Query 036922
Match_columns 135
No_of_seqs 69 out of 71
Neff 2.6
Searched_HMMs 46136
Date Fri Mar 29 06:44:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/036922.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/036922hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0446 Vacuolar sorting prote 99.9 6E-28 1.3E-32 217.2 1.5 120 5-134 176-301 (657)
2 PF01031 Dynamin_M: Dynamin ce 99.6 4.8E-16 1.1E-20 124.2 4.8 82 45-133 1-83 (295)
3 smart00053 DYNc Dynamin, GTPas 99.2 1.2E-11 2.7E-16 99.8 3.8 65 6-80 170-239 (240)
4 PF10662 PduV-EutP: Ethanolami 95.1 0.018 3.9E-07 44.4 2.8 33 23-56 89-121 (143)
5 KOG0447 Dynamin-like GTP bindi 95.0 0.051 1.1E-06 52.1 5.7 68 22-99 478-547 (980)
6 COG4917 EutP Ethanolamine util 89.1 0.31 6.6E-06 38.9 2.3 27 26-54 93-119 (148)
7 COG0699 Predicted GTPases (dyn 81.2 0.65 1.4E-05 38.7 0.8 106 5-130 97-204 (546)
8 cd01857 HSR1_MMR1 HSR1/MMR1. 54.6 32 0.00069 24.4 4.6 18 22-39 41-58 (141)
9 smart00755 Grip golgin-97, Ran 52.7 8.5 0.00018 24.8 1.2 31 90-120 2-33 (46)
10 cd04163 Era Era subfamily. Er 42.6 35 0.00077 22.6 3.1 27 22-48 110-136 (168)
11 PRK15467 ethanolamine utilizat 41.8 29 0.00062 25.3 2.7 19 22-40 90-108 (158)
12 PF12102 DUF3578: Domain of un 41.4 13 0.00029 29.3 1.0 18 54-71 50-67 (188)
13 cd01858 NGP_1 NGP-1. Autoanti 40.1 16 0.00036 26.2 1.2 18 22-39 38-55 (157)
14 PF01465 GRIP: GRIP domain; I 39.8 15 0.00033 23.2 0.9 31 90-120 3-35 (46)
15 cd00880 Era_like Era (E. coli 37.6 22 0.00048 23.0 1.4 20 22-41 103-122 (163)
16 COG0523 Putative GTPases (G3E 37.4 28 0.0006 29.9 2.4 29 28-58 150-178 (323)
17 cd01882 BMS1 Bms1. Bms1 is an 36.6 41 0.0009 26.3 3.1 17 24-40 134-150 (225)
18 PRK11331 5-methylcytosine-spec 36.4 26 0.00057 32.0 2.2 19 54-72 40-58 (459)
19 TIGR03598 GTPase_YsxC ribosome 36.1 20 0.00044 26.0 1.2 18 22-39 128-145 (179)
20 cd01849 YlqF_related_GTPase Yl 36.0 21 0.00046 25.7 1.3 17 22-38 28-44 (155)
21 cd01894 EngA1 EngA1 subfamily. 33.5 26 0.00056 23.6 1.3 20 22-41 104-123 (157)
22 cd04164 trmE TrmE (MnmE, ThdF, 33.0 28 0.0006 23.4 1.4 18 22-39 106-123 (157)
23 cd04165 GTPBP1_like GTPBP1-lik 32.7 45 0.00098 26.3 2.8 29 22-50 137-167 (224)
24 PF10414 CysG_dimeriser: Siroh 32.4 38 0.00082 21.7 1.9 17 115-131 8-24 (60)
25 cd01879 FeoB Ferrous iron tran 32.0 29 0.00063 23.6 1.4 18 22-39 100-117 (158)
26 cd01895 EngA2 EngA2 subfamily. 31.0 65 0.0014 21.8 3.0 30 22-51 112-141 (174)
27 cd04104 p47_IIGP_like p47 (47- 29.9 57 0.0012 24.5 2.8 17 22-38 106-122 (197)
28 cd04178 Nucleostemin_like Nucl 29.5 31 0.00068 26.3 1.3 19 22-40 29-47 (172)
29 cd01855 YqeH YqeH. YqeH is an 29.0 35 0.00076 25.2 1.5 18 22-39 60-77 (190)
30 cd01887 IF2_eIF5B IF2/eIF5B (i 29.0 1.2E+02 0.0027 20.8 4.1 19 22-40 101-119 (168)
31 cd04587 CBS_pair_CAP-ED_DUF294 28.4 33 0.00072 21.9 1.1 14 24-37 99-112 (113)
32 TIGR00073 hypB hydrogenase acc 28.1 77 0.0017 24.1 3.3 26 26-51 151-176 (207)
33 cd04615 CBS_pair_2 The CBS dom 27.2 44 0.00095 21.4 1.5 16 22-37 97-112 (113)
34 KOG1432 Predicted DNA repair e 26.1 65 0.0014 29.3 2.8 36 53-99 127-162 (379)
35 cd01862 Rab7 Rab7 subfamily. 25.6 1.4E+02 0.0031 20.5 3.9 15 23-37 109-123 (172)
36 cd01876 YihA_EngB The YihA (En 25.2 78 0.0017 21.1 2.5 20 22-41 109-128 (170)
37 cd04582 CBS_pair_ABC_OpuCA_ass 25.2 48 0.001 21.0 1.4 16 22-37 90-105 (106)
38 cd04613 CBS_pair_SpoIVFB_EriC_ 25.0 48 0.001 21.0 1.4 15 23-37 99-113 (114)
39 cd01891 TypA_BipA TypA (tyrosi 23.4 2E+02 0.0044 21.1 4.6 29 22-50 116-145 (194)
40 cd04169 RF3 RF3 subfamily. Pe 23.3 76 0.0017 25.8 2.6 40 22-63 122-162 (267)
41 cd01886 EF-G Elongation factor 23.1 72 0.0016 26.0 2.4 40 22-63 115-155 (270)
42 cd04119 RJL RJL (RabJ-Like) su 22.8 1.1E+02 0.0023 20.8 2.9 15 23-37 110-124 (168)
43 cd00882 Ras_like_GTPase Ras-li 22.3 55 0.0012 20.6 1.3 20 22-41 101-120 (157)
44 cd04607 CBS_pair_NTP_transfera 21.9 61 0.0013 20.9 1.5 17 22-38 97-113 (113)
45 PRK05935 biotin--protein ligas 21.7 89 0.0019 24.7 2.6 27 106-132 157-183 (190)
46 cd04605 CBS_pair_MET2_assoc Th 21.2 55 0.0012 20.8 1.1 15 22-36 94-108 (110)
47 TIGR00101 ureG urease accessor 20.9 74 0.0016 24.7 2.0 12 27-38 141-152 (199)
48 COG1162 Predicted GTPases [Gen 20.7 90 0.0019 27.2 2.6 36 16-51 101-138 (301)
49 cd04639 CBS_pair_26 The CBS do 20.6 57 0.0012 20.8 1.1 13 24-36 97-109 (111)
50 cd04594 CBS_pair_EriC_assoc_ar 20.6 56 0.0012 21.0 1.1 15 22-36 88-102 (104)
51 cd04606 CBS_pair_Mg_transporte 20.3 66 0.0014 20.7 1.4 16 22-37 92-107 (109)
52 cd04638 CBS_pair_25 The CBS do 20.2 59 0.0013 20.7 1.1 16 22-37 90-105 (106)
53 cd01856 YlqF YlqF. Proteins o 20.1 63 0.0014 23.7 1.4 17 22-38 45-61 (171)
No 1
>KOG0446 consensus Vacuolar sorting protein VPS1, dynamin, and related proteins [Intracellular trafficking, secretion, and vesicular transport; General function prediction only]
Probab=99.94 E-value=6e-28 Score=217.20 Aligned_cols=120 Identities=23% Similarity=0.278 Sum_probs=113.7
Q ss_pred CCCCCCCcccccccccc-----cCceeeeeeehhhccccchhHHHHHHHHHHhCCCCCCCCCceEEEeccceehhhcccC
Q 036922 5 ELPPCESSITSRVLSFL-----QGTRTVGVISKIDQASADQKALAAVQALLLNQGPPKTADISWVALIGQSVSIATAQSG 79 (135)
Q Consensus 5 ~~Pan~diatS~alkla-----~g~RTiGVitKiD~~~~~t~alaAv~alL~~qG~~~~~~~pWVavInrSq~ia~Adin 79 (135)
-.|||.|++||+|||+| +|.||||||||+|+||+||+ |++. |+ |+.++++.|||++|||+| .+|+
T Consensus 176 v~~an~d~ats~alkiarevDp~g~RTigvitK~DlmdkGt~---~~~~-L~--g~~~~l~~g~v~vvnR~q----~di~ 245 (657)
T KOG0446|consen 176 VTPANSDIATSPALVVAREVDPGGSRTLEVITKFDFMDKGTN---AVTR-LV--GRPITLKVGYVGVVNRSQ----SIID 245 (657)
T ss_pred ccchhhhhhcCHHHHHHHhhCCCccchhHHhhhHHhhhcCCc---ceee-ec--CCccccccceeeeeccch----hhhh
Confidence 46999999999999999 89999999999999999999 7777 54 999999999999999999 8998
Q ss_pred CCCcHHHHHHHHHHHHhhhh-cCCcccchhHHHHHHHHHHHHHHHHHhhccccccC
Q 036922 80 SESSLETAWRAESESLKSIL-TGAPQSKLGRIALVDALAQQIRKRMKVRVPNVLSG 134 (135)
Q Consensus 80 se~~m~tArr~E~E~f~s~~-~g~~~sklG~~~L~~~Lsk~i~~~ik~RlP~ilsg 134 (135)
...+|.+|..+|+.||.+.| |++...++|+.+|++.|.++|...|+.++|.|.+.
T Consensus 246 ~~k~~~~al~~e~~~f~~~p~y~~~~~~~g~p~La~~L~~~l~~hi~~~lP~l~~~ 301 (657)
T KOG0446|consen 246 FKKSILEALNDEVPSFESVPSYPILLTISGVPYLALLLPGYLQSHIRDQLPELKTK 301 (657)
T ss_pred hhhhHHHHHHhhhhhhhccccccccccccCcchHHHHHHHHHHHHHHhcCcHHHHH
Confidence 77799999999999999999 99999999999999999999999999999998753
No 2
>PF01031 Dynamin_M: Dynamin central region; InterPro: IPR000375 Dynamin is a microtubule-associated force-producing protein of 100 Kd which is involved in the production of microtubule bundles. At the N terminus of dynamin is a GTPase domain (see IPR001401 from INTERPRO), and at the C terminus is a PH domain (see IPR001849 from INTERPRO). Between these two domains lies a central region of unknown function, which this entry represents.; GO: 0005525 GTP binding; PDB: 3ZVR_A 2AKA_B 2X2F_D 2X2E_D 3SNH_A 3ZYS_D 3ZYC_D 1JWY_B 1JX2_B 3SZR_A ....
Probab=99.61 E-value=4.8e-16 Score=124.15 Aligned_cols=82 Identities=20% Similarity=0.275 Sum_probs=70.9
Q ss_pred HHHHHHHhCCCCCCCCCceEEEeccceehhhcccCCCCcHHHHHHHHHHHHhhhh-cCCcccchhHHHHHHHHHHHHHHH
Q 036922 45 AVQALLLNQGPPKTADISWVALIGQSVSIATAQSGSESSLETAWRAESESLKSIL-TGAPQSKLGRIALVDALAQQIRKR 123 (135)
Q Consensus 45 Av~alL~~qG~~~~~~~pWVavInrSq~ia~Adinse~~m~tArr~E~E~f~s~~-~g~~~sklG~~~L~~~Lsk~i~~~ 123 (135)
|+++ |. |..+.++++||||+|||| .|++...|++.|+++|.+||++.| |..+++++|+.+|++.|++.|...
T Consensus 1 ~~~i-L~--n~~~pLklGy~~V~nrsq----~di~~~~s~~~a~~~E~~fF~~~~~~~~~~~~~G~~~L~~~L~~~L~~~ 73 (295)
T PF01031_consen 1 AMDI-LR--NKVIPLKLGYVGVKNRSQ----QDINDGKSIEEARQKEKEFFSNHPWYSSPADRCGTPALRKRLSELLVEH 73 (295)
T ss_dssp SHHH-HT--TSSS--TT-EEEE--S-H----HHHHTTEEHHHHHHHHHHHHHHSTTTGGGGGGSSHHHHHHHHHHHHHHH
T ss_pred ChHH-hC--CCeeccCCCeEEEecCCc----cccccCCCHHHHHHHHHHHHhcccccCCcccccchHHHHHHHHHHHHHH
Confidence 4566 64 999999999999999999 999999999999999999999998 888999999999999999999999
Q ss_pred HHhhcccccc
Q 036922 124 MKVRVPNVLS 133 (135)
Q Consensus 124 ik~RlP~ils 133 (135)
|+..||.|.+
T Consensus 74 I~~~LP~l~~ 83 (295)
T PF01031_consen 74 IRKSLPSLKS 83 (295)
T ss_dssp HHHHHHHHHH
T ss_pred HHHhCcHHHH
Confidence 9999999864
No 3
>smart00053 DYNc Dynamin, GTPase. Large GTPases that mediate vesicle trafficking. Dynamin participates in the endocytic uptake of receptors, associated ligands, and plasma membrane following an exocytic event.
Probab=99.19 E-value=1.2e-11 Score=99.78 Aligned_cols=65 Identities=23% Similarity=0.307 Sum_probs=58.4
Q ss_pred CCCCCCcccccccccc-----cCceeeeeeehhhccccchhHHHHHHHHHHhCCCCCCCCCceEEEeccceehhhcccCC
Q 036922 6 LPPCESSITSRVLSFL-----QGTRTVGVISKIDQASADQKALAAVQALLLNQGPPKTADISWVALIGQSVSIATAQSGS 80 (135)
Q Consensus 6 ~Pan~diatS~alkla-----~g~RTiGVitKiD~~~~~t~alaAv~alL~~qG~~~~~~~pWVavInrSq~ia~Adins 80 (135)
.+++.|+++++++++| .|.|||||+||+|..+.+++ +++. |. |..+.++++|++|.|||| +|++.
T Consensus 170 vda~~d~~~~d~l~ia~~ld~~~~rti~ViTK~D~~~~~~~---~~~~-~~--~~~~~l~~g~~~v~nr~~----~d~~~ 239 (240)
T smart00053 170 TPANVDLANSDALKLAKEVDPQGERTIGVITKLDLMDEGTD---ARDI-LE--NKLLPLRRGYIGVVNRSQ----KDIEG 239 (240)
T ss_pred EECCCCCCchhHHHHHHHHHHcCCcEEEEEECCCCCCccHH---HHHH-Hh--CCccccCCCEEEEECCCh----HHhhc
Confidence 3688999999999999 79999999999999999999 7777 65 888999999999999999 88853
No 4
>PF10662 PduV-EutP: Ethanolamine utilisation - propanediol utilisation; InterPro: IPR012381 Members of this family function in ethanolamine [] and propanediol [] degradation pathways. Both pathways require coenzyme B12 (adenosylcobalamin, AdoCbl). Bacteria that harbour these pathways can use ethanolamine as a source of carbon and nitrogen, or propanediol as a sole carbon and energy source, respectively. The exact roles of the EutP and PduV proteins in these respective pathways are not yet determined. Members of this family contain P-loop consensus motifs in the N-terminal part, and are distantly related to various GTPases and ATPases, including ATPase components of transport systems. Propanediol degradation is thought to be important for the natural Salmonella populations, since propanediol is produced by the fermentation of the common plant sugars rhamnose and fucose [, ]. More than 1% of the Salmonella enterica genome is devoted to the utilisation of propanediol and cobalamin biosynthesis. In vivo expression technology has indicated that propanediol utilisation (pdu) genes may be important for growth in host tissues, and competitive index studies with mice have shown that pdu mutations confer a virulence defect [, ]. The pdu operon is contiguous and co-regulated with the cobalamin (B12) biosynthesis cob operon, indicating that propanediol catabolism may be the primary reason for de novo B12 synthesis in Salmonella [, , ]. Please see IPR003207 from INTERPRO, IPR003208 from INTERPRO, IPR009204 from INTERPRO, IPR009191 from INTERPRO, IPR009192 from INTERPRO for more details on the propanediol utilisation pathway and the pdu operon.; GO: 0005524 ATP binding, 0006576 cellular biogenic amine metabolic process
Probab=95.14 E-value=0.018 Score=44.38 Aligned_cols=33 Identities=36% Similarity=0.406 Sum_probs=24.9
Q ss_pred CceeeeeeehhhccccchhHHHHHHHHHHhCCCC
Q 036922 23 GTRTVGVISKIDQASADQKALAAVQALLLNQGPP 56 (135)
Q Consensus 23 g~RTiGVitKiD~~~~~t~alaAv~alL~~qG~~ 56 (135)
..+.||||||+|+..++.+.-.|.+. |.+.|-.
T Consensus 89 ~~pvIGVITK~Dl~~~~~~i~~a~~~-L~~aG~~ 121 (143)
T PF10662_consen 89 NKPVIGVITKIDLPSDDANIERAKKW-LKNAGVK 121 (143)
T ss_pred CCCEEEEEECccCccchhhHHHHHHH-HHHcCCC
Confidence 46899999999999666666667666 6666654
No 5
>KOG0447 consensus Dynamin-like GTP binding protein [General function prediction only]
Probab=94.96 E-value=0.051 Score=52.12 Aligned_cols=68 Identities=24% Similarity=0.377 Sum_probs=51.8
Q ss_pred cCceeeeeeehhhccccchhHHHHHHHHHHhCCCCCCCC-CceEEEe-ccceehhhcccCCCCcHHHHHHHHHHHHhhhh
Q 036922 22 QGTRTVGVISKIDQASADQKALAAVQALLLNQGPPKTAD-ISWVALI-GQSVSIATAQSGSESSLETAWRAESESLKSIL 99 (135)
Q Consensus 22 ~g~RTiGVitKiD~~~~~t~alaAv~alL~~qG~~~~~~-~pWVavI-nrSq~ia~Adinse~~m~tArr~E~E~f~s~~ 99 (135)
.|.|||=|+||+|++.+.--.-.-++-+|+ |.-+.-+ .++.||| ||. ||..|.++.|+-|-+||+++-
T Consensus 478 ~GrRTIfVLTKVDlAEknlA~PdRI~kIle--GKLFPMKALGYfaVVTGrG--------nssdSIdaIR~YEE~FF~nSk 547 (980)
T KOG0447|consen 478 HGRRTIFVLTKVDLAEKNVASPSRIQQIIE--GKLFPMKALGYFAVVTGKG--------NSSESIEAIREYEEEFFQNSK 547 (980)
T ss_pred CCCeeEEEEeecchhhhccCCHHHHHHHHh--cCccchhhcceeEEEecCC--------CcchhHHHHHHHHHHHhhhhH
Confidence 699999999999999884333337777787 7655432 4667776 444 478899999999999999875
No 6
>COG4917 EutP Ethanolamine utilization protein [Amino acid transport and metabolism]
Probab=89.09 E-value=0.31 Score=38.89 Aligned_cols=27 Identities=33% Similarity=0.527 Sum_probs=18.7
Q ss_pred eeeeeehhhccccchhHHHHHHHHHHhCC
Q 036922 26 TVGVISKIDQASADQKALAAVQALLLNQG 54 (135)
Q Consensus 26 TiGVitKiD~~~~~t~alaAv~alL~~qG 54 (135)
+|||+||+|++. +.+. +++.-+|...|
T Consensus 93 vIgvVTK~DLae-d~dI-~~~~~~L~eaG 119 (148)
T COG4917 93 VIGVVTKADLAE-DADI-SLVKRWLREAG 119 (148)
T ss_pred eEEEEecccccc-hHhH-HHHHHHHHHcC
Confidence 999999999995 4443 34555555455
No 7
>COG0699 Predicted GTPases (dynamin-related) [General function prediction only]
Probab=81.25 E-value=0.65 Score=38.67 Aligned_cols=106 Identities=10% Similarity=0.017 Sum_probs=79.3
Q ss_pred CCCCCCCcccccccccc-cCceeeeeeehhhccccchhHHHHHHHHHHhCCCCCCCCCceEEEeccceehhhcccCCCCc
Q 036922 5 ELPPCESSITSRVLSFL-QGTRTVGVISKIDQASADQKALAAVQALLLNQGPPKTADISWVALIGQSVSIATAQSGSESS 83 (135)
Q Consensus 5 ~~Pan~diatS~alkla-~g~RTiGVitKiD~~~~~t~alaAv~alL~~qG~~~~~~~pWVavInrSq~ia~Adinse~~ 83 (135)
...++.+.++..+.+.+ ++.| |.+|+|.++.+++ +... ....-+.+++..+ .++-....
T Consensus 97 ~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~---~~~~----------~~~~~~~~~~~~~----~~~~~~~~ 156 (546)
T COG0699 97 GIAPNADEEAELSIEVIREADR---VPTKINFLNGGTN---LTLI----------LGNGDVLVVDALE----TDIQLLKT 156 (546)
T ss_pred chhhhhhhccchhhHhhhhhcc---hhHHHHHHhcCCc---eeee----------eccccccccCchh----HHHHhccc
Confidence 45677888888888888 6666 9999999999999 4210 1222255555655 55667777
Q ss_pred HHHHHHHHHHHHhhhh-cCCcccchhHHHHHHHHHHHHHHHHHhhccc
Q 036922 84 LETAWRAESESLKSIL-TGAPQSKLGRIALVDALAQQIRKRMKVRVPN 130 (135)
Q Consensus 84 m~tArr~E~E~f~s~~-~g~~~sklG~~~L~~~Lsk~i~~~ik~RlP~ 130 (135)
...+=..|.++|...+ +..-....+..++...+++++...+..-.|-
T Consensus 157 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 204 (546)
T COG0699 157 ALEALVKELEYFAEHPLLEDNEKLVLLPYLKKLLSKILELHLRLLPKY 204 (546)
T ss_pred chHHHHHHHHHhhcCccccccccccCChhhhhhhhhhHHHHHHhcChh
Confidence 8888899999999999 7666667999999999999888877765543
No 8
>cd01857 HSR1_MMR1 HSR1/MMR1. Human HSR1, is localized to the human MHC class I region and is highly homologous to a putative GTP-binding protein, MMR1 from mouse. These proteins represent a new subfamily of GTP-binding proteins that has only eukaryote members. This subfamily shows a circular permutation of the GTPase signature motifs so that the C-terminal strands 5, 6, and 7 (strand 6 contains the G4 box with sequence NKXD) are relocated to the N terminus.
Probab=54.59 E-value=32 Score=24.44 Aligned_cols=18 Identities=11% Similarity=0.276 Sum_probs=14.5
Q ss_pred cCceeeeeeehhhccccc
Q 036922 22 QGTRTVGVISKIDQASAD 39 (135)
Q Consensus 22 ~g~RTiGVitKiD~~~~~ 39 (135)
.+...|=|+||+|+..+.
T Consensus 41 ~~k~~iivlNK~DL~~~~ 58 (141)
T cd01857 41 PRKKNILLLNKADLLTEE 58 (141)
T ss_pred CCCcEEEEEechhcCCHH
Confidence 377889999999997544
No 9
>smart00755 Grip golgin-97, RanBP2alpha,Imh1p and p230/golgin-245.
Probab=52.66 E-value=8.5 Score=24.81 Aligned_cols=31 Identities=23% Similarity=0.248 Sum_probs=23.0
Q ss_pred HHHHHHhhhhcCCcccchh-HHHHHHHHHHHH
Q 036922 90 AESESLKSILTGAPQSKLG-RIALVDALAQQI 120 (135)
Q Consensus 90 ~E~E~f~s~~~g~~~sklG-~~~L~~~Lsk~i 120 (135)
.+.||+|++.++-..++=+ |..|+..|+..|
T Consensus 2 ~n~eYLKNVll~fl~~~e~~r~~ll~vi~tlL 33 (46)
T smart00755 2 ANFEYLKNVLLQFLTLRESERETLLKVISTVL 33 (46)
T ss_pred ccHHHHHHHHHHHhccCcchHHHHHHHHHHHh
Confidence 3689999999655555555 788888887665
No 10
>cd04163 Era Era subfamily. Era (E. coli Ras-like protein) is a multifunctional GTPase found in all bacteria except some eubacteria. It binds to the 16S ribosomal RNA (rRNA) of the 30S subunit and appears to play a role in the assembly of the 30S subunit, possibly by chaperoning the 16S rRNA. It also contacts several assembly elements of the 30S subunit. Era couples cell growth with cytokinesis and plays a role in cell division and energy metabolism. Homologs have also been found in eukaryotes. Era contains two domains: the N-terminal GTPase domain and a C-terminal domain KH domain that is critical for RNA binding. Both domains are important for Era function. Era is functionally able to compensate for deletion of RbfA, a cold-shock adaptation protein that is required for efficient processing of the 16S rRNA.
Probab=42.55 E-value=35 Score=22.64 Aligned_cols=27 Identities=22% Similarity=0.303 Sum_probs=17.9
Q ss_pred cCceeeeeeehhhccccchhHHHHHHH
Q 036922 22 QGTRTVGVISKIDQASADQKALAAVQA 48 (135)
Q Consensus 22 ~g~RTiGVitKiD~~~~~t~alaAv~a 48 (135)
.+...+-|+||+|++..........+.
T Consensus 110 ~~~~~iiv~nK~Dl~~~~~~~~~~~~~ 136 (168)
T cd04163 110 SKTPVILVLNKIDLVKDKEDLLPLLEK 136 (168)
T ss_pred hCCCEEEEEEchhccccHHHHHHHHHH
Confidence 357789999999998644443333334
No 11
>PRK15467 ethanolamine utilization protein EutP; Provisional
Probab=41.84 E-value=29 Score=25.31 Aligned_cols=19 Identities=42% Similarity=0.520 Sum_probs=14.8
Q ss_pred cCceeeeeeehhhccccch
Q 036922 22 QGTRTVGVISKIDQASADQ 40 (135)
Q Consensus 22 ~g~RTiGVitKiD~~~~~t 40 (135)
.+...++|++|+|+.+.+.
T Consensus 90 ~~~~ii~v~nK~Dl~~~~~ 108 (158)
T PRK15467 90 VSKRQIAVISKTDMPDADV 108 (158)
T ss_pred CCCCeEEEEEccccCcccH
Confidence 4567899999999976443
No 12
>PF12102 DUF3578: Domain of unknown function (DUF3578); InterPro: IPR021961 This presumed domain is functionally uncharacterised. This domain is found in bacteria and archaea. This domain is typically between 177 to 191 amino acids in length. ; PDB: 3SSD_B 3SSE_A 3SSC_B.
Probab=41.37 E-value=13 Score=29.27 Aligned_cols=18 Identities=28% Similarity=0.734 Sum_probs=12.6
Q ss_pred CCCCCCCCceEEEeccce
Q 036922 54 GPPKTADISWVALIGQSV 71 (135)
Q Consensus 54 G~~~~~~~pWVavInrSq 71 (135)
|.-.-+++||||+.++.+
T Consensus 50 G~G~wA~iPWIai~d~~i 67 (188)
T PF12102_consen 50 GQGNWAEIPWIAIFDKRI 67 (188)
T ss_dssp ESSSEESSEEEEEE-T--
T ss_pred CCCCccCCeEEEEEcccC
Confidence 444688999999998855
No 13
>cd01858 NGP_1 NGP-1. Autoantigen NGP-1 (Nucleolar G-protein gene 1) has been shown to localize in the nucleolus and nucleolar organizers in all cell types analyzed, which is indicative of a function in ribosomal assembly. NGP-1 and its homologs show a circular permutation of the GTPase signature motifs so that the C-terminal strands 5, 6, and 7 (strand 6 contains the G4 box with NKXD motif) are relocated to the N terminus.
Probab=40.12 E-value=16 Score=26.21 Aligned_cols=18 Identities=17% Similarity=0.075 Sum_probs=14.7
Q ss_pred cCceeeeeeehhhccccc
Q 036922 22 QGTRTVGVISKIDQASAD 39 (135)
Q Consensus 22 ~g~RTiGVitKiD~~~~~ 39 (135)
.+.+.|=|+||+|+.++.
T Consensus 38 ~~~p~ilVlNKiDl~~~~ 55 (157)
T cd01858 38 PHKHLIFVLNKCDLVPTW 55 (157)
T ss_pred CCCCEEEEEEchhcCCHH
Confidence 457899999999997554
No 14
>PF01465 GRIP: GRIP domain; InterPro: IPR000237 The GRIP (golgin-97, RanBP2alpha,Imh1p and p230/golgin-245) domain [, , ] is found in many large coiled-coil proteins. It has been shown to be sufficient for targeting to the Golgi []. The GRIP domain contains a completely conserved tyrosine residue.; GO: 0005515 protein binding, 0000042 protein targeting to Golgi; PDB: 1R4A_H 1UPT_B.
Probab=39.77 E-value=15 Score=23.23 Aligned_cols=31 Identities=26% Similarity=0.236 Sum_probs=20.6
Q ss_pred HHHHHHhhhhcCCccc--chhHHHHHHHHHHHH
Q 036922 90 AESESLKSILTGAPQS--KLGRIALVDALAQQI 120 (135)
Q Consensus 90 ~E~E~f~s~~~g~~~s--klG~~~L~~~Lsk~i 120 (135)
.+.||||++.+.-+.+ .-++..|...|+.-|
T Consensus 3 ~~~eYLKNvl~~fl~~~~~~~~~~llpvi~tlL 35 (46)
T PF01465_consen 3 INLEYLKNVLLQFLESREPSEREQLLPVIATLL 35 (46)
T ss_dssp HHHHHHHHHHHHHHTTSS---HHHHHHHHHHHT
T ss_pred hhHHHHHHHHHHHhcCCchhhHHHHHHHHHHHH
Confidence 4689999999433333 348899998888655
No 15
>cd00880 Era_like Era (E. coli Ras-like protein)-like. This family includes several distinct subfamilies (TrmE/ThdF, FeoB, YihA (EngG), Era, and EngA/YfgK) that generally show sequence conservation in the region between the Walker A and B motifs (G1 and G3 box motifs), to the exclusion of other GTPases. TrmE is ubiquitous in bacteria and is a widespread mitochondrial protein in eukaryotes, but is absent from archaea. The yeast member of TrmE family, MSS1, is involved in mitochondrial translation; bacterial members are often present in translation-related operons. FeoB represents an unusual adaptation of GTPases for high-affinity iron (II) transport. YihA (EngB) family of GTPases is typified by the E. coli YihA, which is an essential protein involved in cell division control. Era is characterized by a distinct derivative of the KH domain (the pseudo-KH domain) which is located C-terminal to the GTPase domain. EngA and its orthologs are composed of two GTPase domains and, since the se
Probab=37.57 E-value=22 Score=23.01 Aligned_cols=20 Identities=25% Similarity=0.449 Sum_probs=16.5
Q ss_pred cCceeeeeeehhhccccchh
Q 036922 22 QGTRTVGVISKIDQASADQK 41 (135)
Q Consensus 22 ~g~RTiGVitKiD~~~~~t~ 41 (135)
.+...|-|+||+|+......
T Consensus 103 ~~~~~ivv~nK~D~~~~~~~ 122 (163)
T cd00880 103 RGKPVLLVLNKIDLLPEEEE 122 (163)
T ss_pred cCCeEEEEEEccccCChhhH
Confidence 57789999999999876544
No 16
>COG0523 Putative GTPases (G3E family) [General function prediction only]
Probab=37.43 E-value=28 Score=29.86 Aligned_cols=29 Identities=31% Similarity=0.384 Sum_probs=21.8
Q ss_pred eeeehhhccccchhHHHHHHHHHHhCCCCCC
Q 036922 28 GVISKIDQASADQKALAAVQALLLNQGPPKT 58 (135)
Q Consensus 28 GVitKiD~~~~~t~alaAv~alL~~qG~~~~ 58 (135)
=||||+|+.+... ++++++.|..-.|..+
T Consensus 150 ivlNK~Dlv~~~~--l~~l~~~l~~lnp~A~ 178 (323)
T COG0523 150 IVLNKTDLVDAEE--LEALEARLRKLNPRAR 178 (323)
T ss_pred EEEecccCCCHHH--HHHHHHHHHHhCCCCe
Confidence 4899999999984 7788877765555543
No 17
>cd01882 BMS1 Bms1. Bms1 is an essential, evolutionarily conserved, nucleolar protein. Its depletion interferes with processing of the 35S pre-rRNA at sites A0, A1, and A2, and the formation of 40S subunits. Bms1, the putative endonuclease Rc11, and the essential U3 small nucleolar RNA form a stable subcomplex that is believed to control an early step in the formation of the 40S subumit. The C-terminal domain of Bms1 contains a GTPase-activating protein (GAP) that functions intramolecularly. It is believed that Rc11 activates Bms1 by acting as a guanine-nucleotide exchange factor (GEF) to promote GDP/GTP exchange, and that activated (GTP-bound) Bms1 delivers Rc11 to the preribosomes.
Probab=36.64 E-value=41 Score=26.27 Aligned_cols=17 Identities=24% Similarity=0.556 Sum_probs=13.0
Q ss_pred ceeeeeeehhhccccch
Q 036922 24 TRTVGVISKIDQASADQ 40 (135)
Q Consensus 24 ~RTiGVitKiD~~~~~t 40 (135)
.+.|+|+||+|+.....
T Consensus 134 p~vi~VvnK~D~~~~~~ 150 (225)
T cd01882 134 PRVMGVLTHLDLFKKNK 150 (225)
T ss_pred CeEEEEEeccccCCcHH
Confidence 45789999999985443
No 18
>PRK11331 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional
Probab=36.40 E-value=26 Score=31.99 Aligned_cols=19 Identities=26% Similarity=0.613 Sum_probs=16.7
Q ss_pred CCCCCCCCceEEEecccee
Q 036922 54 GPPKTADISWVALIGQSVS 72 (135)
Q Consensus 54 G~~~~~~~pWVavInrSq~ 72 (135)
|.-.-.++||||+.|..|+
T Consensus 40 g~g~~a~vpw~a~~~~~~t 58 (459)
T PRK11331 40 GYGNFTSIPWFAFLGEGQE 58 (459)
T ss_pred CCCCcccCceEEeecCCce
Confidence 6666789999999999997
No 19
>TIGR03598 GTPase_YsxC ribosome biogenesis GTP-binding protein YsxC/EngB. Members of this protein family are a GTPase associated with ribosome biogenesis, typified by YsxC from Bacillus subutilis. The family is widely but not universally distributed among bacteria. Members commonly are called EngB based on homology to EngA, one of several other GTPases of ribosome biogenesis. Cutoffs as set find essentially all bacterial members, but also identify large numbers of eukaryotic (probably organellar) sequences. This protein is found in about 80 percent of bacterial genomes.
Probab=36.12 E-value=20 Score=26.01 Aligned_cols=18 Identities=22% Similarity=0.357 Sum_probs=15.0
Q ss_pred cCceeeeeeehhhccccc
Q 036922 22 QGTRTVGVISKIDQASAD 39 (135)
Q Consensus 22 ~g~RTiGVitKiD~~~~~ 39 (135)
.+-+.+.|+||+|+++.+
T Consensus 128 ~~~pviiv~nK~D~~~~~ 145 (179)
T TIGR03598 128 RGIPVLIVLTKADKLKKS 145 (179)
T ss_pred cCCCEEEEEECcccCCHH
Confidence 577899999999998643
No 20
>cd01849 YlqF_related_GTPase YlqF-related GTPases. These proteins are found in bacteria, eukaryotes, and archaea. They all exhibit a circular permutation of the GTPase signature motifs so that the order of the conserved G box motifs is G4-G5-G1-G2-G3, with G4 and G5 being permuted from the C-terminal region of proteins in the Ras superfamily to the N-terminus of YlqF-related GTPases.
Probab=35.97 E-value=21 Score=25.66 Aligned_cols=17 Identities=24% Similarity=0.413 Sum_probs=14.7
Q ss_pred cCceeeeeeehhhcccc
Q 036922 22 QGTRTVGVISKIDQASA 38 (135)
Q Consensus 22 ~g~RTiGVitKiD~~~~ 38 (135)
.+.+.|-|+||+|+...
T Consensus 28 ~~~p~IiVlNK~Dl~~~ 44 (155)
T cd01849 28 KGKKLILVLNKADLVPK 44 (155)
T ss_pred CCCCEEEEEechhcCCH
Confidence 57899999999999754
No 21
>cd01894 EngA1 EngA1 subfamily. This CD represents the first GTPase domain of EngA and its orthologs, which are composed of two adjacent GTPase domains. Since the sequences of the two domains are more similar to each other than to other GTPases, it is likely that an ancient gene duplication, rather than a fusion of evolutionarily distinct GTPases, gave rise to this family. Although the exact function of these proteins has not been elucidated, studies have revealed that the E. coli EngA homolog, Der, and Neisseria gonorrhoeae EngA are essential for cell viability. A recent report suggests that E. coli Der functions in ribosome assembly and stability.
Probab=33.50 E-value=26 Score=23.59 Aligned_cols=20 Identities=15% Similarity=0.338 Sum_probs=16.4
Q ss_pred cCceeeeeeehhhccccchh
Q 036922 22 QGTRTVGVISKIDQASADQK 41 (135)
Q Consensus 22 ~g~RTiGVitKiD~~~~~t~ 41 (135)
.+...|.|+||+|+......
T Consensus 104 ~~~piiiv~nK~D~~~~~~~ 123 (157)
T cd01894 104 SKKPVILVVNKVDNIKEEDE 123 (157)
T ss_pred cCCCEEEEEECcccCChHHH
Confidence 46889999999999876544
No 22
>cd04164 trmE TrmE (MnmE, ThdF, MSS1) is a 3-domain protein found in bacteria and eukaryotes. It controls modification of the uridine at the wobble position (U34) of tRNAs that read codons ending with A or G in the mixed codon family boxes. TrmE contains a GTPase domain that forms a canonical Ras-like fold. It functions a molecular switch GTPase, and apparently uses a conformational change associated with GTP hydrolysis to promote the tRNA modification reaction, in which the conserved cysteine in the C-terminal domain is thought to function as a catalytic residue. In bacteria that are able to survive in extremely low pH conditions, TrmE regulates glutamate-dependent acid resistance.
Probab=32.96 E-value=28 Score=23.36 Aligned_cols=18 Identities=17% Similarity=0.174 Sum_probs=15.2
Q ss_pred cCceeeeeeehhhccccc
Q 036922 22 QGTRTVGVISKIDQASAD 39 (135)
Q Consensus 22 ~g~RTiGVitKiD~~~~~ 39 (135)
.+.+.|-|+||+|+++..
T Consensus 106 ~~~~vi~v~nK~D~~~~~ 123 (157)
T cd04164 106 ADKPIIVVLNKSDLLPDS 123 (157)
T ss_pred cCCCEEEEEEchhcCCcc
Confidence 578889999999998654
No 23
>cd04165 GTPBP1_like GTPBP1-like. Mammalian GTP binding protein 1 (GTPBP1), GTPBP2, and nematode homologs AGP-1 and CGP-1 are GTPases whose specific functions remain unknown. In mouse, GTPBP1 is expressed in macrophages, in smooth muscle cells of various tissues and in some neurons of the cerebral cortex; GTPBP2 tissue distribution appears to overlap that of GTPBP1. In human leukemia and macrophage cell lines, expression of both GTPBP1 and GTPBP2 is enhanced by interferon-gamma (IFN-gamma). The chromosomal location of both genes has been identified in humans, with GTPBP1 located in chromosome 22q12-13.1 and GTPBP2 located in chromosome 6p21-12. Human glioblastoma multiforme (GBM), a highly-malignant astrocytic glioma and the most common cancer in the central nervous system, has been linked to chromosomal deletions and a translocation on chromosome 6. The GBM translocation results in a fusion of GTPBP2 and PTPRZ1, a protein involved in oligodendrocyte differentiation, recovery, and
Probab=32.68 E-value=45 Score=26.31 Aligned_cols=29 Identities=31% Similarity=0.428 Sum_probs=19.5
Q ss_pred cCceeeeeeehhhccccc--hhHHHHHHHHH
Q 036922 22 QGTRTVGVISKIDQASAD--QKALAAVQALL 50 (135)
Q Consensus 22 ~g~RTiGVitKiD~~~~~--t~alaAv~alL 50 (135)
.|-..|-|+||+|+...+ .+.+..+..+|
T Consensus 137 ~~ip~ivvvNK~D~~~~~~~~~~~~~l~~~L 167 (224)
T cd04165 137 LNIPVFVVVTKIDLAPANILQETLKDLKRIL 167 (224)
T ss_pred cCCCEEEEEECccccCHHHHHHHHHHHHHHh
Confidence 577889999999997643 23344444444
No 24
>PF10414 CysG_dimeriser: Sirohaem synthase dimerisation region; InterPro: IPR019478 Bacterial sulphur metabolism depends on the iron-containing porphinoid sirohaem. CysG is a multi-functional enzyme with S-adenosyl-L-methionine (SAM)-dependent bismethyltransferase, dehydrogenase and ferrochelatase activities. CysG synthesizes sirohaem from uroporphyrinogen III via reactions which encompass two branchpoint intermediates in tetrapyrrole biosynthesis, diverting flux first from protoporphyrin IX biosynthesis and then from cobalamin (vitamin B12) biosynthesis. CysG is a dimer. Its dimerisation region is 74 residues long, and acts to hold the two structurally similar protomers held together asymmetrically through a number of salt-bridges across complementary residues within the dimerisation region []. CysG dimerisation produces a series of active sites, accounting for CysG's multi-functionality, catalysing four diverse reactions: Two SAM-dependent methylations NAD+-dependent tetrapyrrole dehydrogenation Metal chelation ; GO: 0006779 porphyrin-containing compound biosynthetic process, 0055114 oxidation-reduction process; PDB: 1PJT_A 1PJS_A 1PJQ_A.
Probab=32.43 E-value=38 Score=21.68 Aligned_cols=17 Identities=41% Similarity=0.749 Sum_probs=13.8
Q ss_pred HHHHHHHHHHHhhcccc
Q 036922 115 ALAQQIRKRMKVRVPNV 131 (135)
Q Consensus 115 ~Lsk~i~~~ik~RlP~i 131 (135)
.|+..+|.++|.+||..
T Consensus 8 ~l~~~~R~~Vk~~l~~~ 24 (60)
T PF10414_consen 8 ELAGRFRERVKQRLPDF 24 (60)
T ss_dssp HHHHHHHHHHHHH-SSH
T ss_pred HHHHHHHHHHHHHCCCc
Confidence 47789999999999974
No 25
>cd01879 FeoB Ferrous iron transport protein B (FeoB) subfamily. E. coli has an iron(II) transport system, known as feo, which may make an important contribution to the iron supply of the cell under anaerobic conditions. FeoB has been identified as part of this transport system. FeoB is a large 700-800 amino acid integral membrane protein. The N terminus contains a P-loop motif suggesting that iron transport may be ATP dependent.
Probab=32.04 E-value=29 Score=23.56 Aligned_cols=18 Identities=28% Similarity=0.327 Sum_probs=15.0
Q ss_pred cCceeeeeeehhhccccc
Q 036922 22 QGTRTVGVISKIDQASAD 39 (135)
Q Consensus 22 ~g~RTiGVitKiD~~~~~ 39 (135)
.+...|-|+||+|+.+..
T Consensus 100 ~~~~~iiv~NK~Dl~~~~ 117 (158)
T cd01879 100 LGLPVVVALNMIDEAEKR 117 (158)
T ss_pred cCCCEEEEEehhhhcccc
Confidence 567899999999997654
No 26
>cd01895 EngA2 EngA2 subfamily. This CD represents the second GTPase domain of EngA and its orthologs, which are composed of two adjacent GTPase domains. Since the sequences of the two domains are more similar to each other than to other GTPases, it is likely that an ancient gene duplication, rather than a fusion of evolutionarily distinct GTPases, gave rise to this family. Although the exact function of these proteins has not been elucidated, studies have revealed that the E. coli EngA homolog, Der, and Neisseria gonorrhoeae EngA are essential for cell viability. A recent report suggests that E. coli Der functions in ribosome assembly and stability.
Probab=30.96 E-value=65 Score=21.77 Aligned_cols=30 Identities=23% Similarity=0.305 Sum_probs=19.3
Q ss_pred cCceeeeeeehhhccccchhHHHHHHHHHH
Q 036922 22 QGTRTVGVISKIDQASADQKALAAVQALLL 51 (135)
Q Consensus 22 ~g~RTiGVitKiD~~~~~t~alaAv~alL~ 51 (135)
.+...|-|+||+|+++......+.+...+.
T Consensus 112 ~~~~~iiv~nK~Dl~~~~~~~~~~~~~~~~ 141 (174)
T cd01895 112 EGKALVIVVNKWDLVEKDSKTMKEFKKEIR 141 (174)
T ss_pred cCCCEEEEEeccccCCccHHHHHHHHHHHH
Confidence 467788999999998774333333333343
No 27
>cd04104 p47_IIGP_like p47 (47-kDa) family. The p47 GTPase family consists of several highly homologous proteins, including IGTP, TGTP/Mg21, IRG-47, GTPI, LRG-47, and IIGP1. They are found in higher eukaryotes where they play a role in immune resistance against intracellular pathogens. p47 proteins exist at low resting levels in mouse cells, but are strongly induced by Type II interferon (IFN-gamma). ITGP is critical for resistance to Toxoplasma gondii infection and in involved in inhibition of Coxsackievirus-B3-induced apoptosis. TGTP was shown to limit vesicular stomatitis virus (VSV) infection of fibroblasts in vitro. IRG-47 is involved in resistance to T. gondii infection. LRG-47 has been implicated in resistance to T. gondii, Listeria monocytogenes, Leishmania, and mycobacterial infections. IIGP1 has been shown to localize to the ER and to the Golgi membranes in IFN-induced cells and inflamed tissues. In macrophages, IIGP1 interacts with hook3, a microtubule binding protei
Probab=29.88 E-value=57 Score=24.52 Aligned_cols=17 Identities=24% Similarity=0.268 Sum_probs=14.2
Q ss_pred cCceeeeeeehhhcccc
Q 036922 22 QGTRTVGVISKIDQASA 38 (135)
Q Consensus 22 ~g~RTiGVitKiD~~~~ 38 (135)
.|.+.+=|+||+|+...
T Consensus 106 ~~~~~ilV~nK~D~~~~ 122 (197)
T cd04104 106 MGKKFYFVRTKVDRDLS 122 (197)
T ss_pred hCCCEEEEEecccchhh
Confidence 47889999999999654
No 28
>cd04178 Nucleostemin_like Nucleostemin-like. Nucleostemin (NS) is a nucleolar protein that functions as a regulator of cell growth and proliferation in stem cells and in several types of cancer cells, but is not expressed in the differentiated cells of most mammalian adult tissues. NS shuttles between the nucleolus and nucleoplasm bidirectionally at a rate that is fast and independent of cell type. Lowering GTP levels decreases the nucleolar retention of NS, and expression of NS is abruptly down-regulated during differentiation prior to terminal cell division. Found only in eukaryotes, NS consists of an N-terminal basic domain, a coiled-coil domain, a GTP-binding domain, an intermediate domain, and a C-terminal acidic domain. Experimental evidence indicates that NS uses its GTP-binding property as a molecular switch to control the transition between the nucleolus and nucleoplasm, and this process involves interaction between the basic, GTP-binding, and intermediate domains of the
Probab=29.52 E-value=31 Score=26.28 Aligned_cols=19 Identities=26% Similarity=0.366 Sum_probs=15.0
Q ss_pred cCceeeeeeehhhccccch
Q 036922 22 QGTRTVGVISKIDQASADQ 40 (135)
Q Consensus 22 ~g~RTiGVitKiD~~~~~t 40 (135)
.+.+.|-||+|+|+.++..
T Consensus 29 ~~kp~IlVlNK~DL~~~~~ 47 (172)
T cd04178 29 GNKKLVLVLNKIDLVPKEN 47 (172)
T ss_pred CCCCEEEEEehhhcCCHHH
Confidence 3578899999999976543
No 29
>cd01855 YqeH YqeH. YqeH is an essential GTP-binding protein. Depletion of YqeH induces an excess initiation of DNA replication, suggesting that it negatively controls initiation of chromosome replication. The YqeH subfamily is common in eukaryotes and sporadically present in bacteria with probable acquisition by plants from chloroplasts. Proteins of the YqeH family contain all sequence motifs typical of the vast class of P-loop-containing GTPases, but show a circular permutation, with a G4-G1-G3 pattern of motifs as opposed to the regular G1-G3-G4 pattern seen in most GTPases.
Probab=28.99 E-value=35 Score=25.20 Aligned_cols=18 Identities=28% Similarity=0.211 Sum_probs=14.8
Q ss_pred cCceeeeeeehhhccccc
Q 036922 22 QGTRTVGVISKIDQASAD 39 (135)
Q Consensus 22 ~g~RTiGVitKiD~~~~~ 39 (135)
.+.+.|-|+||+|+....
T Consensus 60 ~~~~~ilV~NK~Dl~~~~ 77 (190)
T cd01855 60 GNNPVILVGNKIDLLPKD 77 (190)
T ss_pred CCCcEEEEEEchhcCCCC
Confidence 567889999999997644
No 30
>cd01887 IF2_eIF5B IF2/eIF5B (initiation factors 2/ eukaryotic initiation factor 5B) subfamily. IF2/eIF5B contribute to ribosomal subunit joining and function as GTPases that are maximally activated by the presence of both ribosomal subunits. As seen in other GTPases, IF2/IF5B undergoes conformational changes between its GTP- and GDP-bound states. Eukaryotic IF2/eIF5Bs possess three characteristic segments, including a divergent N-terminal region followed by conserved central and C-terminal segments. This core region is conserved among all known eukaryotic and archaeal IF2/eIF5Bs and eubacterial IF2s.
Probab=28.96 E-value=1.2e+02 Score=20.76 Aligned_cols=19 Identities=21% Similarity=0.347 Sum_probs=14.2
Q ss_pred cCceeeeeeehhhccccch
Q 036922 22 QGTRTVGVISKIDQASADQ 40 (135)
Q Consensus 22 ~g~RTiGVitKiD~~~~~t 40 (135)
.+.+.|-|+||+|+.+...
T Consensus 101 ~~~p~ivv~NK~Dl~~~~~ 119 (168)
T cd01887 101 ANVPFIVALNKIDKPNANP 119 (168)
T ss_pred cCCCEEEEEEceecccccH
Confidence 5677888999999875443
No 31
>cd04587 CBS_pair_CAP-ED_DUF294_PBI_assoc This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with either the CAP_ED (cAMP receptor protein effector domain) family of transcription factors and the DUF294 domain or the PB1 (Phox and Bem1p) domain. Members of CAP_ED, include CAP which binds cAMP, FNR (fumarate and nitrate reductase) which uses an iron-sulfur cluster to sense oxygen, and CooA a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. DUF294 is a putative nucleotidyltransferase with a conserved DxD motif. The PB1 domain adopts a beta-grasp fold, similar to that found in ubiquitin and Ras-binding domains. A motif, variously termed OPR, PC and AID, represents the most conserved region of the majority of PB1 domains, and is necessary for PB1 domain function. This function is the formation of PB1 domain heterodimers, although not all PB1 domain pai
Probab=28.42 E-value=33 Score=21.88 Aligned_cols=14 Identities=14% Similarity=0.299 Sum_probs=10.7
Q ss_pred ceeeeeeehhhccc
Q 036922 24 TRTVGVISKIDQAS 37 (135)
Q Consensus 24 ~RTiGVitKiD~~~ 37 (135)
.|.+||||+-|++.
T Consensus 99 ~~~~Gvvs~~dl~~ 112 (113)
T cd04587 99 GQVVGLLDVTKLTH 112 (113)
T ss_pred CCEEEEEEHHHhcc
Confidence 57788888888753
No 32
>TIGR00073 hypB hydrogenase accessory protein HypB. HypB is implicated in insertion of nickel into the large subunit of NiFe hydrogenases.
Probab=28.12 E-value=77 Score=24.07 Aligned_cols=26 Identities=27% Similarity=0.107 Sum_probs=16.4
Q ss_pred eeeeeehhhccccchhHHHHHHHHHH
Q 036922 26 TVGVISKIDQASADQKALAAVQALLL 51 (135)
Q Consensus 26 TiGVitKiD~~~~~t~alaAv~alL~ 51 (135)
.+-|+||+|+.......++.++..+.
T Consensus 151 ~iiv~NK~Dl~~~~~~~~~~~~~~l~ 176 (207)
T TIGR00073 151 DLIVINKADLAEAVGFDVEKMKADAK 176 (207)
T ss_pred CEEEEEHHHccccchhhHHHHHHHHH
Confidence 48999999998654333334444344
No 33
>cd04615 CBS_pair_2 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic genera
Probab=27.18 E-value=44 Score=21.41 Aligned_cols=16 Identities=13% Similarity=0.235 Sum_probs=13.1
Q ss_pred cCceeeeeeehhhccc
Q 036922 22 QGTRTVGVISKIDQAS 37 (135)
Q Consensus 22 ~g~RTiGVitKiD~~~ 37 (135)
++.+.+||||+-|+..
T Consensus 97 ~~g~~~Gvvt~~dl~~ 112 (113)
T cd04615 97 DKGKVGGIVTEDDILR 112 (113)
T ss_pred CCCeEEEEEEHHHhhc
Confidence 4569999999998864
No 34
>KOG1432 consensus Predicted DNA repair exonuclease SIA1 [General function prediction only]
Probab=26.06 E-value=65 Score=29.29 Aligned_cols=36 Identities=22% Similarity=0.307 Sum_probs=29.5
Q ss_pred CCCCCCCCCceEEEeccceehhhcccCCCCcHHHHHHHHHHHHhhhh
Q 036922 53 QGPPKTADISWVALIGQSVSIATAQSGSESSLETAWRAESESLKSIL 99 (135)
Q Consensus 53 qG~~~~~~~pWVavInrSq~ia~Adinse~~m~tArr~E~E~f~s~~ 99 (135)
=+|.....|||+++.|.+- +--++||.|.-.|.+.+
T Consensus 127 vaP~I~~~IPwA~~lGNHD-----------des~ltr~ql~~~i~~l 162 (379)
T KOG1432|consen 127 VAPAIDRKIPWAAVLGNHD-----------DESDLTRLQLMKFISKL 162 (379)
T ss_pred hhhHhhcCCCeEEEecccc-----------cccccCHHHHHHHHhcC
Confidence 3888899999999999765 34467899988888877
No 35
>cd01862 Rab7 Rab7 subfamily. Rab7 is a small Rab GTPase that regulates vesicular traffic from early to late endosomal stages of the endocytic pathway. The yeast Ypt7 and mammalian Rab7 are both involved in transport to the vacuole/lysosome, whereas Ypt7 is also required for homotypic vacuole fusion. Mammalian Rab7 is an essential participant in the autophagic pathway for sequestration and targeting of cytoplasmic components to the lytic compartment. Mammalian Rab7 is also proposed to function as a tumor suppressor. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-
Probab=25.55 E-value=1.4e+02 Score=20.54 Aligned_cols=15 Identities=27% Similarity=0.089 Sum_probs=8.3
Q ss_pred Cceeeeeeehhhccc
Q 036922 23 GTRTVGVISKIDQAS 37 (135)
Q Consensus 23 g~RTiGVitKiD~~~ 37 (135)
+-..+-|+||+|+..
T Consensus 109 ~~p~ilv~nK~Dl~~ 123 (172)
T cd01862 109 NFPFVVLGNKIDLEE 123 (172)
T ss_pred CceEEEEEECccccc
Confidence 344555666666653
No 36
>cd01876 YihA_EngB The YihA (EngB) subfamily. This subfamily of GTPases is typified by the E. coli YihA, an essential protein involved in cell division control. YihA and its orthologs are small proteins that typically contain less than 200 amino acid residues and consists of the GTPase domain only (some of the eukaryotic homologs contain an N-terminal extension of about 120 residues that might be involved in organellar targeting). Homologs of yihA are found in most Gram-positive and Gram-negative pathogenic bacteria, with the exception of Mycobacterium tuberculosis. The broad-spectrum nature of YihA and its essentiality for cell viability in bacteria make it an attractive antibacterial target.
Probab=25.16 E-value=78 Score=21.11 Aligned_cols=20 Identities=20% Similarity=0.247 Sum_probs=15.1
Q ss_pred cCceeeeeeehhhccccchh
Q 036922 22 QGTRTVGVISKIDQASADQK 41 (135)
Q Consensus 22 ~g~RTiGVitKiD~~~~~t~ 41 (135)
-+...+-|+||+|++..+..
T Consensus 109 ~~~~vi~v~nK~D~~~~~~~ 128 (170)
T cd01876 109 LGIPFLVVLTKADKLKKSEL 128 (170)
T ss_pred cCCCEEEEEEchhcCChHHH
Confidence 35667889999999866543
No 37
>cd04582 CBS_pair_ABC_OpuCA_assoc This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with the ABC transporter OpuCA. OpuCA is the ATP binding component of a bacterial solute transporter that serves a protective role to cells growing in a hyperosmolar environment but the function of the CBS domains in OpuCA remains unknown. In the related ABC transporter, OpuA, the tandem CBS domains have been shown to function as sensors for ionic strength, whereby they control the transport activity through an electronic switching mechanism. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. They are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzi
Probab=25.16 E-value=48 Score=20.97 Aligned_cols=16 Identities=25% Similarity=0.351 Sum_probs=12.6
Q ss_pred cCceeeeeeehhhccc
Q 036922 22 QGTRTVGVISKIDQAS 37 (135)
Q Consensus 22 ~g~RTiGVitKiD~~~ 37 (135)
+..+.+||||+-|+..
T Consensus 90 ~~~~~~Gvi~~~~l~~ 105 (106)
T cd04582 90 EDGRYVGEVTQRSIAD 105 (106)
T ss_pred CCCcEEEEEEHHHhhc
Confidence 3468999999998764
No 38
>cd04613 CBS_pair_SpoIVFB_EriC_assoc2 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with either the SpoIVFB domain (sporulation protein, stage IV cell wall formation, F locus, promoter-distal B) or the chloride channel protein EriC. SpoIVFB is one of 4 proteins involved in endospore formation; the others are SpoIVFA (sporulation protein, stage IV cell wall formation, F locus, promoter-proximal A), BofA (bypass-of-forespore A ), and SpoIVB (sporulation protein, stage IV cell wall formation, B locus). SpoIVFB is negatively regulated by SpoIVFA and BofA and activated by SpoIVB. It is thought that SpoIVFB, SpoIVFA, and BofA are located in the mother-cell membrane that surrounds the forespore and that SpoIVB is secreted from the forespore into the space between the two where it activates SpoIVFB. EriC is involved in inorganic ion transport and metabolism. CBS is a small domain originally identified in cystathionine beta-synthase a
Probab=24.98 E-value=48 Score=21.00 Aligned_cols=15 Identities=27% Similarity=0.450 Sum_probs=11.6
Q ss_pred Cceeeeeeehhhccc
Q 036922 23 GTRTVGVISKIDQAS 37 (135)
Q Consensus 23 g~RTiGVitKiD~~~ 37 (135)
..+.+||||+-|++.
T Consensus 99 ~~~~~Gvvt~~di~~ 113 (114)
T cd04613 99 PGKLLGILSRSDLLS 113 (114)
T ss_pred CCEEEEEEEhHHhhc
Confidence 468899999888753
No 39
>cd01891 TypA_BipA TypA (tyrosine phosphorylated protein A)/BipA subfamily. BipA is a protein belonging to the ribosome-binding family of GTPases and is widely distributed in bacteria and plants. BipA was originally described as a protein that is induced in Salmonella typhimurium after exposure to bactericidal/permeability-inducing protein (a cationic antimicrobial protein produced by neutrophils), and has since been identified in E. coli as well. The properties thus far described for BipA are related to its role in the process of pathogenesis by enteropathogenic E. coli. It appears to be involved in the regulation of several processes important for infection, including rearrangements of the cytoskeleton of the host, bacterial resistance to host defense peptides, flagellum-mediated cell motility, and expression of K5 capsular genes. It has been proposed that BipA may utilize a novel mechanism to regulate the expression of target genes. In addition, BipA from enteropathogenic E. co
Probab=23.38 E-value=2e+02 Score=21.09 Aligned_cols=29 Identities=31% Similarity=0.461 Sum_probs=19.0
Q ss_pred cCceeeeeeehhhccccchh-HHHHHHHHH
Q 036922 22 QGTRTVGVISKIDQASADQK-ALAAVQALL 50 (135)
Q Consensus 22 ~g~RTiGVitKiD~~~~~t~-alaAv~alL 50 (135)
.+-+.|-|+||+|+...... .++.+..++
T Consensus 116 ~~~p~iiv~NK~Dl~~~~~~~~~~~~~~~~ 145 (194)
T cd01891 116 LGLKPIVVINKIDRPDARPEEVVDEVFDLF 145 (194)
T ss_pred cCCCEEEEEECCCCCCCCHHHHHHHHHHHH
Confidence 57788999999999755442 233444434
No 40
>cd04169 RF3 RF3 subfamily. Peptide chain release factor 3 (RF3) is a protein involved in the termination step of translation in bacteria. Termination occurs when class I release factors (RF1 or RF2) recognize the stop codon at the A-site of the ribosome and activate the release of the nascent polypeptide. The class II release factor RF3 then initiates the release of the class I RF from the ribosome. RF3 binds to the RF/ribosome complex in the inactive (GDP-bound) state. GDP/GTP exchange occurs, followed by the release of the class I RF. Subsequent hydrolysis of GTP to GDP triggers the release of RF3 from the ribosome. RF3 also enhances the efficiency of class I RFs at less preferred stop codons and at stop codons in weak contexts.
Probab=23.28 E-value=76 Score=25.78 Aligned_cols=40 Identities=18% Similarity=0.188 Sum_probs=26.3
Q ss_pred cCceeeeeeehhhccccch-hHHHHHHHHHHhCCCCCCCCCce
Q 036922 22 QGTRTVGVISKIDQASADQ-KALAAVQALLLNQGPPKTADISW 63 (135)
Q Consensus 22 ~g~RTiGVitKiD~~~~~t-~alaAv~alL~~qG~~~~~~~pW 63 (135)
.+...|-|+||+|+...+. +.++.++..|. -+....++||
T Consensus 122 ~~~P~iivvNK~D~~~a~~~~~~~~l~~~l~--~~~~~~~~Pi 162 (267)
T cd04169 122 RGIPIITFINKLDREGRDPLELLDEIEEELG--IDCTPLTWPI 162 (267)
T ss_pred cCCCEEEEEECCccCCCCHHHHHHHHHHHHC--CCceeEEecc
Confidence 4778899999999876553 44455555442 3555666665
No 41
>cd01886 EF-G Elongation factor G (EF-G) subfamily. Translocation is mediated by EF-G (also called translocase). The structure of EF-G closely resembles that of the complex between EF-Tu and tRNA. This is an example of molecular mimicry; a protein domain evolved so that it mimics the shape of a tRNA molecule. EF-G in the GTP form binds to the ribosome, primarily through the interaction of its EF-Tu-like domain with the 50S subunit. The binding of EF-G to the ribosome in this manner stimulates the GTPase activity of EF-G. On GTP hydrolysis, EF-G undergoes a conformational change that forces its arm deeper into the A site on the 30S subunit. To accommodate this domain, the peptidyl-tRNA in the A site moves to the P site, carrying the mRNA and the deacylated tRNA with it. The ribosome may be prepared for these rearrangements by the initial binding of EF-G as well. The dissociation of EF-G leaves the ribosome ready to accept the next aminoacyl-tRNA into the A site. This group conta
Probab=23.07 E-value=72 Score=26.04 Aligned_cols=40 Identities=15% Similarity=0.301 Sum_probs=24.4
Q ss_pred cCceeeeeeehhhccccch-hHHHHHHHHHHhCCCCCCCCCce
Q 036922 22 QGTRTVGVISKIDQASADQ-KALAAVQALLLNQGPPKTADISW 63 (135)
Q Consensus 22 ~g~RTiGVitKiD~~~~~t-~alaAv~alL~~qG~~~~~~~pW 63 (135)
.|.+.|.||+|+|+...+. +.+..++..+. -+.....+|+
T Consensus 115 ~~~p~ivviNK~D~~~a~~~~~~~~l~~~l~--~~~~~~~~Pi 155 (270)
T cd01886 115 YNVPRIAFVNKMDRTGADFFRVVEQIREKLG--ANPVPLQLPI 155 (270)
T ss_pred cCCCEEEEEECCCCCCCCHHHHHHHHHHHhC--CCceEEEecc
Confidence 5778899999999975443 44455555442 2334444554
No 42
>cd04119 RJL RJL (RabJ-Like) subfamily. RJLs are found in many protists and as chimeras with C-terminal DNAJ domains in deuterostome metazoa. They are not found in plants, fungi, and protostome metazoa, suggesting a horizontal gene transfer between protists and deuterostome metazoa. RJLs lack any known membrane targeting signal and contain a degenerate phosphate/magnesium-binding 3 (PM3) motif, suggesting an impaired ability to hydrolyze GTP. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization.
Probab=22.78 E-value=1.1e+02 Score=20.80 Aligned_cols=15 Identities=27% Similarity=0.202 Sum_probs=12.3
Q ss_pred Cceeeeeeehhhccc
Q 036922 23 GTRTVGVISKIDQAS 37 (135)
Q Consensus 23 g~RTiGVitKiD~~~ 37 (135)
..+.|.|.||.|+..
T Consensus 110 ~~piilv~nK~Dl~~ 124 (168)
T cd04119 110 NIVVVVCANKIDLTK 124 (168)
T ss_pred CceEEEEEEchhccc
Confidence 467899999999874
No 43
>cd00882 Ras_like_GTPase Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulate initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Memb
Probab=22.34 E-value=55 Score=20.62 Aligned_cols=20 Identities=20% Similarity=0.099 Sum_probs=16.9
Q ss_pred cCceeeeeeehhhccccchh
Q 036922 22 QGTRTVGVISKIDQASADQK 41 (135)
Q Consensus 22 ~g~RTiGVitKiD~~~~~t~ 41 (135)
.+...+.|+||+|+......
T Consensus 101 ~~~~~ivv~nk~D~~~~~~~ 120 (157)
T cd00882 101 ENIPIILVGNKIDLPEERVV 120 (157)
T ss_pred CCCcEEEEEeccccccccch
Confidence 68889999999999876554
No 44
>cd04607 CBS_pair_NTP_transferase_assoc This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domain associated with the NTP (Nucleotidyl transferase) domain downstream. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown.
Probab=21.93 E-value=61 Score=20.91 Aligned_cols=17 Identities=29% Similarity=0.292 Sum_probs=13.4
Q ss_pred cCceeeeeeehhhcccc
Q 036922 22 QGTRTVGVISKIDQASA 38 (135)
Q Consensus 22 ~g~RTiGVitKiD~~~~ 38 (135)
+..+.+||||+-|.+.+
T Consensus 97 ~~~~~~Gvit~~di~~~ 113 (113)
T cd04607 97 EEGRVVGLATLDDLLSK 113 (113)
T ss_pred CCCCEEEEEEhHHhccC
Confidence 45688999999998753
No 45
>PRK05935 biotin--protein ligase; Provisional
Probab=21.71 E-value=89 Score=24.72 Aligned_cols=27 Identities=15% Similarity=0.274 Sum_probs=24.5
Q ss_pred chhHHHHHHHHHHHHHHHHHhhccccc
Q 036922 106 KLGRIALVDALAQQIRKRMKVRVPNVL 132 (135)
Q Consensus 106 klG~~~L~~~Lsk~i~~~ik~RlP~il 132 (135)
...+..|...|.++|.++++.|||-++
T Consensus 157 ~~~~~~l~~~l~~~l~~~~~~~~~~~~ 183 (190)
T PRK05935 157 PIDLEEQRERLIKHIKHVLIQTLPKLL 183 (190)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 467899999999999999999999875
No 46
>cd04605 CBS_pair_MET2_assoc This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the MET2 domain. Met2 is a key enzyme in the biosynthesis of methionine. It encodes a homoserine transacetylase involved in converting homoserine to O-acetyl homoserine. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown.
Probab=21.25 E-value=55 Score=20.84 Aligned_cols=15 Identities=27% Similarity=0.530 Sum_probs=9.0
Q ss_pred cCceeeeeeehhhcc
Q 036922 22 QGTRTVGVISKIDQA 36 (135)
Q Consensus 22 ~g~RTiGVitKiD~~ 36 (135)
++.+.+||||+-|+.
T Consensus 94 ~~~~~~G~v~~~di~ 108 (110)
T cd04605 94 AENRVIGIITSEDIS 108 (110)
T ss_pred CCCcEEEEEEHHHhh
Confidence 345666777666653
No 47
>TIGR00101 ureG urease accessory protein UreG. This model represents UreG, a GTP hydrolase that acts in the assembly of the nickel metallocenter of urease. It is found only in urease-positive species, although some urease-positive species (e.g. Bacillus subtilis) lack this protein. A similar protein, hypB, is an accessory protein for expression of hydrogenase, which also uses nickel.
Probab=20.88 E-value=74 Score=24.67 Aligned_cols=12 Identities=50% Similarity=0.504 Sum_probs=10.3
Q ss_pred eeeeehhhcccc
Q 036922 27 VGVISKIDQASA 38 (135)
Q Consensus 27 iGVitKiD~~~~ 38 (135)
+.|+||+|+.+.
T Consensus 141 ~~~~~k~d~~~~ 152 (199)
T TIGR00101 141 LLVINKIDLAPM 152 (199)
T ss_pred EEEEEhhhcccc
Confidence 789999999854
No 48
>COG1162 Predicted GTPases [General function prediction only]
Probab=20.72 E-value=90 Score=27.16 Aligned_cols=36 Identities=25% Similarity=0.279 Sum_probs=24.4
Q ss_pred cccccc--cCceeeeeeehhhccccchhHHHHHHHHHH
Q 036922 16 RVLSFL--QGTRTVGVISKIDQASADQKALAAVQALLL 51 (135)
Q Consensus 16 ~alkla--~g~RTiGVitKiD~~~~~t~alaAv~alL~ 51 (135)
|.|=+| .|-.-|=||||+|+.+.......+...+.+
T Consensus 101 R~Lv~ae~~gi~pvIvlnK~DL~~~~~~~~~~~~~~y~ 138 (301)
T COG1162 101 RYLVLAEAGGIEPVIVLNKIDLLDDEEAAVKELLREYE 138 (301)
T ss_pred HHHHHHHHcCCcEEEEEEccccCcchHHHHHHHHHHHH
Confidence 344444 788889999999999988875433333343
No 49
>cd04639 CBS_pair_26 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic gener
Probab=20.64 E-value=57 Score=20.80 Aligned_cols=13 Identities=23% Similarity=0.388 Sum_probs=9.2
Q ss_pred ceeeeeeehhhcc
Q 036922 24 TRTVGVISKIDQA 36 (135)
Q Consensus 24 ~RTiGVitKiD~~ 36 (135)
.+.+||||+-|+.
T Consensus 97 ~~~~G~it~~dl~ 109 (111)
T cd04639 97 GRLVGLVTLENVG 109 (111)
T ss_pred CCEEEEEEHHHhh
Confidence 5677888777764
No 50
>cd04594 CBS_pair_EriC_assoc_archaea This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the EriC CIC-type chloride channels in archaea. These ion channels are proteins with a seemingly simple task of allowing the passive flow of chloride ions across biological membranes. CIC-type chloride channels come from all kingdoms of life, have several gene families, and can be gated by voltage. The members of the CIC-type chloride channel are double-barreled: two proteins forming homodimers at a broad interface formed by four helices from each protein. The two pores are not found at this interface, but are completely contained within each subunit, as deduced from the mutational analyses, unlike many other channels, in which four or five identical or structurally related subunits jointly form one pore. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS do
Probab=20.59 E-value=56 Score=20.99 Aligned_cols=15 Identities=7% Similarity=0.102 Sum_probs=10.5
Q ss_pred cCceeeeeeehhhcc
Q 036922 22 QGTRTVGVISKIDQA 36 (135)
Q Consensus 22 ~g~RTiGVitKiD~~ 36 (135)
+..+.+||||+-|+.
T Consensus 88 ~~~~~iGvit~~dl~ 102 (104)
T cd04594 88 DDGKFKGIVTLDSIL 102 (104)
T ss_pred ECCEEEEEEEHHHhh
Confidence 445778888877764
No 51
>cd04606 CBS_pair_Mg_transporter This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domain in the magnesium transporter, MgtE. MgtE and its homologs are found in eubacteria, archaebacteria, and eukaryota. Members of this family transport Mg2+ or other divalent cations into the cell via two highly conserved aspartates. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown.
Probab=20.30 E-value=66 Score=20.69 Aligned_cols=16 Identities=31% Similarity=0.401 Sum_probs=13.0
Q ss_pred cCceeeeeeehhhccc
Q 036922 22 QGTRTVGVISKIDQAS 37 (135)
Q Consensus 22 ~g~RTiGVitKiD~~~ 37 (135)
+..+.+||||+-|++.
T Consensus 92 ~~~~~~Gvit~~dll~ 107 (109)
T cd04606 92 EEGRLVGIITVDDVID 107 (109)
T ss_pred CCCcEEEEEEhHHhhh
Confidence 4568999999999863
No 52
>cd04638 CBS_pair_25 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic gener
Probab=20.21 E-value=59 Score=20.71 Aligned_cols=16 Identities=19% Similarity=0.401 Sum_probs=11.1
Q ss_pred cCceeeeeeehhhccc
Q 036922 22 QGTRTVGVISKIDQAS 37 (135)
Q Consensus 22 ~g~RTiGVitKiD~~~ 37 (135)
+..+.+|+||+-|...
T Consensus 90 d~~~~~G~it~~d~~~ 105 (106)
T cd04638 90 DDGKLVGIVTVADIVR 105 (106)
T ss_pred ECCEEEEEEEHHHhhc
Confidence 3347888888877653
No 53
>cd01856 YlqF YlqF. Proteins of the YlqF family contain all sequence motifs typical of the vast class of P-loop-containing GTPases, but show a circular permutation, with a G4-G1-G3 pattern of motifs as opposed to the regular G1-G3-G4 pattern seen in most GTPases. The YlqF subfamily is represented in a phylogenetically diverse array of bacteria (including gram-positive bacteria, proteobacteria, Synechocystis, Borrelia, and Thermotoga) and in all eukaryotes.
Probab=20.07 E-value=63 Score=23.65 Aligned_cols=17 Identities=24% Similarity=0.253 Sum_probs=14.1
Q ss_pred cCceeeeeeehhhcccc
Q 036922 22 QGTRTVGVISKIDQASA 38 (135)
Q Consensus 22 ~g~RTiGVitKiD~~~~ 38 (135)
.+...|=|+||+|+.+.
T Consensus 45 ~~k~~ilVlNK~Dl~~~ 61 (171)
T cd01856 45 GNKPRIIVLNKADLADP 61 (171)
T ss_pred cCCCEEEEEehhhcCCh
Confidence 46789999999999754
Done!