEEEEecCCcEEEEEEechHHHHHHHHHHHHH
Confidence 89999999999999999999999999999999899999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhcCCCeEEEEeeecccCCCCCCCc-cccCCCcchhhhhHhhhhcccccceeeceeEEEeeCCceeEEEEecCcc
Q 029530 81 VRELEKKFSGKDVVLIATRRIVRPPKKGSA-VQRPRSRTLTAVHDAMLEDVVYPAEIVGKRVRYRLDGSKIIKVIFLDPK 159 (192)
Q Consensus 81 v~ELEKKfsg~~Vv~vAqRrIl~kp~~~~~-q~RPRSRTLTaVheaiLeDlV~P~eIVGKR~r~r~DGsk~~KV~~LD~k 159 (192)
+|||||||||+||+|||+|||+|+|++++. |||||||||||||||||||+|||+|||||||||++||++++|| |||++
T Consensus 81 vreleKKF~gk~Vifia~Rrilpkp~rks~~qKRprsrtltaVhdaiLed~vfP~eIvGkR~rv~ldg~ki~kV-~LD~~ 159 (192)
T KOG3320|consen 81 VRELEKKFSGKHVIFIAQRRILPKPTRKSRTQKRPRSRTLTAVHDAILEDLVFPAEIVGKRTRVKLDGSKLVKV-HLDKK 159 (192)
T ss_pred HHHHHHhcCCceEEEEEeeeeccCCCCCcccccCCccchHHHHHHHHHHhccchhhhcceeEEEEecCcEEEEE-Eechh
Confidence 999999999999999999999999999987 8999999999999999999999999999999999999999999 99999
Q ss_pred cccchhhhhhhHHHHHhhhcCCceEEECCCCC
Q 029530 160 ERNNTEYKLESFSGVYRKLTGKDVVFDYPITD 191 (192)
Q Consensus 160 ~~~~ve~Kl~tfs~VYkkLTgK~v~FeFp~~~ 191 (192)
|+|++|||+|+|++||++||||||+||||+..
T Consensus 160 ~~n~~e~K~e~f~~vy~kLtGKdv~fEfp~~~ 191 (192)
T KOG3320|consen 160 QQNNVEHKVETFSAVYKKLTGKDVVFEFPEFT 191 (192)
T ss_pred hccchHHhHHHHHHHHHHhcCCceEEecCccc
Confidence 99999999999999999999999999999864
No 3
>PTZ00389 40S ribosomal protein S7; Provisional
Probab=100.00 E-value=3.3e-89 Score=571.51 Aligned_cols=182 Identities=57% Similarity=0.937 Sum_probs=177.6
Q ss_pred cccCCCCCCCHHHHHHHHHhHhhhcCChHHHhcCcceeeeeeEEEEecCC-eeEEEEEeehhhHHHHHHHHHHHHHHHHh
Q 029530 8 IQKDKDAEPTEFEETVAQALFDLENTNQELKSDLKDLYINQAIQMDVSGN-RKAIVVYVPYRLRKAYRKIHSRLVRELEK 86 (192)
Q Consensus 8 i~k~~~~~p~e~E~~Vaqal~dLe~~~~dLk~~Lr~l~i~~akei~v~~~-kKAivIfVP~~~lk~f~Kiq~rLv~ELEK 86 (192)
+.|++|++|||||.+|||||+|||++|+|||++|++|||++||||||++| ||||||||||||+++|||||.||++||||
T Consensus 1 ~~k~~~~~p~e~E~~vaqal~~le~~~~dlK~~L~~L~i~~akei~v~~~~kkaivIfVP~~~lk~~~kiq~rLv~ELEK 80 (184)
T PTZ00389 1 IKKLKKAEPSELEKQVAKALFELEASSKDLKADLKNLKISSVKEVTVGKDKKKAVVVFVPYRMLMIYRKIQRKLIPELEK 80 (184)
T ss_pred CCCCCCCCCCHHHHHHHHHHHHHHhCcHHHHhhhhccEEeeEEEEEecCCCcEEEEEEecHHHHHHHHHHHHHHHHHHHH
Confidence 46889999999999999999999999999999999999999999999877 99999999999999999999999999999
Q ss_pred hcCCCeEEEEeeecccCCCCCCCc-cccCCCcchhhhhHhhhhcccccceeeceeEEEeeCCceeEEEEecCcccccchh
Q 029530 87 KFSGKDVVLIATRRIVRPPKKGSA-VQRPRSRTLTAVHDAMLEDVVYPAEIVGKRVRYRLDGSKIIKVIFLDPKERNNTE 165 (192)
Q Consensus 87 Kfsg~~Vv~vAqRrIl~kp~~~~~-q~RPRSRTLTaVheaiLeDlV~P~eIVGKR~r~r~DGsk~~KV~~LD~k~~~~ve 165 (192)
|| |+||+|||||||+|+|+++++ |+|||||||||||||||+|||||+|||||||||++|||+++|| |||++|++++|
T Consensus 81 K~-g~~Vv~ia~RrIl~kp~r~~~~q~rPrSRTLTaVhdaiLeDLvyPaeIvGkRir~~~DGsk~~KV-~Ld~~d~~~ve 158 (184)
T PTZ00389 81 KL-KKHVVIVAQRTILKKPVKNYKLKTRPRSRTLTAVHEAILEDLVYPSEIVGKRTRVRVDGSKLLKV-FLDPKDRKNVE 158 (184)
T ss_pred Hh-CCeEEEEEEEEEcCCCCcCccccCCCCccchHHHHHHHHHHhccchheeeeEEEEecCCcEEEEE-EeCHHHhcccc
Confidence 99 999999999999999999886 9999999999999999999999999999999999999999999 99999999999
Q ss_pred hhhhhHHHHHhhhcCCceEEECCCCC
Q 029530 166 YKLESFSGVYRKLTGKDVVFDYPITD 191 (192)
Q Consensus 166 ~Kl~tfs~VYkkLTgK~v~FeFp~~~ 191 (192)
||+|+|++||++|||+||+||||++.
T Consensus 159 ~Kletf~~VykkLTgkdV~fefp~~~ 184 (184)
T PTZ00389 159 EKLDAFSAVYKKLTGRDVVFEFPWDP 184 (184)
T ss_pred hhHHHHHHHHHHHhCCCeEEEecCCC
Confidence 99999999999999999999999863
No 4
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=99.77 E-value=2.2e-18 Score=142.90 Aligned_cols=137 Identities=23% Similarity=0.389 Sum_probs=108.3
Q ss_pred CCCHHHHHHHHHhHhhhcCChHHHhcCcceeeeeeEEEEecCCeeEEEEEe--ehhhHHHHHHHHHHHHHHHHhhcCCCe
Q 029530 15 EPTEFEETVAQALFDLENTNQELKSDLKDLYINQAIQMDVSGNRKAIVVYV--PYRLRKAYRKIHSRLVRELEKKFSGKD 92 (192)
Q Consensus 15 ~p~e~E~~Vaqal~dLe~~~~dLk~~Lr~l~i~~akei~v~~~kKAivIfV--P~~~lk~f~Kiq~rLv~ELEKKfsg~~ 92 (192)
.-+++|-.|+.+|++||-+ ..|++..+-.|-++ ++ + |||| |=. =.+..| -...++.|++++ ||+
T Consensus 27 ~v~~~dv~i~~~l~~l~~~-----~~l~~~~~~k~~~~--dd-r---vIfvV~~gd-g~aIGk-~G~~ik~l~~~l-gk~ 92 (166)
T PRK06418 27 EVTELDVEVSKVLLKLEED-----KELKDVEYKKAYEV--DD-L---VILLVTSGP-RIPIGK-GGKIAKALSRKL-GKK 92 (166)
T ss_pred ceEEeehHHHHHHHHhhcc-----ccccCceEEEEEEe--CC-E---EEEEEeCCC-cccccc-cchHHHHHHHHh-CCc
Confidence 5689999999999999833 34566655555544 43 2 3333 222 223333 467888899999 889
Q ss_pred EEEEeeecccCCCCCCCccccCCCcchhhhhHhhhhcccccceeeceeEEEeeCCceeEEEEecCcccccchhhhhhhHH
Q 029530 93 VVLIATRRIVRPPKKGSAVQRPRSRTLTAVHDAMLEDVVYPAEIVGKRVRYRLDGSKIIKVIFLDPKERNNTEYKLESFS 172 (192)
Q Consensus 93 Vv~vAqRrIl~kp~~~~~q~RPRSRTLTaVheaiLeDlV~P~eIVGKR~r~r~DGsk~~KV~~LD~k~~~~ve~Kl~tfs 172 (192)
|=+|- .|-+ -+.+|+||+||++|+|+|++++.||+..+|| ++|++|++++++|+++|+
T Consensus 93 VevVE-----------------~s~d----~~~fl~Nl~~PA~V~gV~i~~~~dG~~~~kV-~Vd~~Dk~~l~~k~e~~~ 150 (166)
T PRK06418 93 VRVVE-----------------KTND----IKKLAVQLLSPARVLGVNTVWLPDGTVQYVI-RVSRRDRRRLPAKPELLE 150 (166)
T ss_pred EEEEE-----------------cCCC----HHHHHHhcCCCcEEEEEEEEEeCCCcEEEEE-EECHHHhhcccccHHHHH
Confidence 87775 1111 4679999999999999999999999999999 999999999999999999
Q ss_pred HHHhhhcCCceEEEC
Q 029530 173 GVYRKLTGKDVVFDY 187 (192)
Q Consensus 173 ~VYkkLTgK~v~FeF 187 (192)
+||++|||++|.|+|
T Consensus 151 ~v~~kltgk~v~~~f 165 (166)
T PRK06418 151 SILSKITGTEVKIRV 165 (166)
T ss_pred HHHHHHHCCcEEEEe
Confidence 999999999999998
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=83.73 E-value=6.1 Score=34.18 Aligned_cols=93 Identities=19% Similarity=0.290 Sum_probs=62.2
Q ss_pred hhHHHHHHHHHHHH---HHHHhhcCCCeEEEEeeecccCCCCCCCccccCCCcchhhhhHhhhhcccccceeeceeEEEe
Q 029530 68 RLRKAYRKIHSRLV---RELEKKFSGKDVVLIATRRIVRPPKKGSAVQRPRSRTLTAVHDAMLEDVVYPAEIVGKRVRYR 144 (192)
Q Consensus 68 ~~lk~f~Kiq~rLv---~ELEKKfsg~~Vv~vAqRrIl~kp~~~~~q~RPRSRTLTaVheaiLeDlV~P~eIVGKR~r~r 144 (192)
+.+..|.+.+.++. ..| +- .|++|+|+|.+..-..+- .--.+.+|=....++.+.+.+.--+++|| |+.+.
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-SNKNIYATAWELTNQSSG---ESGQIYNRYQPDIREKVLNAFLGLTDVVG-RIVLN 183 (220)
T ss_pred cccccHHHHHHHHHHHHHHH-Hh-CCCcEEEEEeeccccccC---CCCCCcceechhhhhhHHHhhcccccEEE-EEEEc
Confidence 35678888876654 555 23 599999999987521111 11224456666778888899999999999 56554
Q ss_pred e-CCceeEEEEecCcccccchhhhhh
Q 029530 145 L-DGSKIIKVIFLDPKERNNTEYKLE 169 (192)
Q Consensus 145 ~-DGsk~~KV~~LD~k~~~~ve~Kl~ 169 (192)
- +|. +.+.+++.+.....++||
T Consensus 184 ~~~g~---R~~~~~~~~~~~AKNrld 206 (220)
T TIGR01618 184 GETGE---RGFILDPSKGNYAKNRLD 206 (220)
T ss_pred cCCCc---eEEEECCCCCcccccccc
Confidence 4 466 454678877766666665
No 6
>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=66.29 E-value=21 Score=24.60 Aligned_cols=66 Identities=18% Similarity=0.358 Sum_probs=46.6
Q ss_pred HHHHHHHhHhhhcCChHHHhcCcceeeeeeEEEEecCCeeEEEEEeehhhHHHHHHHHHHHHHHHHhhcCC
Q 029530 20 EETVAQALFDLENTNQELKSDLKDLYINQAIQMDVSGNRKAIVVYVPYRLRKAYRKIHSRLVRELEKKFSG 90 (192)
Q Consensus 20 E~~Vaqal~dLe~~~~dLk~~Lr~l~i~~akei~v~~~kKAivIfVP~~~lk~f~Kiq~rLv~ELEKKfsg 90 (192)
|++|-+||-.+. .+++..+|-++.+ .+++++.+|+=.+.+.+|+|-...+..++..+..-|. .++|
T Consensus 1 k~~V~~aL~~v~--dP~~~~~iv~~g~--V~~i~i~~~~V~v~l~l~~~~~~~~~~l~~~i~~~l~-~l~g 66 (72)
T PF01883_consen 1 KQAVRDALKQVK--DPELGKDIVELGM--VRDISIEGGKVSVSLELPTPACPAAEPLREEIREALK-ALPG 66 (72)
T ss_dssp HHHHHHHHTT-B--ETTTSSBTTTTTS--EEEEEECTCEEEEEE--SSTTHTTHHHHHHHHHHHHH-TSTT
T ss_pred CHHHHHHHhCCC--CCCCCCCHHHcCC--eeEEEEECCEEEEEEEECCCCchHHHHHHHHHHHHHH-hCCC
Confidence 456667776666 2555555555444 6789999999999999999999888888888888777 5555
No 7
>TIGR02945 SUF_assoc FeS assembly SUF system protein. Members of this family belong to the broader Pfam family pfam01883, or Domain of Unknown Function DUF59. Many members of DUF59 are candidate ring hydroxylating complex subunits. However, members of the narrower family defined here all are found in genomes that carry the FeS assembly SUF system. For 70 % of these species, the member of this protein family is found as part of the SUF locus, usually immediately downstream of the sufS gene.
Probab=58.43 E-value=33 Score=25.19 Aligned_cols=69 Identities=13% Similarity=0.173 Sum_probs=51.3
Q ss_pred HHHHHHHHhHhhhcCChHHHhcCcceeeeeeEEEEecC-CeeEEEEEeehhhHHHHHHHHHHHHHHHHhhcCCCe
Q 029530 19 FEETVAQALFDLENTNQELKSDLKDLYINQAIQMDVSG-NRKAIVVYVPYRLRKAYRKIHSRLVRELEKKFSGKD 92 (192)
Q Consensus 19 ~E~~Vaqal~dLe~~~~dLk~~Lr~l~i~~akei~v~~-~kKAivIfVP~~~lk~f~Kiq~rLv~ELEKKfsg~~ 92 (192)
.+.+|.++|-.+. .+++...|-++. .++.+++.+ ++--|.+..|+|.......++..+...|+. ++|-.
T Consensus 2 ~~~~I~~~L~~v~--dP~l~~~lv~~g--~V~~i~v~~~~~v~i~l~l~~p~~~~~~~l~~~i~~al~~-l~gv~ 71 (99)
T TIGR02945 2 LKDAVIEALKTVY--DPEIPVNIYELG--LIYDIDVDDDGHVDIQMTLTAPNCPVAGSMPGEVENAVRA-VPGVG 71 (99)
T ss_pred HHHHHHHHHcCCC--CCCCCCCeecCC--CeeEEEECCCCeEEEEEEECCCCCChHHHHHHHHHHHHHh-CCCCc
Confidence 4677888888777 366666665553 347788885 888999999999888888888888888865 44544
No 8
>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=50.61 E-value=51 Score=25.01 Aligned_cols=45 Identities=9% Similarity=0.267 Sum_probs=35.8
Q ss_pred eEEEEEeehhhHHHHHHHHHHHHHHHHhhcCCCeEEEEeeecccC
Q 029530 59 KAIVVYVPYRLRKAYRKIHSRLVRELEKKFSGKDVVLIATRRIVR 103 (192)
Q Consensus 59 KAivIfVP~~~lk~f~Kiq~rLv~ELEKKfsg~~Vv~vAqRrIl~ 103 (192)
-++|+.+-..-..+|..+...+..++.+..++.++++|+.-.=++
T Consensus 71 d~~ilv~d~~~~~s~~~~~~~~~~~i~~~~~~~piilv~nK~Dl~ 115 (174)
T smart00174 71 DVFLICFSVDSPASFENVKEKWYPEVKHFCPNTPIILVGTKLDLR 115 (174)
T ss_pred CEEEEEEECCCHHHHHHHHHHHHHHHHhhCCCCCEEEEecChhhh
Confidence 466666677778999998877788888888899999998865443
No 9
>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=48.44 E-value=24 Score=29.88 Aligned_cols=40 Identities=33% Similarity=0.549 Sum_probs=26.3
Q ss_pred CcchhhhhHhhhhccc-------ccceeeceeE---E---EeeCCceeEEEEec
Q 029530 116 SRTLTAVHDAMLEDVV-------YPAEIVGKRV---R---YRLDGSKIIKVIFL 156 (192)
Q Consensus 116 SRTLTaVheaiLeDlV-------~P~eIVGKR~---r---~r~DGsk~~KV~~L 156 (192)
.-++++-.+.++.+++ .|-||||||- + ++.+|+...|| .|
T Consensus 102 ~~~~~~~~~~l~~~v~~i~~~~~~~vEiIgKrk~~~~~~~~~~~~~~~~kv-~~ 154 (245)
T PF01577_consen 102 KVKMSDTFDNLIRQVLKIAKKKGKPVEIIGKRKKRTRARYKRRGGKRYLKV-ET 154 (245)
T ss_pred ccccchhHHHHHHHHHHHHHhcCCeEEEEecCCceEEEEEEEECCEEEEEE-EC
Confidence 3334432455555543 4999999974 2 56789999999 53
No 10
>PF02154 FliM: Flagellar motor switch protein FliM; InterPro: IPR001689 The flagellar motor switch in Escherichia coli and Salmonella typhimurium regulates the direction of flagellar rotation and hence controls swimming behaviour []. The switch is a complex apparatus that responds to signals transduced by the chemotaxis sensory signalling system during chemotactic behaviour []. CheY, the chemotaxis response regulator, is believed to act directly on the switch to induce tumbles in the swimming pattern, but no physical interactions of CheY and switch proteins have yet been demonstrated. The switch complex comprises at least three proteins - FliG, FliM and FliN. It has been shown that FliG interacts with FliM, FliM interacts with itself, and FliM interacts with FliN []. Several residues within the middle third of FliG appear to be strongly involved in the FliG-FliM interaction, with residues near the N or C termini being less important []. Such clustering suggests that FliG-FliM interaction plays a central role in switching. Analysis of the FliG, FliM and FliN sequences shows that none are especially hydrophobic or appear to be integral membrane proteins []. This result is consistent with other evidence suggesting that the proteins may be peripheral to the membrane, possibly mounted on the basal body M ring [, ].; GO: 0003774 motor activity, 0001539 ciliary or flagellar motility, 0006935 chemotaxis, 0009425 bacterial-type flagellum basal body; PDB: 3SOH_C 2HP7_A.
Probab=38.78 E-value=2.2e+02 Score=23.28 Aligned_cols=62 Identities=18% Similarity=0.353 Sum_probs=41.6
Q ss_pred CCCCCCHHHHHHHHHhHhh----------------------hcCChHHHhcC--cceeeeeeEEEEecCCeeEEEEEeeh
Q 029530 12 KDAEPTEFEETVAQALFDL----------------------ENTNQELKSDL--KDLYINQAIQMDVSGNRKAIVVYVPY 67 (192)
Q Consensus 12 ~~~~p~e~E~~Vaqal~dL----------------------e~~~~dLk~~L--r~l~i~~akei~v~~~kKAivIfVP~ 67 (192)
.+.+.|++|..+.+-+++. | +|+++.+-. .+..+...=++++++..-.+-|.+|+
T Consensus 104 ~~R~~T~iE~~i~~~v~~~~~~~l~~aw~~v~~~~~~~~~~E-~np~~~~i~~~~e~vv~~~f~i~i~~~~g~~~i~~P~ 182 (192)
T PF02154_consen 104 EGREFTEIEQRILRRVVERILEALREAWQPVVPLEFELERIE-TNPQFVQIVPPNEPVVVITFEIKIGGREGMMNICIPY 182 (192)
T ss_dssp -SS---HHHHHHHHHHHHHHHHHHHHHCTTTH---EEEEEEE-SSGGGT-SS-TTSEEEEEEEEEEETTEEEEEEEEEEH
T ss_pred ccccCcHHHHHHHHHHHHHHHHHHHHHHhhceeeeeEeeeEe-cCHHHHcccCCCCeEEEEEEEEEECCcEEEEEEEecH
Confidence 4668999999998755542 2 345544333 56677777899999888899999999
Q ss_pred hhHHHHH
Q 029530 68 RLRKAYR 74 (192)
Q Consensus 68 ~~lk~f~ 74 (192)
..+...+
T Consensus 183 ~~lepi~ 189 (192)
T PF02154_consen 183 STLEPIR 189 (192)
T ss_dssp HHHHHHH
T ss_pred HHHHHHH
Confidence 8887654
No 11
>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=37.77 E-value=1.1e+02 Score=22.87 Aligned_cols=45 Identities=9% Similarity=0.307 Sum_probs=35.7
Q ss_pred eEEEEEeehhhHHHHHHHHHHHHHHHHhhcCCCeEEEEeeecccC
Q 029530 59 KAIVVYVPYRLRKAYRKIHSRLVRELEKKFSGKDVVLIATRRIVR 103 (192)
Q Consensus 59 KAivIfVP~~~lk~f~Kiq~rLv~ELEKKfsg~~Vv~vAqRrIl~ 103 (192)
-++++.+.......|......+..++....++..+++|+.-.=++
T Consensus 73 ~~~i~v~d~~~~~s~~~~~~~~~~~~~~~~~~~p~ivv~nK~Dl~ 117 (171)
T cd00157 73 DVFLICFSVDSPSSFENVKTKWIPEIRHYCPNVPIILVGTKIDLR 117 (171)
T ss_pred CEEEEEEECCCHHHHHHHHHHHHHHHHhhCCCCCEEEEEccHHhh
Confidence 477777777778889888877788888887889999998866443
No 12
>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=33.46 E-value=72 Score=28.50 Aligned_cols=31 Identities=26% Similarity=0.350 Sum_probs=27.3
Q ss_pred hhHHHHHHHHHHHHHHHHhhcCCCeEEEEee
Q 029530 68 RLRKAYRKIHSRLVRELEKKFSGKDVVLIAT 98 (192)
Q Consensus 68 ~~lk~f~Kiq~rLv~ELEKKfsg~~Vv~vAq 98 (192)
+.+.+.++.|.+.+.++++.|+|.+|+-+-.
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 5689999999999999999999999887754
No 13
>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=31.65 E-value=59 Score=22.57 Aligned_cols=21 Identities=24% Similarity=0.409 Sum_probs=15.4
Q ss_pred eeEEEEEeehhhH-HHHHHHHH
Q 029530 58 RKAIVVYVPYRLR-KAYRKIHS 78 (192)
Q Consensus 58 kKAivIfVP~~~l-k~f~Kiq~ 78 (192)
+..-..+|||.+| ..+|.||.
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 4456667999999 56688774
No 14
>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=29.81 E-value=1.1e+02 Score=23.04 Aligned_cols=47 Identities=19% Similarity=0.295 Sum_probs=31.7
Q ss_pred EEEEecC--CeeEEEEEeehhhHHHHHHHHHHHHHHHHhhcCCCeEEEEe
Q 029530 50 IQMDVSG--NRKAIVVYVPYRLRKAYRKIHSRLVRELEKKFSGKDVVLIA 97 (192)
Q Consensus 50 kei~v~~--~kKAivIfVP~~~lk~f~Kiq~rLv~ELEKKfsg~~Vv~vA 97 (192)
+.+..+. ||..+|.|.+..-...+++-.. .+.+|-+++.++.|-+|+
T Consensus 19 ~~~~l~~~~gk~~vv~f~~~~~Cp~C~~~~p-~l~~l~~~~~~~~v~~v~ 67 (146)
T PF08534_consen 19 KPVSLSDFKGKPVVVNFWASAWCPPCRKELP-YLNELQEKYKDKGVDVVG 67 (146)
T ss_dssp EEEEGGGGTTSEEEEEEESTTTSHHHHHHHH-HHHHHHHHHHTTTCEEEE
T ss_pred CEecHHHhCCCeEEEEEEccCCCCcchhhhh-hHHhhhhhhccCceEEEE
Confidence 4555544 7889999998756666776444 778887776666554443
No 15
>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=29.45 E-value=1e+02 Score=31.19 Aligned_cols=49 Identities=29% Similarity=0.548 Sum_probs=37.5
Q ss_pred EEEEecCCeeEEEEEeehh--h---HHHHH--------HHHHHHHHHHHhhcCCCeEEEEeeeccc
Q 029530 50 IQMDVSGNRKAIVVYVPYR--L---RKAYR--------KIHSRLVRELEKKFSGKDVVLIATRRIV 102 (192)
Q Consensus 50 kei~v~~~kKAivIfVP~~--~---lk~f~--------Kiq~rLv~ELEKKfsg~~Vv~vAqRrIl 102 (192)
.++.++|+-.|+++|.|.| . ..++| ...+||--|| .. | +|||.+-|++-
T Consensus 607 ~~~~~~~~e~alllf~p~~~~~~~~~aa~rlla~l~~~~f~qrlRve~--ql-G-Y~v~~~~~~~~ 668 (696)
T TIGR02110 607 VPLACDGGEQALLLFCPLPTADVASEAAWRLLAQLLEPPFFQRLRVEL--QL-G-YVVFCRYRRVA 668 (696)
T ss_pred EeccCCCCCcEEEEEecCCCCCHHHHHHHHHHHHHhchhHHHHHHHhh--cc-c-eEEEEeeEEcC
Confidence 5677788899999999999 3 45565 2356777665 44 6 99999999985
No 16
>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=28.97 E-value=1.8e+02 Score=21.58 Aligned_cols=43 Identities=9% Similarity=0.303 Sum_probs=34.9
Q ss_pred eEEEEEeehhhHHHHHHHHHHHHHHHHhhcC-CCeEEEEeeeccc
Q 029530 59 KAIVVYVPYRLRKAYRKIHSRLVRELEKKFS-GKDVVLIATRRIV 102 (192)
Q Consensus 59 KAivIfVP~~~lk~f~Kiq~rLv~ELEKKfs-g~~Vv~vAqRrIl 102 (192)
.+++|..-+....+|+.++ .+..++.+..+ +.++++++...=+
T Consensus 73 ~~~ii~fd~~~~~S~~~~~-~~~~~i~~~~~~~~~iivvg~K~D~ 116 (162)
T PF00071_consen 73 DAIIIVFDVTDEESFENLK-KWLEEIQKYKPEDIPIIVVGNKSDL 116 (162)
T ss_dssp SEEEEEEETTBHHHHHTHH-HHHHHHHHHSTTTSEEEEEEETTTG
T ss_pred ccccccccccccccccccc-cccccccccccccccceeeeccccc
Confidence 5777777888899999999 77778888887 6889999876533
No 17
>PF03799 FtsQ: Cell division protein FtsQ; InterPro: IPR005548 FtsQ is one of several cell division proteins. FtsQ interacts with other Fts proteins, reviewed in []. The precise function of FtsQ is unknown.; PDB: 2VH1_B 2VH2_B 2ALJ_A 1YR1_A.
Probab=28.15 E-value=1.4e+02 Score=21.41 Aligned_cols=39 Identities=21% Similarity=0.310 Sum_probs=25.6
Q ss_pred eEEEeeCCceeEEEEecCcccccchhhhhhhHHHHHhhhc---CCceE
Q 029530 140 RVRYRLDGSKIIKVIFLDPKERNNTEYKLESFSGVYRKLT---GKDVV 184 (192)
Q Consensus 140 R~r~r~DGsk~~KV~~LD~k~~~~ve~Kl~tfs~VYkkLT---gK~v~ 184 (192)
.+.+.+++...++. .. .+.+.|+..|..+|..+. ++++.
T Consensus 71 ~~~l~l~dg~~V~l---g~---~~~~~kl~~~~~i~~~~~~~~~~~i~ 112 (117)
T PF03799_consen 71 SWTLYLDDGVEVKL---GR---SDLAEKLQRLVKILPQLEKSKGKKIA 112 (117)
T ss_dssp CEEEE-SSS-EEEE---ES---STHHHHHHHHHHHHHCCC-HHCCCEE
T ss_pred eEEEEECCCcEEEE---cC---cCHHHHHHHHHHHHHHHHHhhcCCCe
Confidence 37777754443444 32 348999999999999886 55553
No 18
>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=27.74 E-value=2.1e+02 Score=21.64 Aligned_cols=41 Identities=12% Similarity=0.222 Sum_probs=30.5
Q ss_pred EEEEEeehhhHHHHHHHHHHHHHHHHhhcCCCeEEEEeeec
Q 029530 60 AIVVYVPYRLRKAYRKIHSRLVRELEKKFSGKDVVLIATRR 100 (192)
Q Consensus 60 AivIfVP~~~lk~f~Kiq~rLv~ELEKKfsg~~Vv~vAqRr 100 (192)
++++.+-+.-..+|+.+...+.++|.+..++.++++++...
T Consensus 74 ~~ilv~~~~~~~s~~~~~~~~~~~l~~~~~~~piivv~nK~ 114 (174)
T cd04135 74 VFLICFSVVNPASFQNVKEEWVPELKEYAPNVPYLLVGTQI 114 (174)
T ss_pred EEEEEEECCCHHHHHHHHHHHHHHHHhhCCCCCEEEEeEch
Confidence 34433445556889999888888888777889999998764
No 19
>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=27.46 E-value=2.1e+02 Score=21.66 Aligned_cols=43 Identities=9% Similarity=0.232 Sum_probs=31.6
Q ss_pred EEEEEeehhhHHHHHHHHHHHHHHHHhhcCCCeEEEEeeeccc
Q 029530 60 AIVVYVPYRLRKAYRKIHSRLVRELEKKFSGKDVVLIATRRIV 102 (192)
Q Consensus 60 AivIfVP~~~lk~f~Kiq~rLv~ELEKKfsg~~Vv~vAqRrIl 102 (192)
++++.+.+.-..+|..+...+..++.+..++.++++++...=+
T Consensus 75 ~~i~v~~~~~~~s~~~~~~~~~~~~~~~~~~~piilv~nK~Dl 117 (175)
T cd01870 75 VILMCFSIDSPDSLENIPEKWTPEVKHFCPNVPIILVGNKKDL 117 (175)
T ss_pred EEEEEEECCCHHHHHHHHHHHHHHHHhhCCCCCEEEEeeChhc
Confidence 4555566666678888877778888777778899999876544
No 20
>cd01893 Miro1 Miro1 subfamily. Miro (mitochondrial Rho) proteins have tandem GTP-binding domains separated by a linker region containing putative calcium-binding EF hand motifs. Genes encoding Miro-like proteins were found in several eukaryotic organisms. This CD represents the N-terminal GTPase domain of Miro proteins. These atypical Rho GTPases have roles in mitochondrial homeostasis and apoptosis. Most Rho proteins contain a lipid modification site at the C-terminus; however, Miro is one of few Rho subfamilies that lack this feature.
Probab=27.32 E-value=2.2e+02 Score=21.72 Aligned_cols=42 Identities=7% Similarity=0.135 Sum_probs=29.9
Q ss_pred EEEEEeehhhHHHHHHHHHHHHHHHHhhcCCCeEEEEeeecc
Q 029530 60 AIVVYVPYRLRKAYRKIHSRLVRELEKKFSGKDVVLIATRRI 101 (192)
Q Consensus 60 AivIfVP~~~lk~f~Kiq~rLv~ELEKKfsg~~Vv~vAqRrI 101 (192)
++++.+......+|..+...+..+++....+.++++++...=
T Consensus 73 ~~ilv~d~~~~~s~~~~~~~~~~~i~~~~~~~pviiv~nK~D 114 (166)
T cd01893 73 VICLVYSVDRPSTLERIRTKWLPLIRRLGVKVPIILVGNKSD 114 (166)
T ss_pred EEEEEEECCCHHHHHHHHHHHHHHHHHhCCCCCEEEEEEchh
Confidence 455555666678888877777777776556789999987543
No 21
>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=27.14 E-value=2e+02 Score=22.05 Aligned_cols=43 Identities=12% Similarity=0.276 Sum_probs=32.2
Q ss_pred EEEEEeehhhHHHHHHHHHHHHHHHHhhcCCCeEEEEeeeccc
Q 029530 60 AIVVYVPYRLRKAYRKIHSRLVRELEKKFSGKDVVLIATRRIV 102 (192)
Q Consensus 60 AivIfVP~~~lk~f~Kiq~rLv~ELEKKfsg~~Vv~vAqRrIl 102 (192)
++|+-+.+.-..+|+.+...+..++.+..++..+++++...=+
T Consensus 74 ~~i~v~d~~~~~sf~~~~~~~~~~~~~~~~~~piilv~nK~Dl 116 (173)
T cd04130 74 VFLLCFSVVNPSSFQNISEKWIPEIRKHNPKAPIILVGTQADL 116 (173)
T ss_pred EEEEEEECCCHHHHHHHHHHHHHHHHhhCCCCCEEEEeeChhh
Confidence 5555556666778988877777888877778899999886644
No 22
>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=26.54 E-value=93 Score=22.24 Aligned_cols=25 Identities=20% Similarity=0.371 Sum_probs=20.1
Q ss_pred HHHHHHHHHHHHhhcCCCeEEEEee
Q 029530 74 RKIHSRLVRELEKKFSGKDVVLIAT 98 (192)
Q Consensus 74 ~Kiq~rLv~ELEKKfsg~~Vv~vAq 98 (192)
-.-|..|-+|+..-|+++.++.|..
T Consensus 31 ie~Q~~L~~~ik~~F~~~P~i~V~n 55 (58)
T PF06858_consen 31 IEEQLSLFKEIKPLFPNKPVIVVLN 55 (58)
T ss_dssp HHHHHHHHHHHHHHTTTS-EEEEE-
T ss_pred HHHHHHHHHHHHHHcCCCCEEEEEe
Confidence 3558999999999999999998864
No 23
>PF13479 AAA_24: AAA domain
Probab=26.00 E-value=3.3e+02 Score=22.53 Aligned_cols=90 Identities=20% Similarity=0.363 Sum_probs=46.6
Q ss_pred HHHHHHHHHHHHHHHHhh--cCCCeEEEEeeecccCCCCCC-CccccCCCcchhhhhHhhhhcccccceeeceeEEEee-
Q 029530 70 RKAYRKIHSRLVRELEKK--FSGKDVVLIATRRIVRPPKKG-SAVQRPRSRTLTAVHDAMLEDVVYPAEIVGKRVRYRL- 145 (192)
Q Consensus 70 lk~f~Kiq~rLv~ELEKK--fsg~~Vv~vAqRrIl~kp~~~-~~q~RPRSRTLTaVheaiLeDlV~P~eIVGKR~r~r~- 145 (192)
++.|..++..+.+-+.+- ..|+||||+|.-..-.-+..+ ..+.+|. .+....+-+.+-+++|| |++...
T Consensus 105 ~~~yg~~~~~~~~~i~~l~~~~~~~VI~tah~~~~~~~~~~~~~~~~~~------l~~k~~~~l~~~~D~V~-~l~~~~~ 177 (213)
T PF13479_consen 105 GKGYGELQQEFMRFIDKLLNALGKNVIFTAHAKEEEDEDGGKYTRYKPK------LGKKVRNELPGWFDVVG-RLRVETV 177 (213)
T ss_pred cchHHHHHHHHHHHHHHHHHHCCCcEEEEEEEEEEEcCCCCceeEEeec------cChhHHhhhhecccEEE-EEEEEEe
Confidence 567777765555555432 249999999977654432211 1233332 33355566777778883 344332
Q ss_pred -CCceeEEEEecCcccccchhhh
Q 029530 146 -DGSKIIKVIFLDPKERNNTEYK 167 (192)
Q Consensus 146 -DGsk~~KV~~LD~k~~~~ve~K 167 (192)
|++.- +++++.+.+.....++
T Consensus 178 ~~~~~~-R~~~~~~~~~~~aKnR 199 (213)
T PF13479_consen 178 DDETGK-RVIYFQPSPSYFAKNR 199 (213)
T ss_pred cCCCCc-eEEEECCCCceEccCC
Confidence 22211 4445555544444333
No 24
>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=25.59 E-value=2.3e+02 Score=22.44 Aligned_cols=44 Identities=18% Similarity=0.339 Sum_probs=32.4
Q ss_pred EEEEEeehhhHHHHHHHHHHHHHHHHhhcCCCeEEEEeeecccC
Q 029530 60 AIVVYVPYRLRKAYRKIHSRLVRELEKKFSGKDVVLIATRRIVR 103 (192)
Q Consensus 60 AivIfVP~~~lk~f~Kiq~rLv~ELEKKfsg~~Vv~vAqRrIl~ 103 (192)
++|+.+-+.-..+|+.+....+.++....++.++++||...=|+
T Consensus 74 ~~ilv~dv~~~~sf~~~~~~~~~~i~~~~~~~piilvgNK~Dl~ 117 (189)
T cd04134 74 VIMLCFSVDSPDSLENVESKWLGEIREHCPGVKLVLVALKCDLR 117 (189)
T ss_pred EEEEEEECCCHHHHHHHHHHHHHHHHHhCCCCCEEEEEEChhhc
Confidence 55555556677899888765677887777788999999876554
No 25
>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=25.43 E-value=1.3e+02 Score=22.13 Aligned_cols=42 Identities=21% Similarity=0.188 Sum_probs=25.6
Q ss_pred CCeeEEEEEeehhhHHHHHHHHHHHHHHHHhhcCCCeEEEEee
Q 029530 56 GNRKAIVVYVPYRLRKAYRKIHSRLVRELEKKFSGKDVVLIAT 98 (192)
Q Consensus 56 ~~kKAivIfVP~~~lk~f~Kiq~rLv~ELEKKfsg~~Vv~vAq 98 (192)
++++.+|+|+|-.-....+. +..-+.++-.+|.++.|-+||-
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 35788999998766666664 3344455666664444555543
No 26
>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=23.96 E-value=2.5e+02 Score=21.65 Aligned_cols=44 Identities=14% Similarity=0.298 Sum_probs=33.9
Q ss_pred eEEEEEeehhhHHHHHHHHHHHHHHHHhhcCCCeEEEEeeecccC
Q 029530 59 KAIVVYVPYRLRKAYRKIHSRLVRELEKKFSGKDVVLIATRRIVR 103 (192)
Q Consensus 59 KAivIfVP~~~lk~f~Kiq~rLv~ELEKKfsg~~Vv~vAqRrIl~ 103 (192)
-|+|+.+-+....+|+.++. .+.++.+...+.++++||...=++
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 46777778888889988864 667888777688999998866543
No 27
>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=23.72 E-value=2.6e+02 Score=21.96 Aligned_cols=44 Identities=11% Similarity=0.237 Sum_probs=31.6
Q ss_pred eEEEEEeehhhHHHHHHHHHHHHHHHHhhcCCCeEEEEeeeccc
Q 029530 59 KAIVVYVPYRLRKAYRKIHSRLVRELEKKFSGKDVVLIATRRIV 102 (192)
Q Consensus 59 KAivIfVP~~~lk~f~Kiq~rLv~ELEKKfsg~~Vv~vAqRrIl 102 (192)
.++|+.+=+.-..+|..+...+..++++.-++.++++|+...=+
T Consensus 74 ~~~ilv~d~~~~~s~~~~~~~w~~~i~~~~~~~piilvgnK~Dl 117 (175)
T cd01874 74 DVFLVCFSVVSPSSFENVKEKWVPEITHHCPKTPFLLVGTQIDL 117 (175)
T ss_pred CEEEEEEECCCHHHHHHHHHHHHHHHHHhCCCCCEEEEEECHhh
Confidence 35555555566788998876667888776677899999886543
No 28
>TIGR01397 fliM_switch flagellar motor switch protein FliM. Members of this family are the flagellar motor switch protein FliM. The family excludes FliM homologs that lack an N-terminal region critical to interaction with phosphorylated CheY. One set lacking this N-terminal region is found in Rhizobium meliloti, in which the direction of flagellar rotation is not reversible (i.e. the FliM homolog does not act to reverse the motor direction), and in related species. Another is found in Buchnera, an obligate intracellular endosymbiont with genes for many of the components of the flagellar apparatus, but not, apparently, for flagellin iself.
Probab=21.24 E-value=5.7e+02 Score=22.51 Aligned_cols=62 Identities=19% Similarity=0.295 Sum_probs=41.9
Q ss_pred CCCCCCHHHHHHHHHhHhhhc---------------------CChHHHh--cCcceeeeeeEEEEecCCeeEEEEEeehh
Q 029530 12 KDAEPTEFEETVAQALFDLEN---------------------TNQELKS--DLKDLYINQAIQMDVSGNRKAIVVYVPYR 68 (192)
Q Consensus 12 ~~~~p~e~E~~Vaqal~dLe~---------------------~~~dLk~--~Lr~l~i~~akei~v~~~kKAivIfVP~~ 68 (192)
.+.++|++|..+.+-+++.-. +|+.+-+ .-.+..+...=++++++..--+-+.+|+.
T Consensus 138 ~~R~lT~iE~~i~~~~~~~~~~~l~~aw~~~~~~~~~~~~~e~np~~~~i~~~~e~vv~~~f~v~i~~~~g~~~l~lP~~ 217 (320)
T TIGR01397 138 EGREFTEIERRVIDRILDRVLEDLKEAWSPVMPLEPELDRSETNPQFAQIVPPNEIVVLVSFSVEVGETEGMINICLPYS 217 (320)
T ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHhhCceeeeeEEEEEEcCHHHHhccCCCcEEEEEEEEEEECCceEEEEEEeeHH
Confidence 456889999999887665321 2233221 12345566677889988778888999998
Q ss_pred hHHHH
Q 029530 69 LRKAY 73 (192)
Q Consensus 69 ~lk~f 73 (192)
.+...
T Consensus 218 ~lepi 222 (320)
T TIGR01397 218 TLEPI 222 (320)
T ss_pred HHHHH
Confidence 87654
No 29
>COG4496 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.17 E-value=29 Score=27.35 Aligned_cols=31 Identities=29% Similarity=0.506 Sum_probs=24.7
Q ss_pred ccCCCcchhhhhHhhh------------hcccccceee--ceeEE
Q 029530 112 QRPRSRTLTAVHDAML------------EDVVYPAEIV--GKRVR 142 (192)
Q Consensus 112 ~RPRSRTLTaVheaiL------------eDlV~P~eIV--GKR~r 142 (192)
.+||+.+|.+..|||| +|||-|.||- ..|++
T Consensus 4 ~klr~~~Ld~l~dailtL~n~eecy~FfdDlcTinEiqslaqRlq 48 (100)
T COG4496 4 EKLRGAALDELFDAILTLENLEECYAFFDDLCTINEIQSLAQRLQ 48 (100)
T ss_pred cchhhHHHHHHHHHHHHhccHHHHHHHHHhhcCHHHHHHHHHHHH
Confidence 4688999999999985 7999999983 44554
No 30
>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=21.14 E-value=3e+02 Score=22.14 Aligned_cols=44 Identities=7% Similarity=0.196 Sum_probs=33.8
Q ss_pred eEEEEEeehhhHHHHHHHHHHHHHHHHhhcCCCeEEEEeeeccc
Q 029530 59 KAIVVYVPYRLRKAYRKIHSRLVRELEKKFSGKDVVLIATRRIV 102 (192)
Q Consensus 59 KAivIfVP~~~lk~f~Kiq~rLv~ELEKKfsg~~Vv~vAqRrIl 102 (192)
-++++.+-+.-..+|..+..+.+.++.+-.++.++++||...=|
T Consensus 78 d~~ilvyDit~~~Sf~~~~~~w~~~i~~~~~~~piilVgNK~DL 121 (182)
T cd04172 78 DAVLICFDISRPETLDSVLKKWKGEIQEFCPNTKMLLVGCKSDL 121 (182)
T ss_pred CEEEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCEEEEeEChhh
Confidence 46666666777899999877777888776678889999976554
No 31
>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=21.10 E-value=3.1e+02 Score=21.83 Aligned_cols=45 Identities=11% Similarity=0.304 Sum_probs=33.4
Q ss_pred eEEEEEeehhhHHHHHHHHHHHHHHHHhhcCCCeEEEEeeecccC
Q 029530 59 KAIVVYVPYRLRKAYRKIHSRLVRELEKKFSGKDVVLIATRRIVR 103 (192)
Q Consensus 59 KAivIfVP~~~lk~f~Kiq~rLv~ELEKKfsg~~Vv~vAqRrIl~ 103 (192)
.++|+.+-+.-..+|..++..+..++....++-++++||.-.=|+
T Consensus 76 ~~~ilvydit~~~Sf~~~~~~w~~~i~~~~~~~piilvgNK~DL~ 120 (191)
T cd01875 76 NVFIICFSIASPSSYENVRHKWHPEVCHHCPNVPILLVGTKKDLR 120 (191)
T ss_pred CEEEEEEECCCHHHHHHHHHHHHHHHHhhCCCCCEEEEEeChhhh
Confidence 355655566667889998766667776666788999999887764
No 32
>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=20.69 E-value=2.9e+02 Score=23.43 Aligned_cols=44 Identities=11% Similarity=0.172 Sum_probs=35.1
Q ss_pred eEEEEEeehhhHHHHHHHHHHHHHHHHhhcCCCeEEEEeeeccc
Q 029530 59 KAIVVYVPYRLRKAYRKIHSRLVRELEKKFSGKDVVLIATRRIV 102 (192)
Q Consensus 59 KAivIfVP~~~lk~f~Kiq~rLv~ELEKKfsg~~Vv~vAqRrIl 102 (192)
-++++.+-+.-..+|..+...+..|+....++-++++|+.-.=|
T Consensus 74 d~illvfdis~~~Sf~~i~~~w~~~~~~~~~~~piiLVgnK~DL 117 (222)
T cd04173 74 DAVLICFDISRPETLDSVLKKWQGETQEFCPNAKVVLVGCKLDM 117 (222)
T ss_pred CEEEEEEECCCHHHHHHHHHHHHHHHHhhCCCCCEEEEEECccc
Confidence 47777777888899999987777888777788899999876544
No 33
>smart00175 RAB Rab subfamily of small GTPases. Rab GTPases are implicated in vesicle trafficking.
Probab=20.06 E-value=3.6e+02 Score=19.78 Aligned_cols=40 Identities=10% Similarity=0.274 Sum_probs=29.3
Q ss_pred eEEEEEeehhhHHHHHHHHHHHHHHHHhhc-CCCeEEEEeee
Q 029530 59 KAIVVYVPYRLRKAYRKIHSRLVRELEKKF-SGKDVVLIATR 99 (192)
Q Consensus 59 KAivIfVP~~~lk~f~Kiq~rLv~ELEKKf-sg~~Vv~vAqR 99 (192)
-++++.+......+|..+.. +..++++-- ++.++++++..
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 36777777788888988876 556666544 57899999874
Done!