Query 030908
Match_columns 169
No_of_seqs 146 out of 1016
Neff 6.6
Searched_HMMs 46136
Date Fri Mar 29 06:23:58 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030908.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030908hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01152 Bac_globin: Bacterial 100.0 2.4E-36 5.2E-41 223.5 10.2 119 26-147 1-120 (120)
2 COG2346 Truncated hemoglobins 100.0 4E-35 8.6E-40 221.6 12.6 124 23-150 5-129 (133)
3 cd00454 Trunc_globin Truncated 100.0 9E-33 1.9E-37 202.9 13.9 115 26-147 1-116 (116)
4 cd01067 globin_like superfamil 99.3 8.3E-12 1.8E-16 91.7 6.2 97 38-140 1-115 (117)
5 cd01068 sensor_globin Globin d 98.6 1.1E-07 2.4E-12 71.8 5.3 103 33-140 28-137 (147)
6 PF11563 Protoglobin: Protoglo 97.7 6.8E-05 1.5E-09 57.0 5.2 105 33-141 30-141 (158)
7 cd01040 globin Globins are hem 97.3 0.00035 7.6E-09 51.2 4.6 106 34-143 17-139 (140)
8 COG1017 Hmp Hemoglobin-like fl 96.9 0.0029 6.4E-08 48.6 6.4 107 34-148 19-137 (150)
9 PRK13289 bifunctional nitric o 96.8 0.0065 1.4E-07 52.9 8.3 113 28-148 14-137 (399)
10 PF00042 Globin: Globin plant 91.1 0.22 4.7E-06 35.0 2.8 77 35-115 15-109 (110)
11 KOG3378 Globins and related he 83.9 3.3 7.2E-05 35.7 6.0 92 39-147 24-136 (385)
12 PHA02928 Hypothetical protein; 68.4 4 8.6E-05 31.8 2.1 65 26-94 95-160 (214)
13 cd01220 PH_CDEP Chondrocyte-de 47.0 20 0.00043 25.5 2.6 19 103-121 81-99 (99)
14 cd07925 LigA_like_1 The A subu 43.2 50 0.0011 24.2 4.2 32 103-135 24-55 (106)
15 cd01219 PH_FGD FGD (faciogenit 42.4 26 0.00057 24.6 2.6 19 103-121 83-101 (101)
16 PRK10455 periplasmic protein; 41.7 99 0.0022 24.0 6.0 27 96-122 50-76 (161)
17 KOG0763 Mitochondrial ornithin 41.4 53 0.0012 27.5 4.6 72 65-141 10-82 (301)
18 PRK13378 protocatechuate 4,5-d 40.3 57 0.0012 24.3 4.1 32 103-135 35-66 (117)
19 PF08671 SinI: Anti-repressor 38.4 75 0.0016 17.9 3.5 26 109-136 3-28 (30)
20 cd07923 Gallate_dioxygenase_C 37.5 56 0.0012 23.4 3.6 32 103-135 16-47 (94)
21 cd07321 Extradiol_Dioxygenase_ 36.9 57 0.0012 22.2 3.5 33 102-135 13-45 (77)
22 PF06628 Catalase-rel: Catalas 36.8 1.2E+02 0.0026 19.8 6.1 44 103-149 20-64 (68)
23 TIGR02792 PCA_ligA protocatech 36.2 69 0.0015 23.9 4.0 32 103-135 29-60 (117)
24 PF07631 PSD4: Protein of unkn 35.3 49 0.0011 24.7 3.2 60 6-82 5-66 (128)
25 cd07924 PCA_45_Doxase_A The A 33.6 84 0.0018 23.6 4.2 32 103-135 32-63 (121)
26 PRK13379 protocatechuate 4,5-d 33.4 76 0.0016 23.7 3.9 32 103-135 36-67 (119)
27 cd07921 PCA_45_Doxase_A_like S 33.1 72 0.0016 23.4 3.7 32 103-135 24-55 (106)
28 PRK13377 protocatechuate 4,5-d 33.0 82 0.0018 23.9 4.1 32 103-135 35-66 (129)
29 PF03126 Plus-3: Plus-3 domain 29.8 40 0.00086 24.1 1.9 16 102-117 92-107 (108)
30 PF07637 PSD5: Protein of unkn 29.4 1.4E+02 0.003 19.3 4.3 21 102-122 18-38 (64)
31 PF13297 Telomere_Sde2_2: Telo 28.6 32 0.0007 22.7 1.1 13 3-15 34-46 (60)
32 PRK13756 tetracycline represso 28.4 3E+02 0.0065 21.8 11.6 105 22-143 36-143 (205)
33 COG3265 GntK Gluconate kinase 27.8 99 0.0021 24.3 3.8 50 70-121 10-62 (161)
34 PRK14974 cell division protein 26.5 3E+02 0.0065 23.9 7.1 39 100-139 55-93 (336)
35 PF00169 PH: PH domain; Inter 26.1 75 0.0016 20.7 2.7 17 103-119 87-103 (104)
36 COG4103 Uncharacterized protei 25.3 1.4E+02 0.0031 23.1 4.3 68 69-141 5-79 (148)
37 PF07746 LigA: Aromatic-ring-o 25.1 1.5E+02 0.0032 20.8 4.0 32 103-135 9-40 (88)
38 PF14968 CCDC84: Coiled coil p 25.0 2E+02 0.0043 25.3 5.6 45 65-122 87-131 (336)
39 smart00719 Plus3 Short conserv 25.0 59 0.0013 23.4 2.1 14 102-115 95-108 (109)
40 PRK13754 conjugal transfer fer 24.7 3.7E+02 0.0081 21.6 10.3 112 2-122 41-173 (186)
41 PF07862 Nif11: Nitrogen fixat 24.3 60 0.0013 19.7 1.7 19 40-60 6-24 (49)
42 cd01251 PH_centaurin_alpha Cen 22.4 88 0.0019 22.0 2.5 20 102-121 83-102 (103)
43 cd01264 PH_melted Melted pleck 22.2 65 0.0014 23.1 1.8 18 102-119 84-101 (101)
44 PRK15114 tRNA (cytidine/uridin 21.5 1.7E+02 0.0036 24.2 4.3 39 103-141 179-217 (245)
45 TIGR00050 rRNA_methyl_1 RNA me 20.7 1.9E+02 0.004 23.6 4.5 39 103-141 170-208 (233)
46 PF02881 SRP54_N: SRP54-type p 20.3 2.5E+02 0.0055 18.1 5.7 37 102-139 17-53 (75)
47 PF15409 PH_8: Pleckstrin homo 20.0 85 0.0018 22.1 2.0 17 102-118 72-88 (89)
No 1
>PF01152 Bac_globin: Bacterial-like globin; InterPro: IPR001486 Globins are haem-containing proteins involved in binding and/or transporting oxygen. They belong to a very large and well studied family that is widely distributed in many organisms []. Globins have evolved from a common ancestor and can be divided into three groups: single-domain globins, and two types of chimeric globins, flavohaemoglobins and globin-coupled sensors. Bacteria have all three types of globins, while archaea lack flavohaemoglobins, and eukaryotes lack globin-coupled sensors []. Several functionally different haemoglobins can coexist in the same species. The major types of globins include: Haemoglobin (Hb): trimer of two alpha and two beta chains, although embryonic and foetal forms can substitute the alpha or beta chain for ones with higher oxygen affinity, such as gamma, delta, epsilon or zeta chains. Hb transports oxygen from lungs to other tissues in vertebrates []. Hb proteins are also present in unicellular organisms where they act as enzymes or sensors []. Myoglobin (Mb): monomeric protein responsible for oxygen storage in vertebrate muscle []. Neuroglobin: a myoglobin-like haemprotein expressed in vertebrate brain and retina, where it is involved in neuroprotection from damage due to hypoxia or ischemia []. Neuroglobin belongs to a branch of the globin family that diverged early in evolution. Cytoglobin: an oxygen sensor expressed in multiple tissues. Related to neuroglobin []. Erythrocruorin: highly cooperative extracellular respiratory proteins found in annelids and arthropods that are assembled from as many as 180 subunit into hexagonal bilayers []. Leghaemoglobin (legHb or symbiotic Hb): occurs in the root nodules of leguminous plants, where it facilitates the diffusion of oxygen to symbiotic bacteriods in order to promote nitrogen fixation. Non-symbiotic haemoglobin (NsHb): occurs in non-leguminous plants, and can be over-expressed in stressed plants []. Flavohaemoglobins (FHb): chimeric, with an N-terminal globin domain and a C-terminal ferredoxin reductase-like NAD/FAD-binding domain. FHb provides protection against nitric oxide via its C-terminal domain, which transfers electrons to haem in the globin []. Globin-coupled sensors: chimeric, with an N-terminal myoglobin-like domain and a C-terminal domain that resembles the cytoplasmic signalling domain of bacterial chemoreceptors. They bind oxygen, and act to initiate an aerotactic response or regulate gene expression [, ]. Protoglobin: a single domain globin found in archaea that is related to the N-terminal domain of globin-coupled sensors []. Truncated 2/2 globin: lack the first helix, giving them a 2-over-2 instead of the canonical 3-over-3 alpha-helical sandwich fold. Can be divided into three main groups (I, II and II) based on structural features []. This entry represents a group of haemoglobin-like proteins found in eubacteria, cyanobacteria, protozoa, algae and plants, but not in animals or yeast. These proteins have a truncated 2-over-2 rather than the canonical 3-over-3 alpha-helical sandwich fold []. This entry includes: HbN (or GlbN): a truncated haemoglobin-like protein that binds oxygen cooperatively with a very high affinity and a slow dissociation rate, which may exclude it from oxygen transport. It appears to be involved in bacterial nitric oxide detoxification and in nitrosative stress []. Cyanoglobin (or GlbN): a truncated haemoprotein found in cyanobacteria that has high oxygen affinity, and which appears to serve as part of a terminal oxidase, rather than as a respiratory pigment []. HbO (or GlbO): a truncated haemoglobin-like protein with a lower oxygen affinity than HbN. HbO associates with the bacterial cell membrane, where it significantly increases oxygen uptake over membranes lacking this protein. HbO appears to interact with a terminal oxidase, and could participate in an oxygen/electron-transfer process that facilitates oxygen transfer during aerobic metabolism []. Glb3: a nuclear-encoded truncated haemoglobin from plants that appears more closely related to HbO than HbN. Glb3 from Arabidopsis thaliana (Mouse-ear cress) exhibits an unusual concentration-independent binding of oxygen and carbon dioxide []. ; GO: 0019825 oxygen binding, 0015671 oxygen transport; PDB: 2BKM_B 1UVY_A 1DLW_A 2XYK_B 2IG3_A 2GKM_B 1S61_A 1S56_B 1RTE_B 2GLN_A ....
Probab=100.00 E-value=2.4e-36 Score=223.52 Aligned_cols=119 Identities=29% Similarity=0.525 Sum_probs=113.0
Q ss_pred cHHHHcC-HHHHHHHHHHHHHHHhcChhhhhhcccCCCCHHHHHHHHHHHHHHHhCCCCccCCCCCCCcccCCCCCCCCC
Q 030908 26 NLFRKLG-LQTFINLSTNFYTRVYDDEEEWFRSIFANSNKEEAIQNQYEFFVQRMGGPPLYSQRKGHPALIGRHRPFPVT 104 (169)
Q Consensus 26 sLYe~iG-~~~I~~LV~~FY~rv~~D~~~~l~~~F~~~d~~~~~~~l~~Fl~~~lGGP~~Y~g~~G~p~m~~~H~~l~It 104 (169)
|||++|| +++|++||+.||+||.+||. |+++|.+.|++.++.++++|||+++|||+.|+++.|+|.|+.+|++++||
T Consensus 1 slye~lGG~~~I~~lv~~fY~rv~~d~~--l~~~F~~~d~~~~~~~~~~fl~~~~GGp~~Y~~~~G~p~m~~~H~~l~it 78 (120)
T PF01152_consen 1 SLYERLGGEEGIRALVDAFYDRVLADPR--LKPFFEGIDLEKHKEKQAEFLSQLLGGPPLYTGRDGHPMMREAHAHLGIT 78 (120)
T ss_dssp CHHHHCTHHHHHHHHHHHHHHHHHT-TT--TGGGGTTSCHHHHHHHHHHHHHHHTTSSSHHHHHHSSH-HHHHHTTS-BB
T ss_pred CHHHHhcCHHHHHHHHHHHHHHHHcCHH--HHhhcCCCCHHHHHHHHHHHHHHHhCCCCCCcccCCCchHHHHHhCCCCC
Confidence 7999999 99999999999999999999 99999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHHcc
Q 030908 105 HQAAERWLHHMQIALDSTPEIDADSKIKMMNFFRHTAFFLVAG 147 (169)
Q Consensus 105 ~~~fd~Wl~~~~~aLd~~~~~~~~~~~~l~~~~~~~a~~iv~~ 147 (169)
++||++|++||.+||+++ +++++.++++++.++.++..|+|.
T Consensus 79 ~~~f~~~~~~~~~al~~~-~v~~~~~~~~~~~~~~~~~~i~n~ 120 (120)
T PF01152_consen 79 EEHFDRWLELLKQALDEL-GVPEELIDELLARLESLRDDIVNK 120 (120)
T ss_dssp HHHHHHHHHHHHHHHHHT-TCTHHHHHHHHHHHHHHHHHHHH-
T ss_pred HHHHHHHHHHHHHHHHHh-CCCHHHHHHHHHHHHHHHHHhcCC
Confidence 999999999999999999 699999999999999999999984
No 2
>COG2346 Truncated hemoglobins [General function prediction only]
Probab=100.00 E-value=4e-35 Score=221.57 Aligned_cols=124 Identities=31% Similarity=0.511 Sum_probs=118.8
Q ss_pred CcccHHHHcC-HHHHHHHHHHHHHHHhcChhhhhhcccCCCCHHHHHHHHHHHHHHHhCCCCccCCCCCCCcccCCCCCC
Q 030908 23 DETNLFRKLG-LQTFINLSTNFYTRVYDDEEEWFRSIFANSNKEEAIQNQYEFFVQRMGGPPLYSQRKGHPALIGRHRPF 101 (169)
Q Consensus 23 ~~~sLYe~iG-~~~I~~LV~~FY~rv~~D~~~~l~~~F~~~d~~~~~~~l~~Fl~~~lGGP~~Y~g~~G~p~m~~~H~~l 101 (169)
..+|+||.|| ++.|++||+.||++|.+||. |+|+|+ .|++....++..||++++|||..|+|+||||.|+..|.+.
T Consensus 5 ~~~t~yd~iGg~~~i~~Lv~~FY~rV~~d~~--l~piF~-~dl~~~~~k~~afl~~f~gGp~~y~e~~ghp~lr~~h~~~ 81 (133)
T COG2346 5 RPTTLYDAIGGDETIDLLVERFYERVLEDPR--LGPIFP-ADLAGTWPKQKAFLTQFWGGPPLYTERYGHPPLRARHLPF 81 (133)
T ss_pred cchhhHHHhCchhHHHHHHHHHHHHHhcCcc--ccccCC-CccccchHHHHHHHHHHhcCCcccccccCCccHHHHccCC
Confidence 4468999999 88999999999999999999 999999 8899999999999999999999999999999999999999
Q ss_pred CCCHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHHccHhh
Q 030908 102 PVTHQAAERWLHHMQIALDSTPEIDADSKIKMMNFFRHTAFFLVAGDEL 150 (169)
Q Consensus 102 ~It~~~fd~Wl~~~~~aLd~~~~~~~~~~~~l~~~~~~~a~~iv~~~~~ 150 (169)
+||+++|++||.||..||+++ +++++.++.++++++++|.+|+|....
T Consensus 82 ~it~~~~d~WL~~~~~al~ei-~~~~e~~~~i~~~~~~~A~~~~n~~~~ 129 (133)
T COG2346 82 GITPEEFDAWLGLFADALDEI-GLPEELREEILARAERIAHHMVNSLFT 129 (133)
T ss_pred CCCHHHHHHHHHHHHHHHHHh-CCCHHHHHHHHHHHHHHHHHHHccccc
Confidence 999999999999999999999 599999999999999999999998653
No 3
>cd00454 Trunc_globin Truncated hemoglobins (trHbs) are a family of oxygen-binding heme proteins found in cyanobacteria, eubacteria, unicellular eukaryotes, and plants. The truncated hemoglobins have a characteristic two-over-two alpha helical folding pattern that is distinct from the three-over-three pattern found in other globins. A subset of these have been demonstrated to form homodimers.
Probab=100.00 E-value=9e-33 Score=202.89 Aligned_cols=115 Identities=30% Similarity=0.541 Sum_probs=109.2
Q ss_pred cHHHHcC-HHHHHHHHHHHHHHHhcChhhhhhcccCCCCHHHHHHHHHHHHHHHhCCCCccCCCCCCCcccCCCCCCCCC
Q 030908 26 NLFRKLG-LQTFINLSTNFYTRVYDDEEEWFRSIFANSNKEEAIQNQYEFFVQRMGGPPLYSQRKGHPALIGRHRPFPVT 104 (169)
Q Consensus 26 sLYe~iG-~~~I~~LV~~FY~rv~~D~~~~l~~~F~~~d~~~~~~~l~~Fl~~~lGGP~~Y~g~~G~p~m~~~H~~l~It 104 (169)
||||+|| +++|++||+.||++|.+||. |+++|.+.+++.++.++++|||+++|||+.|+|+ ++ +.+|++++|+
T Consensus 1 slye~lGG~~~i~~lv~~FY~~i~~dp~--i~~~F~~~~~~~~~~~~~~fl~~~~gg~~~y~g~---~~-~~~H~~~~I~ 74 (116)
T cd00454 1 TLYERLGGEEAIRALVDRFYARVAADPR--LGPIFPADDLEEHRAKLADFLTQVLGGPGLYRGH---PM-LRRHLPFPIT 74 (116)
T ss_pred CHHHHhCCHHHHHHHHHHHHHHHhcChH--HHHhcCCcchHHHHHHHHHHHHHHcCCCCCCCCC---Ch-hhhhcCCCCC
Confidence 7999999 99999999999999999999 9999999889999999999999999999999854 54 4699999999
Q ss_pred HHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHHcc
Q 030908 105 HQAAERWLHHMQIALDSTPEIDADSKIKMMNFFRHTAFFLVAG 147 (169)
Q Consensus 105 ~~~fd~Wl~~~~~aLd~~~~~~~~~~~~l~~~~~~~a~~iv~~ 147 (169)
++||++|++||.+||+++ +++.+.++++++.+++++..|+++
T Consensus 75 ~~~f~~~l~~l~~al~~~-~~~~~~~~~~~~~~~~~~~~~v~~ 116 (116)
T cd00454 75 EEEFDAWLELLRDALDEL-GVPAELADALLARAERIADHMVNK 116 (116)
T ss_pred HHHHHHHHHHHHHHHHHh-CCCHHHHHHHHHHHHHHHHHHhcC
Confidence 999999999999999999 699999999999999999999874
No 4
>cd01067 globin_like superfamily containing globins and truncated hemoglobins
Probab=99.27 E-value=8.3e-12 Score=91.74 Aligned_cols=97 Identities=14% Similarity=0.136 Sum_probs=86.5
Q ss_pred HHHHHHHHHHhcCh-hhhhhcccCC-----------CCHHHHHHHHHHHHHHHhCCCCc----cCCCCCCCcccCCCCCC
Q 030908 38 NLSTNFYTRVYDDE-EEWFRSIFAN-----------SNKEEAIQNQYEFFVQRMGGPPL----YSQRKGHPALIGRHRPF 101 (169)
Q Consensus 38 ~LV~~FY~rv~~D~-~~~l~~~F~~-----------~d~~~~~~~l~~Fl~~~lGGP~~----Y~g~~G~p~m~~~H~~l 101 (169)
++|+.||.++.+++ . ++.+|.. .+++.++.++..+|+.+++|+.. |..+ .|..+|.++
T Consensus 1 ~~v~~fy~~lf~~~P~--~~~~F~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~----~l~~~H~~~ 74 (117)
T cd01067 1 ADVDDFYKHLFENYPP--LRKYFKSREEYTADVQNDPFFKKQGQKILLAIHVACAGYDDREFNAKTR----ELASRHKRD 74 (117)
T ss_pred CcHHHHHHHHHHhChh--HHHHCCCCCCCHHhccCCHHHHHHHHHHHHHHHHHHHccCcHhHHHHHH----HHHHHHhhc
Confidence 47999999999886 6 9999996 67999999999999999999998 8876 799999999
Q ss_pred CC--CHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHH
Q 030908 102 PV--THQAAERWLHHMQIALDSTPEIDADSKIKMMNFFRHT 140 (169)
Q Consensus 102 ~I--t~~~fd~Wl~~~~~aLd~~~~~~~~~~~~l~~~~~~~ 140 (169)
+| ++.+|+.|.+++..+|.+++..+++..+.+.+.+...
T Consensus 75 gi~~~~~~f~~~~~~L~~~l~~~~~~~~~~~~Aw~~~~~~~ 115 (117)
T cd01067 75 HVHMPPEVFTAFWKLLEEYLGKKTTLDEPTIQAWHEIGREF 115 (117)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhh
Confidence 99 9999999999999999999534889888888777654
No 5
>cd01068 sensor_globin Globin domain present in Globin-Coupled-Sensors (GCS). These domains detect changes in intracellular concentrations of oxygen, carbon monoxyde, or nitrous oxide, which result in aerotaxis and/or gene regulation. One subgroup, the HemATs, are aerotactic heme sensors combining a globin with an MCP signaling domain, others function as gene regulators, by direct combination with DNA-binding domains, with domains modulating 2nd messengers, or with domains interacting with transcription factors or regulators.
Probab=98.56 E-value=1.1e-07 Score=71.76 Aligned_cols=103 Identities=16% Similarity=0.131 Sum_probs=83.0
Q ss_pred HHHHHHHHHHHHHHHhcChhhhhhcccC-CCCHHHHHHHHHHHHHHHhCCC--CccCCCCCCCcccCCCCCCCCCHHHH-
Q 030908 33 LQTFINLSTNFYTRVYDDEEEWFRSIFA-NSNKEEAIQNQYEFFVQRMGGP--PLYSQRKGHPALIGRHRPFPVTHQAA- 108 (169)
Q Consensus 33 ~~~I~~LV~~FY~rv~~D~~~~l~~~F~-~~d~~~~~~~l~~Fl~~~lGGP--~~Y~g~~G~p~m~~~H~~l~It~~~f- 108 (169)
++.+..+|+.||+++..+|. ++.+|. ....+..+..+.++|..+++|+ ..|..+ .-.+-.+|..++|++..+
T Consensus 28 ~~~~~~i~~~FY~~l~~~p~--~~~~~~~~~~~~~l~~~~~~~~~~l~~~~~d~~y~~~--~~~iG~~H~~igl~~~~~~ 103 (147)
T cd01068 28 EANADELVDRFYDHLRRTPE--TAAFLGDESVVERLKSTQRRHWVELFSGVYDEAYIAQ--RVRIGEVHARIGLEPKWYL 103 (147)
T ss_pred HHHHHHHHHHHHHHHhcChH--HHHHhCCchHHHHHHHHHHHHHHHHhCCCCCHHHHHH--HHHHHHHHHHcCCCCcchH
Confidence 67899999999999999998 999998 4458999999999999999999 556543 123667999999999888
Q ss_pred ---HHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHH
Q 030908 109 ---ERWLHHMQIALDSTPEIDADSKIKMMNFFRHT 140 (169)
Q Consensus 109 ---d~Wl~~~~~aLd~~~~~~~~~~~~l~~~~~~~ 140 (169)
......+.+++.+. ..+++....+...+.++
T Consensus 104 ~~~~~~~~~l~~~l~~~-~~~~~~~~~~~~al~k~ 137 (147)
T cd01068 104 GGYAVLLELLIGALRES-ILSADELAQALRALIKL 137 (147)
T ss_pred HHHHHHHHHHHHHHHHH-ccCHHHHHHHHHHHHHH
Confidence 58888888888877 35666666665555444
No 6
>PF11563 Protoglobin: Protoglobin; PDB: 2VEE_G 3QZZ_A 3R0G_A 3QZX_A 2VEB_A 1OR6_A 1OR4_B 2W31_B.
Probab=97.71 E-value=6.8e-05 Score=56.96 Aligned_cols=105 Identities=12% Similarity=0.133 Sum_probs=73.1
Q ss_pred HHHHHHHHHHHHHHHhcChhhhhhcccCC-CCHHHHHHHHHHHHHHHhCCCCccCCCCC--CCcccCCCCCCCCCHHHHH
Q 030908 33 LQTFINLSTNFYTRVYDDEEEWFRSIFAN-SNKEEAIQNQYEFFVQRMGGPPLYSQRKG--HPALIGRHRPFPVTHQAAE 109 (169)
Q Consensus 33 ~~~I~~LV~~FY~rv~~D~~~~l~~~F~~-~d~~~~~~~l~~Fl~~~lGGP~~Y~g~~G--~p~m~~~H~~l~It~~~fd 109 (169)
++.+..+|++||+++..+|. ++.+|.. ...++.+..+..||..++.|+ |...|= --.+-..|..++|++..+.
T Consensus 30 ~~~~~~iv~~FY~~l~~~pe--~~~~~~~~~~~~~lk~~q~~~~~~l~s~~--~d~~y~~~~~~iG~~H~~igl~~~~~~ 105 (158)
T PF11563_consen 30 EPHAPEIVDDFYDHLLRFPE--TARIFDSESTIERLKATQRRHWRELFSGD--FDEEYVERRRRIGQVHARIGLPPRWYI 105 (158)
T ss_dssp HCTHHHHHHHHHHHHHTSHH--HHGGGCCHCCHHHHHHHHHHHHHHCTSS---CSHHHHHHHHHHHHHHHHCT--HHHHH
T ss_pred HHHHHHHHHHHHHHHHCCHH--HHHHhCChHHHHHHHHHHHHHHHHHhCCC--chHHHHHHHHHHHHHHhHcCCCHHHHH
Confidence 56789999999999999998 9999997 779999999999999999998 433211 0124568999999997765
Q ss_pred HHH----HHHHHHHhhCCCCCHHHHHHHHHHHHHHH
Q 030908 110 RWL----HHMQIALDSTPEIDADSKIKMMNFFRHTA 141 (169)
Q Consensus 110 ~Wl----~~~~~aLd~~~~~~~~~~~~l~~~~~~~a 141 (169)
.-. ..+...+.+....+++.+..++..+.++.
T Consensus 106 ~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~a~~k~~ 141 (158)
T PF11563_consen 106 GAYSFLREFLLEALAEEYRLDPEERADLLRALSKLL 141 (158)
T ss_dssp HHHHHHHHHHHHHHHHHS--SHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHH
Confidence 544 44445555541246666666666655543
No 7
>cd01040 globin Globins are heme proteins, which bind and transport oxygen. This family summarizes a diverse set of homologous protein domains, including: (1) tetrameric vertebrate hemoglobins, which are the major protein component of erythrocytes and transport oxygen in the bloodstream, (2) microorganismal flavohemoglobins, which are linked to C-terminal FAD-dependend reductase domains, (3) homodimeric bacterial hemoglobins, such as from Vitreoscilla, (4) plant leghemoglobins (symbiotic hemoglobins, involved in nitrogen metabolism in plant rhizomes), (5) plant non-symbiotic hexacoordinate globins and hexacoordinate globins from bacteria and animals, such as neuroglobin, (6) invertebrate hemoglobins, which may occur in tandem-repeat arrangements, and (7) monomeric myoglobins found in animal muscle tissue.
Probab=97.33 E-value=0.00035 Score=51.24 Aligned_cols=106 Identities=11% Similarity=0.077 Sum_probs=79.8
Q ss_pred HHHHHHHHHHHHHHhc-ChhhhhhcccCCC-----------CHHHHHHHHHHHHHHHhCC---CCccCCCCCCCcccCCC
Q 030908 34 QTFINLSTNFYTRVYD-DEEEWFRSIFANS-----------NKEEAIQNQYEFFVQRMGG---PPLYSQRKGHPALIGRH 98 (169)
Q Consensus 34 ~~I~~LV~~FY~rv~~-D~~~~l~~~F~~~-----------d~~~~~~~l~~Fl~~~lGG---P~~Y~g~~G~p~m~~~H 98 (169)
.....+...||.++.+ +|. +..+|... ++..|..++.+++..+... +...... =..+...|
T Consensus 17 ~~~~~~g~~~f~~lf~~~P~--~~~~F~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~v~~l~~~~~l~~~--l~~lg~~H 92 (140)
T cd01040 17 ADREEIGLEFYERLFKAHPE--TRALFSRFGGLSAALKGSPKFKAHGKRVLNALDEAIKNLDDLEALKAL--LAKLGRKH 92 (140)
T ss_pred ccHHhHHHHHHHHHHHHChh--HHHHhHHhCCchHhHccCHHHHHHHHHHHHHHHHHHHhccChHHHHHH--HHHHHHHH
Confidence 3567788889999987 676 99999842 5788888888888777643 3211100 01366799
Q ss_pred CCCCCCHHHHHHHHHHHHHHHhhCCC--CCHHHHHHHHHHHHHHHHH
Q 030908 99 RPFPVTHQAAERWLHHMQIALDSTPE--IDADSKIKMMNFFRHTAFF 143 (169)
Q Consensus 99 ~~l~It~~~fd~Wl~~~~~aLd~~~~--~~~~~~~~l~~~~~~~a~~ 143 (169)
..++|++++|+.+.++|..++.+..+ ++++..+.+...+..++..
T Consensus 93 ~~~~v~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~aW~~~~~~i~~~ 139 (140)
T cd01040 93 AKRGVDPEHFKLFGEALLEVLAEVLGDDFTPEVKAAWDKLLDVIADA 139 (140)
T ss_pred HHhCCCHHHHHHHHHHHHHHHHHHhCCcCCHHHHHHHHHHHHHHHHh
Confidence 99999999999999999999998744 5888888888888777654
No 8
>COG1017 Hmp Hemoglobin-like flavoprotein [Energy production and conversion]
Probab=96.95 E-value=0.0029 Score=48.59 Aligned_cols=107 Identities=11% Similarity=0.163 Sum_probs=70.4
Q ss_pred HHHHHHHHHHHHHHhcC-hhhhhhcccCCCC------HHHHHHHHHHHHHHHhCCCC---ccCCCCCCCcccCCCCCCCC
Q 030908 34 QTFINLSTNFYTRVYDD-EEEWFRSIFANSN------KEEAIQNQYEFFVQRMGGPP---LYSQRKGHPALIGRHRPFPV 103 (169)
Q Consensus 34 ~~I~~LV~~FY~rv~~D-~~~~l~~~F~~~d------~~~~~~~l~~Fl~~~lGGP~---~Y~g~~G~p~m~~~H~~l~I 103 (169)
+.-..|...||+||.++ |. +.++|+..+ -.....-+..|=.. ..-+. ..-+ .....|..++|
T Consensus 19 ~~G~~iT~~FY~~MF~~hPE--l~niFN~~nQ~~G~Q~~aLA~ai~ayA~n-Idnl~~l~~~v~-----rIa~KHvsl~I 90 (150)
T COG1017 19 EHGETITAHFYKRMFAHHPE--LKNIFNMANQKNGDQPKALANAILAYAKN-IDNLEALLPVVE-----RIAHKHVSLQI 90 (150)
T ss_pred hcchHHHHHHHHHHHhhCHH--HHHHHhHhhhcccccHHHHHHHHHHHHHh-cCCHHHHHHHHH-----HHHHHHHhcCC
Confidence 34567899999999998 76 999999421 11111112222111 11110 0011 23458999999
Q ss_pred CHHHHHHHHHHHHHHHhhCCC--CCHHHHHHHHHHHHHHHHHHHccH
Q 030908 104 THQAAERWLHHMQIALDSTPE--IDADSKIKMMNFFRHTAFFLVAGD 148 (169)
Q Consensus 104 t~~~fd~Wl~~~~~aLd~~~~--~~~~~~~~l~~~~~~~a~~iv~~~ 148 (169)
.++|+...=+|+-.|++++-+ ..+++.+.|-+.-..+|.-++...
T Consensus 91 ~pEhYpIVge~LL~aI~evlgd~at~evl~AW~~AY~~lA~~lI~~E 137 (150)
T COG1017 91 KPEHYPIVGEHLLAAIKEVLGDAATPEVLEAWGEAYGVLADVLIDRE 137 (150)
T ss_pred ChhhccHHHHHHHHHHHHHhCccccHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999998822 235677777778888899888873
No 9
>PRK13289 bifunctional nitric oxide dioxygenase/dihydropteridine reductase 2; Provisional
Probab=96.80 E-value=0.0065 Score=52.95 Aligned_cols=113 Identities=12% Similarity=0.129 Sum_probs=82.6
Q ss_pred HHHcCHHHHHHHHHHHHHHHhc-ChhhhhhcccCCC--CHHHHHHHHHHHHHHHh---CCCC---ccCCCCCCCcccCCC
Q 030908 28 FRKLGLQTFINLSTNFYTRVYD-DEEEWFRSIFANS--NKEEAIQNQYEFFVQRM---GGPP---LYSQRKGHPALIGRH 98 (169)
Q Consensus 28 Ye~iG~~~I~~LV~~FY~rv~~-D~~~~l~~~F~~~--d~~~~~~~l~~Fl~~~l---GGP~---~Y~g~~G~p~m~~~H 98 (169)
+..+ ......+...||.++.+ +|. +..+|... +...+..++..-+..+. +-+. .+-. .|-..|
T Consensus 14 w~~~-~~~~~~~~~~fy~~lF~~~P~--~~~~F~~~~~~~~~~~~~~~~~l~~~v~~ld~~~~l~~~l~-----~L~~~H 85 (399)
T PRK13289 14 VPLL-EEHGEALTAHFYDRMFSHNPE--LKNIFNQSNQRNGDQPEALANAVLAYARNIDNLEALLPAVE-----RIAQKH 85 (399)
T ss_pred HHHH-HHhHHHHHHHHHHHHHhhChH--HHHhcCcccccchhHHHHHHHHHHHHHHhcCChHHHHHHHH-----HHHHHH
Confidence 3444 34577899999999654 566 99999843 24445555555555443 3333 2221 355789
Q ss_pred CCCCCCHHHHHHHHHHHHHHHhhCCC--CCHHHHHHHHHHHHHHHHHHHccH
Q 030908 99 RPFPVTHQAAERWLHHMQIALDSTPE--IDADSKIKMMNFFRHTAFFLVAGD 148 (169)
Q Consensus 99 ~~l~It~~~fd~Wl~~~~~aLd~~~~--~~~~~~~~l~~~~~~~a~~iv~~~ 148 (169)
..++|++++|+.|-++|..+|.++.+ ++++..+.|...+..++..|+...
T Consensus 86 ~~~gV~~~~f~~~~~~ll~~l~~~~~~~~t~~~~~AW~~~~~~l~~~~~~~~ 137 (399)
T PRK13289 86 VSLQIKPEHYPIVGEHLLAAIREVLGDAATDEVLDAWGEAYGVLADVFIGRE 137 (399)
T ss_pred HHcCCChHHhHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999998633 789999999999999999998773
No 10
>PF00042 Globin: Globin plant globin signature erythrocruorin family signature alpha hemoglobin signature myoglobin signature thalassemia.; InterPro: IPR000971 Globins are haem-containing proteins involved in binding and/or transporting oxygen. They belong to a very large and well studied family that is widely distributed in many organisms []. Globins have evolved from a common ancestor and can be divided into three groups: single-domain globins, and two types of chimeric globins, flavohaemoglobins and globin-coupled sensors. Bacteria have all three types of globins, while archaea lack flavohaemoglobins, and eukaryotes lack globin-coupled sensors []. Several functionally different haemoglobins can coexist in the same species. The major types of globins include: Haemoglobin (Hb): trimer of two alpha and two beta chains, although embryonic and foetal forms can substitute the alpha or beta chain for ones with higher oxygen affinity, such as gamma, delta, epsilon or zeta chains. Hb transports oxygen from lungs to other tissues in vertebrates []. Hb proteins are also present in unicellular organisms where they act as enzymes or sensors []. Myoglobin (Mb): monomeric protein responsible for oxygen storage in vertebrate muscle []. Neuroglobin: a myoglobin-like haemprotein expressed in vertebrate brain and retina, where it is involved in neuroprotection from damage due to hypoxia or ischemia []. Neuroglobin belongs to a branch of the globin family that diverged early in evolution. Cytoglobin: an oxygen sensor expressed in multiple tissues. Related to neuroglobin []. Erythrocruorin: highly cooperative extracellular respiratory proteins found in annelids and arthropods that are assembled from as many as 180 subunit into hexagonal bilayers []. Leghaemoglobin (legHb or symbiotic Hb): occurs in the root nodules of leguminous plants, where it facilitates the diffusion of oxygen to symbiotic bacteriods in order to promote nitrogen fixation. Non-symbiotic haemoglobin (NsHb): occurs in non-leguminous plants, and can be over-expressed in stressed plants []. Flavohaemoglobins (FHb): chimeric, with an N-terminal globin domain and a C-terminal ferredoxin reductase-like NAD/FAD-binding domain. FHb provides protection against nitric oxide via its C-terminal domain, which transfers electrons to haem in the globin []. Globin-coupled sensors: chimeric, with an N-terminal myoglobin-like domain and a C-terminal domain that resembles the cytoplasmic signalling domain of bacterial chemoreceptors. They bind oxygen, and act to initiate an aerotactic response or regulate gene expression [, ]. Protoglobin: a single domain globin found in archaea that is related to the N-terminal domain of globin-coupled sensors []. Truncated 2/2 globin: lack the first helix, giving them a 2-over-2 instead of the canonical 3-over-3 alpha-helical sandwich fold. Can be divided into three main groups (I, II and II) based on structural features []. This entry covers most of the globin family of proteins, but it omits some bacterial globins and the protoglobins. More information about these proteins can be found at Protein of the Month: Haemoglobin [].; GO: 0005506 iron ion binding, 0020037 heme binding; PDB: 2WTH_A 2WTG_A 3A59_G 3FS4_C 3CY5_C 3D1A_B 2RI4_J 3EU1_B 1JEB_A 2Z6N_B ....
Probab=91.06 E-value=0.22 Score=35.03 Aligned_cols=77 Identities=14% Similarity=0.195 Sum_probs=57.6
Q ss_pred HHHHHHHHHHHHHhc-ChhhhhhcccCC-CC------------HHHHHHHHHHHHHHHhCCCCcc---CCCCCCCcccCC
Q 030908 35 TFINLSTNFYTRVYD-DEEEWFRSIFAN-SN------------KEEAIQNQYEFFVQRMGGPPLY---SQRKGHPALIGR 97 (169)
Q Consensus 35 ~I~~LV~~FY~rv~~-D~~~~l~~~F~~-~d------------~~~~~~~l~~Fl~~~lGGP~~Y---~g~~G~p~m~~~ 97 (169)
....+...||.++.+ +|. +..+|.. .+ +..|..++..++..+...-..- ... =..|-..
T Consensus 15 ~~~~~g~~~f~~lF~~~P~--~~~~F~~~~~~~~~~~l~~~~~~~~h~~~v~~~l~~~v~~l~~~~~l~~~--l~~lg~~ 90 (110)
T PF00042_consen 15 DKDEFGSEFFQRLFEEYPD--YKKLFPKFKDIVPLEELKNNPEFKAHAQRVMEALDEAVDNLDDPESLEAM--LRKLGRR 90 (110)
T ss_dssp GHHHHHHHHHHHHHHHSGG--GGGGGTTGTTTSSHHHHTTSHHHHHHHHHHHHHHHHHHHTTTSTHGHHHH--HHHHHHH
T ss_pred cHHHHHHHHHHHHHHHCHH--HHhhcccccccchHHHHhccchHHHHHHHHHHHHHHHHHccCChHhHHHH--HHHHHHH
Confidence 566788889998876 676 9999993 23 8999999999999888774111 100 0125678
Q ss_pred CCCCC-CCHHHHHHHHHHH
Q 030908 98 HRPFP-VTHQAAERWLHHM 115 (169)
Q Consensus 98 H~~l~-It~~~fd~Wl~~~ 115 (169)
|..++ |++++|+.+-++|
T Consensus 91 H~~~~~v~~~~f~~~~~~l 109 (110)
T PF00042_consen 91 HKKRGGVTPEHFELFGEAL 109 (110)
T ss_dssp HHHTTTSSTHHHHHHHHHH
T ss_pred hHCcCCCCHHHHHHHHHHH
Confidence 99999 9999999998876
No 11
>KOG3378 consensus Globins and related hemoproteins [Energy production and conversion]
Probab=83.94 E-value=3.3 Score=35.68 Aligned_cols=92 Identities=13% Similarity=0.191 Sum_probs=66.1
Q ss_pred HHHHHHHHHhcChhhhhhcccCCCC-----HHH--------------HHHHHHHHHHHHhCCCCccCCCCCCCcccCCCC
Q 030908 39 LSTNFYTRVYDDEEEWFRSIFANSN-----KEE--------------AIQNQYEFFVQRMGGPPLYSQRKGHPALIGRHR 99 (169)
Q Consensus 39 LV~~FY~rv~~D~~~~l~~~F~~~d-----~~~--------------~~~~l~~Fl~~~lGGP~~Y~g~~G~p~m~~~H~ 99 (169)
+...||.||++.. |++-|+|...+ -+. -...+.+|+.+ +...|.
T Consensus 24 ~t~~fy~~ml~~~-pelLp~Fn~~~q~~~sqpr~la~~ilaaakNIdDLssL~~~l~q----------------ig~KHr 86 (385)
T KOG3378|consen 24 HTTVFYARMLALE-PELLPLFNYNCQQFSSQPRKLALVILAAAKNIDDLSSLEEYLAQ----------------IGRKHR 86 (385)
T ss_pred HHHHHHHHHHhcC-hhhHHHHHHHHHHhcCChhHHHHHHHHHhcChhhHHHHHHHHHH----------------Hhhhhh
Confidence 5678999998875 24889998311 000 01122233332 335899
Q ss_pred CCCCCHHHHHHHHHHHHHHHhhCCC--CCHHHHHHHHHHHHHHHHHHHcc
Q 030908 100 PFPVTHQAAERWLHHMQIALDSTPE--IDADSKIKMMNFFRHTAFFLVAG 147 (169)
Q Consensus 100 ~l~It~~~fd~Wl~~~~~aLd~~~~--~~~~~~~~l~~~~~~~a~~iv~~ 147 (169)
++.|..+||...=+|+-.+|.++-+ ..|+.++.|-+.-..+|..|+..
T Consensus 87 alqIK~ehypiVGe~LL~~l~e~LgdaaTPa~~~AWs~aYgava~i~i~~ 136 (385)
T KOG3378|consen 87 ALQIKLEHYPIVGESLLYMLEECLGDAATPATRAAWSQAYGAVAQIMIDS 136 (385)
T ss_pred heeechhhCccHHHHHHHHHHHHcCcccCHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999998888887622 57899999999999999999855
No 12
>PHA02928 Hypothetical protein; Provisional
Probab=68.37 E-value=4 Score=31.80 Aligned_cols=65 Identities=12% Similarity=0.265 Sum_probs=53.2
Q ss_pred cHHHHcC-HHHHHHHHHHHHHHHhcChhhhhhcccCCCCHHHHHHHHHHHHHHHhCCCCccCCCCCCCcc
Q 030908 26 NLFRKLG-LQTFINLSTNFYTRVYDDEEEWFRSIFANSNKEEAIQNQYEFFVQRMGGPPLYSQRKGHPAL 94 (169)
Q Consensus 26 sLYe~iG-~~~I~~LV~~FY~rv~~D~~~~l~~~F~~~d~~~~~~~l~~Fl~~~lGGP~~Y~g~~G~p~m 94 (169)
...+++. .-.+..||..++.-+.+|-. +||+|.. ++..+.+-.+-.+.-+|-...|..+|||-+.
T Consensus 95 aildkmtadikltdlvrhyfryieqdip--lgplfkk--idsyrirainkyskelglateyfnkyghlmf 160 (214)
T PHA02928 95 AILDKMTADIKLTDLVRHYFRYIEQDIP--LGPLFKK--IDSYRIRAINKYSKELGLATEYFNKYGHLMF 160 (214)
T ss_pred eehhhhcccccHHHHHHHHHHHhhccCC--CchHHhh--hhhHHhHHHHhhhHHhhhHHHHHhhcCeEEE
Confidence 3567777 77889999999999999976 9999985 4566667777788889999999999998764
No 13
>cd01220 PH_CDEP Chondrocyte-derived ezrin-like domain containing protein (CDEP) Pleckstrin homology (PH) domain. Chondrocyte-derived ezrin-like domain containing protein (CDEP) Pleckstrin homology (PH) domain. CDEP consists of a Ferm domain, a rhoGEF (DH) domain followed by two PH domains. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes.
Probab=47.03 E-value=20 Score=25.49 Aligned_cols=19 Identities=26% Similarity=0.560 Sum_probs=17.0
Q ss_pred CCHHHHHHHHHHHHHHHhh
Q 030908 103 VTHQAAERWLHHMQIALDS 121 (169)
Q Consensus 103 It~~~fd~Wl~~~~~aLd~ 121 (169)
=|+++.+.|++.+.+|+++
T Consensus 81 ~s~~Ek~~Wi~~i~~aI~~ 99 (99)
T cd01220 81 STRAEKEKWLADLSKAIAD 99 (99)
T ss_pred CCHHHHHHHHHHHHHHhhC
Confidence 5789999999999999874
No 14
>cd07925 LigA_like_1 The A subunit of Uncharacterized proteins with similarity to Protocatechuate 4,5-dioxygenase (LigAB). The proteins of unknown function in this subfamily are similar to the A subunit of the Protocatechuate (PCA) 4,5-dioxygenase (LigAB). LigAB belongs to the class III extradiol dioxygenase family, composed of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Dioxygenases play key roles in the degradation of aromatic compounds. PCA 4,5-dioxygenase catalyzes the oxidization and subsequent ring-opening of PCA (or 3,4-dihydroxybenzoic acid), which is an intermediate in the breakdown of lignin and other compounds.
Probab=43.19 E-value=50 Score=24.23 Aligned_cols=32 Identities=13% Similarity=0.124 Sum_probs=29.4
Q ss_pred CCHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHH
Q 030908 103 VTHQAAERWLHHMQIALDSTPEIDADSKIKMMN 135 (169)
Q Consensus 103 It~~~fd~Wl~~~~~aLd~~~~~~~~~~~~l~~ 135 (169)
+.++.+++|+..-..-+++. +++++.++.+.+
T Consensus 24 ~~~~nRe~F~aD~~Ay~~~~-~Lteeqr~av~~ 55 (106)
T cd07925 24 NDAANREAFLADEEAYCEKF-GLTPEQKQAVRN 55 (106)
T ss_pred CCHHHHHHHHhCHHHHHHHc-CCCHHHHHHHHH
Confidence 67999999999999999999 699999988876
No 15
>cd01219 PH_FGD FGD (faciogenital dysplasia protein) pleckstrin homology (PH) domain. FGD (faciogenital dysplasia protein) pleckstrin homology (PH) domain. FGD has a RhoGEF (DH) domain, followed by a PH domain, a FYVE domain and a C-terminal PH domain. FGD is a guanine nucleotide exchange factor that activates the Rho GTPase Cdc42. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes.
Probab=42.44 E-value=26 Score=24.64 Aligned_cols=19 Identities=16% Similarity=0.436 Sum_probs=17.1
Q ss_pred CCHHHHHHHHHHHHHHHhh
Q 030908 103 VTHQAAERWLHHMQIALDS 121 (169)
Q Consensus 103 It~~~fd~Wl~~~~~aLd~ 121 (169)
=|+++.+.|++.+..++++
T Consensus 83 ~s~eEk~~W~~ai~~~i~~ 101 (101)
T cd01219 83 RTQKEKNDWVQAIFSIIDE 101 (101)
T ss_pred CCHHHHHHHHHHHHHHhhC
Confidence 5899999999999999874
No 16
>PRK10455 periplasmic protein; Reviewed
Probab=41.70 E-value=99 Score=24.04 Aligned_cols=27 Identities=11% Similarity=0.065 Sum_probs=22.8
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHHHhhC
Q 030908 96 GRHRPFPVTHQAAERWLHHMQIALDST 122 (169)
Q Consensus 96 ~~H~~l~It~~~fd~Wl~~~~~aLd~~ 122 (169)
....+|++|++....|-..|++.-.+.
T Consensus 50 ~m~~~L~LT~~Qrqqir~im~~~r~~~ 76 (161)
T PRK10455 50 MMFKGLNLTDAQKQQIRDIMKAQRDQM 76 (161)
T ss_pred hhhhhCCCCHHHHHHHHHHHHHHHHhh
Confidence 456789999999999999998887664
No 17
>KOG0763 consensus Mitochondrial ornithine transporter [Energy production and conversion]
Probab=41.40 E-value=53 Score=27.55 Aligned_cols=72 Identities=11% Similarity=0.080 Sum_probs=50.4
Q ss_pred HHHHHHHHHHHHHHhCCC-CccCCCCCCCcccCCCCCCCCCHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHH
Q 030908 65 EEAIQNQYEFFVQRMGGP-PLYSQRKGHPALIGRHRPFPVTHQAAERWLHHMQIALDSTPEIDADSKIKMMNFFRHTA 141 (169)
Q Consensus 65 ~~~~~~l~~Fl~~~lGGP-~~Y~g~~G~p~m~~~H~~l~It~~~fd~Wl~~~~~aLd~~~~~~~~~~~~l~~~~~~~a 141 (169)
-..++-..+++.+..||. +.|.|+ .+...-..+.-=++.+.-|++|+..|-... ++-+=.+-.+=+.+..+|
T Consensus 10 ~~fi~g~IDllAGaaGG~A~Vy~gQ----PlDTvKVK~QTFP~lYrg~~dC~l~TY~~d-GlRGlYaGt~PAl~AnvA 82 (301)
T KOG0763|consen 10 INFIQGAIDLLAGAAGGTACVYTGQ----PLDTVKVKMQTFPDLYRGLTDCFLKTYRQD-GLRGLYAGTVPALFANVA 82 (301)
T ss_pred hhHHHHHHHHhccccCCceeeeeCC----CcceeeeehccChHHHhhHHHHHHHHHHHh-hhhhhhcCccHHHHHHHH
Confidence 456788999999999996 689975 444555566667899999999999999887 354433333333333333
No 18
>PRK13378 protocatechuate 4,5-dioxygenase subunit alpha; Provisional
Probab=40.32 E-value=57 Score=24.34 Aligned_cols=32 Identities=9% Similarity=0.060 Sum_probs=29.3
Q ss_pred CCHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHH
Q 030908 103 VTHQAAERWLHHMQIALDSTPEIDADSKIKMMN 135 (169)
Q Consensus 103 It~~~fd~Wl~~~~~aLd~~~~~~~~~~~~l~~ 135 (169)
+.++.+++|+..-..-+++. +++++.++.+++
T Consensus 35 ~~~~nRe~F~ade~Ay~~~~-~Lteeqk~aV~~ 66 (117)
T PRK13378 35 NDAANRAAFLADEAAYCRKY-GLNEEQKEAIRN 66 (117)
T ss_pred CCHHHHHHHHhCHHHHHHHc-CCCHHHHHHHHh
Confidence 67999999999999999999 699999988876
No 19
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=38.43 E-value=75 Score=17.93 Aligned_cols=26 Identities=19% Similarity=0.501 Sum_probs=17.8
Q ss_pred HHHHHHHHHHHhhCCCCCHHHHHHHHHH
Q 030908 109 ERWLHHMQIALDSTPEIDADSKIKMMNF 136 (169)
Q Consensus 109 d~Wl~~~~~aLd~~~~~~~~~~~~l~~~ 136 (169)
.-|+.++.+|+.. |++.+...+|+..
T Consensus 3 ~EW~~Li~eA~~~--Gls~eeir~FL~~ 28 (30)
T PF08671_consen 3 EEWVELIKEAKES--GLSKEEIREFLEF 28 (30)
T ss_dssp HHHHHHHHHHHHT--T--HHHHHHHHHH
T ss_pred HHHHHHHHHHHHc--CCCHHHHHHHHHh
Confidence 3699999999964 4887777766653
No 20
>cd07923 Gallate_dioxygenase_C The C-terminal domain of Gallate Dioxygenase, which catalyzes the oxidization and subsequent ring-opening of gallate. Gallate Dioxygenase catalyzes the oxidization and subsequent ring-opening of gallate, an intermediate in the degradation of the aromatic compound, syringate. The reaction product of gallate dioxygenase is 4-oxalomesaconate. The amino acid sequence of the N-terminal and C-terminal regions of gallate dioxygenase exhibits homology with the sequence of the PCA 4,5-dioxygenase B (catalytic) and A subunits, respectively. This model represents the C-terminal domain, which is similar to the A subunit of PCA 4,5-dioxygenase (or LigAB). The enzyme is estimated to be a homodimer according to the Escherichia coli enzyme. Since enzymes in this subfamily have fused A and B subunits, the dimer interface may resemble the tetramer interface of classical LigAB enzymes. This enzyme belongs to the class III extradiol dioxygenase family, composed of enzymes whi
Probab=37.45 E-value=56 Score=23.43 Aligned_cols=32 Identities=16% Similarity=0.328 Sum_probs=29.2
Q ss_pred CCHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHH
Q 030908 103 VTHQAAERWLHHMQIALDSTPEIDADSKIKMMN 135 (169)
Q Consensus 103 It~~~fd~Wl~~~~~aLd~~~~~~~~~~~~l~~ 135 (169)
|.++.+++|++.-...|++. ++.++.++.+..
T Consensus 16 ~~a~~RerF~~D~ea~~~e~-gLt~Ee~~av~~ 47 (94)
T cd07923 16 IEPAHRERFLEDPEALFDEA-GLTEEERTLIRN 47 (94)
T ss_pred CCHHHHHHHHhCHHHHHHHc-CCCHHHHHHHHc
Confidence 68999999999999999999 699999988765
No 21
>cd07321 Extradiol_Dioxygenase_3A_like Subunit A of Class III extradiol dioxygenases. Extradiol dioxygenases catalyze the incorporation of both atoms of molecular oxygen into substrates using a variety of reaction mechanisms, resulting in the cleavage of aromatic rings. There are two major groups of dioxygenases according to the cleavage site of the aromatic ring. Intradiol enzymes cleave the aromatic ring between two hydroxyl groups, whereas extradiol enzymes cleave the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Extradiol dioxygenases can be divided into three classes. Class I and II enzymes are evolutionary related and show sequence similarity, with the two domain class II enzymes evolving from the class I enzyme through gene duplication. Class III enzymes are different in sequence and structure and usually have two subunits, designated A and B, which form a tetramer composed of two copies of each subunit. This model represents subunit A of c
Probab=36.92 E-value=57 Score=22.19 Aligned_cols=33 Identities=15% Similarity=0.244 Sum_probs=28.9
Q ss_pred CCCHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHH
Q 030908 102 PVTHQAAERWLHHMQIALDSTPEIDADSKIKMMN 135 (169)
Q Consensus 102 ~It~~~fd~Wl~~~~~aLd~~~~~~~~~~~~l~~ 135 (169)
.+.++.+++|++.=...|++. +++++.++.++.
T Consensus 13 ~~~~~~re~f~~dp~a~~~~~-~Lt~eE~~al~~ 45 (77)
T cd07321 13 LVKPEVKERFKADPEAVLAEY-GLTPEEKAALLA 45 (77)
T ss_pred hcCHHHHHHHHhCHHHHHHHc-CCCHHHHHHHHc
Confidence 477889999999999999999 599999988875
No 22
>PF06628 Catalase-rel: Catalase-related immune-responsive; InterPro: IPR010582 Catalases (1.11.1.6 from EC) are antioxidant enzymes that catalyse the conversion of hydrogen peroxide to water and molecular oxygen, serving to protect cells from its toxic effects []. Hydrogen peroxide is produced as a consequence of oxidative cellular metabolism and can be converted to the highly reactive hydroxyl radical via transition metals, this radical being able to damage a wide variety of molecules within a cell, leading to oxidative stress and cell death. Catalases act to neutralise hydrogen peroxide toxicity, and are produced by all aerobic organisms ranging from bacteria to man. Most catalases are mono-functional, haem-containing enzymes, although there are also bifunctional haem-containing peroxidase/catalases (IPR000763 from INTERPRO) that are closely related to plant peroxidases, and non-haem, manganese-containing catalases (IPR007760 from INTERPRO) that are found in bacteria []. This entry represents a small conserved region within catalase enzymes that carries the immune-responsive amphipathic octa-peptide that is recognised by T cells [].; PDB: 2CAH_A 1NM0_A 1H7K_A 1E93_A 1H6N_A 3HB6_A 2CAG_A 1M85_A 1MQF_A 1A4E_C ....
Probab=36.78 E-value=1.2e+02 Score=19.82 Aligned_cols=44 Identities=11% Similarity=0.178 Sum_probs=35.1
Q ss_pred CCHHHHHHHHHHHHHHHhhCCCCCHH-HHHHHHHHHHHHHHHHHccHh
Q 030908 103 VTHQAAERWLHHMQIALDSTPEIDAD-SKIKMMNFFRHTAFFLVAGDE 149 (169)
Q Consensus 103 It~~~fd~Wl~~~~~aLd~~~~~~~~-~~~~l~~~~~~~a~~iv~~~~ 149 (169)
+++.+.++++..+...|..+ +.+ +++.++.++..+-..+-.+.+
T Consensus 20 l~~~er~~lv~nia~~l~~v---~~~~i~~r~l~~f~~vd~~lg~~v~ 64 (68)
T PF06628_consen 20 LSDEERERLVENIAGHLSGV---SDEEIQERVLAYFYKVDPDLGQRVA 64 (68)
T ss_dssp SSHHHHHHHHHHHHHHHTTS---SHHHHHHHHHHHHHHH-HHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHHccC---ChhhHHHHHHHHHHHhCHHHHHHHH
Confidence 58999999999999999655 655 999999999887776655543
No 23
>TIGR02792 PCA_ligA protocatechuate 4,5-dioxygenase, alpha subunit. Protocatechuate (PCA) 4,5-dioxygenase is the first enzyme in the PCA 4,5-cleavage pathway that is an alternative to PCA 3,4-cleavage and PCA 2,3 cleavage pathways. PCA is an intermediate in the breakdown of lignin (hence the gene symbol ligA) and other compounds. Members of this family are the alpha chain of PCA 4,5-dioxygenase, or the equivalent domain of a fusion protein.
Probab=36.22 E-value=69 Score=23.89 Aligned_cols=32 Identities=16% Similarity=0.217 Sum_probs=29.3
Q ss_pred CCHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHH
Q 030908 103 VTHQAAERWLHHMQIALDSTPEIDADSKIKMMN 135 (169)
Q Consensus 103 It~~~fd~Wl~~~~~aLd~~~~~~~~~~~~l~~ 135 (169)
+.++.+++|+..-..-+++. ++.++.++.+++
T Consensus 29 ~~~~nRerF~ade~Ay~d~~-~Lt~eqk~av~~ 60 (117)
T TIGR02792 29 MKAENRERFKADESAYLDEW-NLTPAQKQAVLA 60 (117)
T ss_pred cCHHHHHHHHhCHHHHHHHc-CCCHHHHHHHHh
Confidence 78899999999999999999 699999988876
No 24
>PF07631 PSD4: Protein of unknown function (DUF1592); InterPro: IPR013042 A region of similarity shared by several Rhodopirellula baltica cytochrome-like proteins that are predicted to be secreted. These proteins also contain IPR011478 from INTERPRO, IPR013036 from INTERPRO, IPR013039 from INTERPRO and IPR013043 from INTERPRO.
Probab=35.31 E-value=49 Score=24.74 Aligned_cols=60 Identities=17% Similarity=-0.007 Sum_probs=34.8
Q ss_pred HHHHHhhCCCCCCcccCCcccHHHHcCHHHH--HHHHHHHHHHHhcChhhhhhcccCCCCHHHHHHHHHHHHHHHhCCC
Q 030908 6 EKASEWSGVDPADAFAIDETNLFRKLGLQTF--INLSTNFYTRVYDDEEEWFRSIFANSNKEEAIQNQYEFFVQRMGGP 82 (169)
Q Consensus 6 ~~~~~~~~~~~~~~~~~~~~sLYe~iG~~~I--~~LV~~FY~rv~~D~~~~l~~~F~~~d~~~~~~~l~~Fl~~~lGGP 82 (169)
+.|++++-.. -...++..|++....-.+ ...+..--+||++||+ . +..+..|+.+|++=.
T Consensus 5 ElAsrLSYfL---w~s~PD~~L~~aA~~g~L~~~~~l~~q~~RML~dpr--~------------~~~~~~F~~qWL~l~ 66 (128)
T PF07631_consen 5 ELASRLSYFL---WGSPPDAELLDAAAAGELRTPEQLRAQAERMLADPR--A------------RRFVERFFRQWLDLD 66 (128)
T ss_pred HHHHHHHHHH---hcCCCCHHHHHHHHhCCCCCHHHHHHHHHHHHcCcc--H------------HHHHHHHHHHHhCCC
Confidence 3455554431 222455667765442233 4455555668889997 3 345678999997643
No 25
>cd07924 PCA_45_Doxase_A The A subunit of Protocatechuate 4,5-dioxygenase (LigAB) is the smaller, non-catalytic subunit. The A subunit is the non-catalytic subunit of Protocatechuate (PCA) 4,5-dioxygenase (LigAB), which is composed of A and B subunits that form a tetramer. PCA 4,5-dioxygenase catalyzes the oxidization and subsequent ring-opening of PCA (or 3,4-dihydroxybenzoic acid), which is an intermediate in the breakdown of lignin and other compounds. PCA 4,5-dioxygenase is one of the aromatic ring opening dioxygenases which play key roles in the degradation of aromatic compounds. As a member of the Class III extradiol dioxygenase family, LigAB uses a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon.
Probab=33.64 E-value=84 Score=23.59 Aligned_cols=32 Identities=16% Similarity=0.239 Sum_probs=29.4
Q ss_pred CCHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHH
Q 030908 103 VTHQAAERWLHHMQIALDSTPEIDADSKIKMMN 135 (169)
Q Consensus 103 It~~~fd~Wl~~~~~aLd~~~~~~~~~~~~l~~ 135 (169)
+.++.+++|+..-..-+++. ++.++.++.+++
T Consensus 32 ~~~~nRerF~ade~Ay~~~~-~Lteeqr~aV~~ 63 (121)
T cd07924 32 MKAENRERFKADERAYLDKW-PMTEEQKQAVLA 63 (121)
T ss_pred CCHHHHHHHHhCHHHHHHHc-CCCHHHHHHHHH
Confidence 78899999999999999999 699999988876
No 26
>PRK13379 protocatechuate 4,5-dioxygenase subunit alpha; Provisional
Probab=33.35 E-value=76 Score=23.74 Aligned_cols=32 Identities=9% Similarity=0.208 Sum_probs=29.5
Q ss_pred CCHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHH
Q 030908 103 VTHQAAERWLHHMQIALDSTPEIDADSKIKMMN 135 (169)
Q Consensus 103 It~~~fd~Wl~~~~~aLd~~~~~~~~~~~~l~~ 135 (169)
|.++.+++|+..-..-|++. ++.++.++.+.+
T Consensus 36 ~~~~~RerF~aDe~ay~~~~-~Lt~eqk~aV~~ 67 (119)
T PRK13379 36 IRAPWRDRFLQDAEALMQEA-GLTEQEKELIRA 67 (119)
T ss_pred ccHHHHHHHHhCHHHHHHHc-CCCHHHHHHHHh
Confidence 88999999999999999999 699999988776
No 27
>cd07921 PCA_45_Doxase_A_like Subunit A of the Class III Extradiol dioxygenase, Protocatechuate 4,5-dioxygenase, and similar enzymes. This subfamily includes the A subunit of protocatechuate (PCA) 4,5-dioxygenase (LigAB) and two subfamilies of unknown function. The A subunit is the smaller, non-catalytic subunit of LigAB. PCA 4,5-dioxygenase catalyzes the oxidization and subsequent ring-opening of PCA (or 3,4-dihydroxybenzoic acid), which is an intermediate in the breakdown of lignin and other compounds. PCA 4,5-dioxygenase is one of the aromatic ring opening dioxygenases which play key roles in the degradation of aromatic compounds. As members of the Class III extradiol dioxygenase family, the enzymes use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. LigAB-like class III enzymes are usually composed of two subunits, designated A and B, which form a tetramer composed of two copies of each subunit.
Probab=33.08 E-value=72 Score=23.37 Aligned_cols=32 Identities=9% Similarity=0.129 Sum_probs=29.3
Q ss_pred CCHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHH
Q 030908 103 VTHQAAERWLHHMQIALDSTPEIDADSKIKMMN 135 (169)
Q Consensus 103 It~~~fd~Wl~~~~~aLd~~~~~~~~~~~~l~~ 135 (169)
+.++.+++|+..=..-|++. +++++.++.++.
T Consensus 24 ~~a~~Re~F~aD~eAy~~~~-gLTeEe~~AV~~ 55 (106)
T cd07921 24 NKAENREAFKADEEAYCDKF-GLTEEQKQAVLD 55 (106)
T ss_pred CCHHHHHHHHhCHHHHHHHc-CCCHHHHHHHHh
Confidence 58999999999999999999 699999988876
No 28
>PRK13377 protocatechuate 4,5-dioxygenase subunit alpha; Provisional
Probab=33.05 E-value=82 Score=23.88 Aligned_cols=32 Identities=16% Similarity=0.240 Sum_probs=29.3
Q ss_pred CCHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHH
Q 030908 103 VTHQAAERWLHHMQIALDSTPEIDADSKIKMMN 135 (169)
Q Consensus 103 It~~~fd~Wl~~~~~aLd~~~~~~~~~~~~l~~ 135 (169)
+.++.+++|+..-..-+++. ++.++.++.+++
T Consensus 35 ~~~~nRerF~ade~Ay~de~-~Lteeqr~aV~~ 66 (129)
T PRK13377 35 MKAENRERFKADERAYLDEW-PMTEEQKQAVLA 66 (129)
T ss_pred CCHHHHHHHHhCHHHHHHHc-CCCHHHHHHHHh
Confidence 78899999999999999999 699999988876
No 29
>PF03126 Plus-3: Plus-3 domain; InterPro: IPR004343 The yeast Paf1 complex consists of Pfa1, Rtf1, Cdc73, Ctr9, and Leo1. The complex regulates histone H2B ubiquitination, histone H3 methylation, RNA polymerase II carboxy-terminal domain (CTD) Ser2 phosphorylation, and RNA 3' end processing. The conservation of Paf1 complex function in higher eukaryotes has been confirmed in human cells, Drosophila and Arabidopsis. The Plus3 domain spans the most conserved regions of the Rtf1 protein and is surrounded by regions of low complexity and coiled-coil propensity []. It contains only a limited number of highly conserved amino acids, among which are three positively charged residues that gave the Plus3 domain its name. The capacity to bind single-stranded DNA is at least one function of the Plus3 domain []. The plus-3 domain is about 90 residues in length and is often found associated with the GYF domain (IPR003169 from INTERPRO). The Plus3 domain structure consists of six alpha helices intervened by a sequence of six beta strands in a mixed alpha/beta topology. Beta strands 1, 2, 5, and 6 compose a four-stranded antiparallel beta sheet with a beta-hairpin insertion formed by strands 3 and 4. The N-terminal helices alpha1-alpha3 and C-terminal helix alpha6 pack together to form an alpha subdomain, while the beta strands and the small 3(10) helix alpha 4 form a beta subdomain. The two subdomains pack together to form a compact, globular protein [].; GO: 0003677 DNA binding, 0006352 transcription initiation, DNA-dependent, 0016570 histone modification, 0005634 nucleus; PDB: 2BZE_A 3U1U_B 2DB9_A.
Probab=29.84 E-value=40 Score=24.08 Aligned_cols=16 Identities=31% Similarity=0.627 Sum_probs=10.4
Q ss_pred CCCHHHHHHHHHHHHH
Q 030908 102 PVTHQAAERWLHHMQI 117 (169)
Q Consensus 102 ~It~~~fd~Wl~~~~~ 117 (169)
+||+++|++|+..+.+
T Consensus 92 ~~te~E~~~w~~~~~~ 107 (108)
T PF03126_consen 92 PFTEEEFERWKQSCEK 107 (108)
T ss_dssp ---HHHHHHHHHHH--
T ss_pred CCCHHHHHHHHHHhcc
Confidence 7999999999988754
No 30
>PF07637 PSD5: Protein of unknown function (DUF1595); InterPro: IPR013043 A region of similarity shared by several Rhodopirellula baltica cytochrome-like proteins that are predicted to be secreted. These proteins also contain IPR011478 from INTERPRO, IPR013036 from INTERPRO, IPR013039 from INTERPRO and IPR013042 from INTERPRO.
Probab=29.35 E-value=1.4e+02 Score=19.31 Aligned_cols=21 Identities=24% Similarity=0.395 Sum_probs=19.0
Q ss_pred CCCHHHHHHHHHHHHHHHhhC
Q 030908 102 PVTHQAAERWLHHMQIALDST 122 (169)
Q Consensus 102 ~It~~~fd~Wl~~~~~aLd~~ 122 (169)
++++++.+.+++.+..+.++-
T Consensus 18 p~~~~e~~~~~~~~~~~~~~g 38 (64)
T PF07637_consen 18 PLTDEEVDRYLALYDSARAQG 38 (64)
T ss_pred CCCHHHHHHHHHHHHHHHHcC
Confidence 689999999999999999863
No 31
>PF13297 Telomere_Sde2_2: Telomere stability C-terminal
Probab=28.60 E-value=32 Score=22.66 Aligned_cols=13 Identities=46% Similarity=0.519 Sum_probs=11.0
Q ss_pred chHHHHHHhhCCC
Q 030908 3 TLQEKASEWSGVD 15 (169)
Q Consensus 3 ~~~~~~~~~~~~~ 15 (169)
|+||||+++.-+.
T Consensus 34 Tl~ERA~RLfs~k 46 (60)
T PF13297_consen 34 TLQERAARLFSVK 46 (60)
T ss_pred CHHHHHHHHHHhc
Confidence 7999999998753
No 32
>PRK13756 tetracycline repressor protein TetR; Provisional
Probab=28.40 E-value=3e+02 Score=21.80 Aligned_cols=105 Identities=10% Similarity=0.049 Sum_probs=61.4
Q ss_pred CCcccHHHHcC-HHHH-HHHHHHHHHHHhcChhhhhhcccCCCCHHHHHHHHHHHHHHHhC-CCCccCCCCCCCcccCCC
Q 030908 22 IDETNLFRKLG-LQTF-INLSTNFYTRVYDDEEEWFRSIFANSNKEEAIQNQYEFFVQRMG-GPPLYSQRKGHPALIGRH 98 (169)
Q Consensus 22 ~~~~sLYe~iG-~~~I-~~LV~~FY~rv~~D~~~~l~~~F~~~d~~~~~~~l~~Fl~~~lG-GP~~Y~g~~G~p~m~~~H 98 (169)
+...|+|-.++ ++.| ..+++..++.+..... +. ...+|..........+...+. -|..- .+ +
T Consensus 36 v~~~slY~hf~~K~~Ll~~~~~~~~~~~~~~~~----~~-~~~~w~~~l~~~~~~~~~~l~~~p~~~-------~~---~ 100 (205)
T PRK13756 36 VEQPTLYWHVKNKRALLDALAIEILDRHHTHFL----PL-EGESWQDFLRNNAKSFRCALLSYRDGA-------KV---H 100 (205)
T ss_pred CCchHHHHHcCCHHHHHHHHHHHHHHHHHhhcc----CC-CCCCHHHHHHHHHHHHHHHHHHCcchh-------HH---H
Confidence 67789999999 5554 6677777777643221 11 245787666666555554442 22111 11 1
Q ss_pred CCCCCCHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHHHH
Q 030908 99 RPFPVTHQAAERWLHHMQIALDSTPEIDADSKIKMMNFFRHTAFF 143 (169)
Q Consensus 99 ~~l~It~~~fd~Wl~~~~~aLd~~~~~~~~~~~~l~~~~~~~a~~ 143 (169)
.+-..++..+ ++++.+-.+|.+. |++++.+......+..+.-.
T Consensus 101 ~~~~~~~~~l-~~~e~~l~~L~~a-G~~~~~a~~~~~~l~~~v~G 143 (205)
T PRK13756 101 LGTRPTEKQY-ETLENQLAFLCQQ-GFSLENALYALSAVGHFTLG 143 (205)
T ss_pred hcCCCCchhH-HHHHHHHHHHHHc-CCCHHHHHHHHHHHHHHHHH
Confidence 1111233444 5678888889999 59998887666555554433
No 33
>COG3265 GntK Gluconate kinase [Carbohydrate transport and metabolism]
Probab=27.77 E-value=99 Score=24.33 Aligned_cols=50 Identities=18% Similarity=0.308 Sum_probs=35.0
Q ss_pred HHHHHHHHHhCCCCccCCCCC-CC--cccCCCCCCCCCHHHHHHHHHHHHHHHhh
Q 030908 70 NQYEFFVQRMGGPPLYSQRKG-HP--ALIGRHRPFPVTHQAAERWLHHMQIALDS 121 (169)
Q Consensus 70 ~l~~Fl~~~lGGP~~Y~g~~G-~p--~m~~~H~~l~It~~~fd~Wl~~~~~aLd~ 121 (169)
.+..=++..|| ..|.+--- || +...+..+.|+|++++-=||+.+..++..
T Consensus 10 tvg~~lA~~lg--~~fidGDdlHp~aNi~KM~~GiPL~DdDR~pWL~~l~~~~~~ 62 (161)
T COG3265 10 TVGSALAERLG--AKFIDGDDLHPPANIEKMSAGIPLNDDDRWPWLEALGDAAAS 62 (161)
T ss_pred HHHHHHHHHcC--CceecccccCCHHHHHHHhCCCCCCcchhhHHHHHHHHHHHH
Confidence 34445556666 44544101 44 35557889999999999999999999987
No 34
>PRK14974 cell division protein FtsY; Provisional
Probab=26.46 E-value=3e+02 Score=23.91 Aligned_cols=39 Identities=8% Similarity=0.239 Sum_probs=33.8
Q ss_pred CCCCCHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHH
Q 030908 100 PFPVTHQAAERWLHHMQIALDSTPEIDADSKIKMMNFFRH 139 (169)
Q Consensus 100 ~l~It~~~fd~Wl~~~~~aLd~~~~~~~~~~~~l~~~~~~ 139 (169)
...|+++..+.+++.+..+|-+. ++..++++++.+.+..
T Consensus 55 ~~~~~~~~~~~~l~~l~~~Ll~~-dv~~~~a~~i~~~~~~ 93 (336)
T PRK14974 55 ITEIKEKDIEDLLEELELELLES-DVALEVAEEILESLKE 93 (336)
T ss_pred hcccCHHHHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHH
Confidence 33499999999999999999999 6999999999887643
No 35
>PF00169 PH: PH domain; InterPro: IPR001849 The pleckstrin homology (PH) domain is a domain of about 100 residues that occurs in a wide range of proteins involved in intracellular signalling or as constituents of the cytoskeleton [, , , , , , ]. The pleckstrin homology domain commonly found in eukaryotic signalling proteins. The domain family possesses multiple functions including the abilities to bind inositol phosphates, and various proteins. PH domains have been found to possess inserted domains (such as in PLC gamma, syntrophins) and to be inserted within other domains. Mutations in Brutons tyrosine kinase (Btk) within its PH domain cause X-linked agammaglobulinaemia (XLA) in patients. Point mutations cluster into the positively charged end of the molecule around the predicted binding site for phosphatidylinositol lipids. The 3D structure of several PH domains has been determined []. All known cases have a common structure consisting of two perpendicular anti-parallel beta sheets, followed by a C-terminal amphipathic helix. The loops connecting the beta-strands differ greatly in length, making the PH domain relatively difficult to detect. There are no totally invariant residues within the PH domain. Proteins reported to contain one more PH domains belong to the following families: Pleckstrin, the protein where this domain was first detected, is the major substrate of protein kinase C in platelets. Pleckstrin is one of the rare proteins to contains two PH domains. Ser/Thr protein kinases such as the Akt/Rac family, the beta-adrenergic receptor kinases, the mu isoform of PKC and the trypanosomal NrkA family. Tyrosine protein kinases belonging to the Btk/Itk/Tec subfamily. Insulin Receptor Substrate 1 (IRS-1). Regulators of small G-proteins like guanine nucleotide releasing factor GNRP (Ras-GRF) (which contains 2 PH domains), guanine nucleotide exchange proteins like vav, dbl, SoS and Saccharomyces cerevisiae CDC24, GTPase activating proteins like rasGAP and BEM2/IPL2, and the human break point cluster protein bcr. Cytoskeletal proteins such as dynamin (see IPR001401 from INTERPRO), Caenorhabditis elegans kinesin-like protein unc-104 (see IPR001752 from INTERPRO), spectrin beta-chain, syntrophin (2 PH domains) and S. cerevisiae nuclear migration protein NUM1. Mammalian phosphatidylinositol-specific phospholipase C (PI-PLC) (see IPR000909 from INTERPRO) isoforms gamma and delta. Isoform gamma contains two PH domains, the second one is split into two parts separated by about 400 residues. Oxysterol binding proteins OSBP, S. cerevisiae OSH1 and YHR073w. Mouse protein citron, a putative rho/rac effector that binds to the GTP-bound forms of rho and rac. Several S. cerevisiae proteins involved in cell cycle regulation and bud formation like BEM2, BEM3, BUD4 and the BEM1-binding proteins BOI2 (BEB1) and BOI1 (BOB1). C. elegans protein MIG-10. C. elegans hypothetical proteins C04D8.1, K06H7.4 and ZK632.12. S. cerevisiae hypothetical proteins YBR129c and YHR155w. ; GO: 0005515 protein binding; PDB: 1DYN_B 2DYN_B 3SNH_A 3ZYS_C 1X05_A 2I5F_A 1ZM0_B 1XX0_A 2I5C_C 3A8P_D ....
Probab=26.11 E-value=75 Score=20.67 Aligned_cols=17 Identities=24% Similarity=0.642 Sum_probs=15.2
Q ss_pred CCHHHHHHHHHHHHHHH
Q 030908 103 VTHQAAERWLHHMQIAL 119 (169)
Q Consensus 103 It~~~fd~Wl~~~~~aL 119 (169)
=+++++..|+..++.++
T Consensus 87 ~s~~~~~~W~~~i~~~~ 103 (104)
T PF00169_consen 87 ESEEERKRWIQAIQKAI 103 (104)
T ss_dssp SSHHHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHh
Confidence 48899999999999886
No 36
>COG4103 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.28 E-value=1.4e+02 Score=23.08 Aligned_cols=68 Identities=15% Similarity=0.146 Sum_probs=39.3
Q ss_pred HHHHHHHHHHhCCCCccCCCCCCCcccCC-------CCCCCCCHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHH
Q 030908 69 QNQYEFFVQRMGGPPLYSQRKGHPALIGR-------HRPFPVTHQAAERWLHHMQIALDSTPEIDADSKIKMMNFFRHTA 141 (169)
Q Consensus 69 ~~l~~Fl~~~lGGP~~Y~g~~G~p~m~~~-------H~~l~It~~~fd~Wl~~~~~aLd~~~~~~~~~~~~l~~~~~~~a 141 (169)
.++..||.++.||+..=.+. +.|.+-.. -++=.+++.++.++...+.+.+ +++++..+.+..+++...
T Consensus 5 ~~~~sfl~~l~~~~~~~~~a-dDP~lAa~~Llf~Vm~ADG~v~~~E~~a~r~il~~~f----~i~~~~l~ali~~~e~~~ 79 (148)
T COG4103 5 ERLLSFLKQLPGGLDGDNSA-DDPRLAAAALLFHVMEADGTVSESEREAFRAILKENF----GIDGEELDALIEAGEEAG 79 (148)
T ss_pred HHHHHHHHhccCccccCcCC-CCHHHHHHHHHHHHHhcccCcCHHHHHHHHHHHHHHc----CCCHHHHHHHHHHHHHhh
Confidence 36677777777776544432 34443111 1111477777777777666654 367777777776665543
No 37
>PF07746 LigA: Aromatic-ring-opening dioxygenase LigAB, LigA subunit; InterPro: IPR011986 Dioxygenases catalyse the incorporation of both atoms of molecular oxygen into substrates using a variety of reaction mechanisms. Cleavage of aromatic rings is one of the most important functions of dioxygenases, which play key roles in the degradation of aromatic compounds. The substrates of ring-cleavage dioxygenases can be classified into two groups according to the mode of scission of the aromatic ring. Intradiol enzymes (IPR000627 from INTERPRO) use a non-haem Fe(III) to cleave the aromatic ring between two hydroxyl groups (ortho-cleavage), whereas extradiol enzymes use a non-haem Fe(II) to cleave the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon (meta-cleavage) [, ]. These two subfamilies differ in sequence, structural fold, iron ligands, and the orientation of second sphere active site amino acid residues. Extradiol dioxygenases are usually homo-multimeric, bind one atom of ferrous ion per subunit and have a subunit size of about 33 kDa. Extradiol dioxygenases can be divided into three classes. Class I and II enzymes (IPR000486 from INTERPRO) show sequence similarity, with the two-domain class II enzymes having evolved from a class I enzyme through gene duplication. Class III enzymes are different in sequence and structure, but they do share several common active-site characteristics with the class II enzymes, in particular the coordination sphere and the disposition of the putative catalytic base are very similar. Class III enzymes usually have two subunits, designated A (IPR004183 from INTERPRO) and B (IPR004183 from INTERPRO). LigAB is a protocatechuate 4,5-dioxygenase (1.13.11.8 from EC) that belongs to the extradiol class III enzyme family. The LigA subunit of this enzyme is multi-helical, containing a compact array of 6 short helices [].; PDB: 1BOU_A 1B4U_A.
Probab=25.10 E-value=1.5e+02 Score=20.85 Aligned_cols=32 Identities=16% Similarity=0.295 Sum_probs=26.1
Q ss_pred CCHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHH
Q 030908 103 VTHQAAERWLHHMQIALDSTPEIDADSKIKMMN 135 (169)
Q Consensus 103 It~~~fd~Wl~~~~~aLd~~~~~~~~~~~~l~~ 135 (169)
++++.+++|++.=...+++. +++++.++.+.+
T Consensus 9 ~~~~~r~~F~~D~~a~~~~~-~Lt~eer~av~~ 40 (88)
T PF07746_consen 9 NDPENRERFLADPEAYLDEY-GLTEEERQAVLD 40 (88)
T ss_dssp GSHHHHHHHHH-HHHHHHCC-T--HHHHHHHHC
T ss_pred cCHHHHHHHHHCHHHHHHHc-CCCHHHHHHHHc
Confidence 78999999999999999999 699999988764
No 38
>PF14968 CCDC84: Coiled coil protein 84
Probab=25.03 E-value=2e+02 Score=25.29 Aligned_cols=45 Identities=20% Similarity=0.255 Sum_probs=34.8
Q ss_pred HHHHHHHHHHHHHHhCCCCccCCCCCCCcccCCCCCCCCCHHHHHHHHHHHHHHHhhC
Q 030908 65 EEAIQNQYEFFVQRMGGPPLYSQRKGHPALIGRHRPFPVTHQAAERWLHHMQIALDST 122 (169)
Q Consensus 65 ~~~~~~l~~Fl~~~lGGP~~Y~g~~G~p~m~~~H~~l~It~~~fd~Wl~~~~~aLd~~ 122 (169)
+.|+..+..||..-=|++ +++. .+-|+++++++|-..+..+|++.
T Consensus 87 ~eH~k~vk~F~w~~g~~~----------d~~d---~f~Is~~d~~r~kk~~~~~l~~~ 131 (336)
T PF14968_consen 87 PEHRKNVKKFWWKNGADM----------DLKD---KFRISEEDYARFKKKCEKALDEY 131 (336)
T ss_pred HHHHHHHHHHHHHcCCCc----------cccc---ceeecHHHHHHHHHHHHHHHHHH
Confidence 678899999998754444 3222 56799999999999999999654
No 39
>smart00719 Plus3 Short conserved domain in transcriptional regulators. Plus3 domains occur in the Saccharomyces cerevisiae Rtf1p protein, which interacts with Spt6p, and in parsley CIP, which interacts with the bZIP protein CPRF1.
Probab=24.99 E-value=59 Score=23.38 Aligned_cols=14 Identities=21% Similarity=0.551 Sum_probs=12.4
Q ss_pred CCCHHHHHHHHHHH
Q 030908 102 PVTHQAAERWLHHM 115 (169)
Q Consensus 102 ~It~~~fd~Wl~~~ 115 (169)
++|+++|++|...+
T Consensus 95 ~fte~E~~~w~~~~ 108 (109)
T smart00719 95 DFTEEEFQRWKQAI 108 (109)
T ss_pred CCCHHHHHHHHHHh
Confidence 79999999999765
No 40
>PRK13754 conjugal transfer fertility inhibition protein FinO; Provisional
Probab=24.72 E-value=3.7e+02 Score=21.62 Aligned_cols=112 Identities=12% Similarity=0.138 Sum_probs=70.4
Q ss_pred cchHHHHHHhhCCCCCCcccCCcccHHHHcC--HHHHHHHHHHHHHHHhcCh--hh-hhh---cccCC-------CCHHH
Q 030908 2 QTLQEKASEWSGVDPADAFAIDETNLFRKLG--LQTFINLSTNFYTRVYDDE--EE-WFR---SIFAN-------SNKEE 66 (169)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~sLYe~iG--~~~I~~LV~~FY~rv~~D~--~~-~l~---~~F~~-------~d~~~ 66 (169)
|.|.++||+-+..-..-+...++.+.|+++- .+.|..|+..|=. +.... .| .|| .+|.+ .+-..
T Consensus 41 ~~~a~~a~~~~~~~~~~a~~~~~~~~y~Kl~~~keaI~~Lae~wP~-lF~~g~~kPLKIGI~eDL~qDi~~r~~~lSk~~ 119 (186)
T PRK13754 41 QKLAEKAAREAELAAKKAQARQALSIYLNLPPLDEAVNTLKPWWPG-LFDGDTPRLLACGIREVLLEDVAQRNIPLSHKK 119 (186)
T ss_pred HHHHHHHHHhhhhhHHhhhccCCchhhhhcCCHHHHHHHHHHhhHH-hcCCCCCCccccCcHHHHHHHHHhccCCCCHHH
Confidence 4577888877776555566677779999988 7888888876654 44332 22 111 12321 11122
Q ss_pred HHH------HHHHHHHHHhCCCCccCCCCCCCcccCCCCCCCCCHHHHHHHHHHHHHHHhhC
Q 030908 67 AIQ------NQYEFFVQRMGGPPLYSQRKGHPALIGRHRPFPVTHQAAERWLHHMQIALDST 122 (169)
Q Consensus 67 ~~~------~l~~Fl~~~lGGP~~Y~g~~G~p~m~~~H~~l~It~~~fd~Wl~~~~~aLd~~ 122 (169)
.+. +-..||..+..|-.+|.=. |+|.= .||++|.+-=.+.+.+-....
T Consensus 120 LR~ALr~yT~S~rYL~avk~Ga~R~DLd-G~pvG-------eVT~Ee~~hA~~rL~E~~kr~ 173 (186)
T PRK13754 120 LRRALKAITRSESYLCAMKAGACRYDTE-GYVTE-------HISQEEEAYAAERLDKIRRQN 173 (186)
T ss_pred HHHHHHHHhCCHHHHHHHHcCCeeeCCC-CCCcc-------ccCHHHHHHHHHHHHHHHHhh
Confidence 222 2346888888998888754 77762 499999887777666555443
No 41
>PF07862 Nif11: Nitrogen fixation protein of unknown function; InterPro: IPR012903 This domain is found in the cyanobacteria, and the nitrogen-fixing proteobacterium Azotobacter vinelandii and may be involved in nitrogen fixation, but no role has been assigned [].
Probab=24.32 E-value=60 Score=19.67 Aligned_cols=19 Identities=26% Similarity=0.413 Sum_probs=15.6
Q ss_pred HHHHHHHHhcChhhhhhcccC
Q 030908 40 STNFYTRVYDDEEEWFRSIFA 60 (169)
Q Consensus 40 V~~FY~rv~~D~~~~l~~~F~ 60 (169)
+..|+.++.+||. ++.-..
T Consensus 6 l~~Fl~~~~~d~~--l~~~l~ 24 (49)
T PF07862_consen 6 LKAFLEKVKSDPE--LREQLK 24 (49)
T ss_pred HHHHHHHHhcCHH--HHHHHH
Confidence 7889999999997 766555
No 42
>cd01251 PH_centaurin_alpha Centaurin alpha Pleckstrin homology (PH) domain. Centaurin alpha Pleckstrin homology (PH) domain. Centaurin alpha is a phophatidlyinositide binding protein consisting of an N-terminal ArfGAP domain and two PH domains. In response to growth factor activation, PI3K phosphorylates phosphatidylinositol 4,5-bisphosphate to phosphatidylinositol 3,4,5-trisphosphate. Centaurin alpha 1 is recruited to the plasma membrane following growth factor stimulation by specific binding of its PH domain to phosphatidylinositol 3,4,5-trisphosphate. Centaurin alpha 2 is constitutively bound to the plasma membrane since it binds phosphatidylinositol 4,5-bisphosphate and phosphatidylinositol 3,4,5-trisphosphate with equal affinity. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specifici
Probab=22.41 E-value=88 Score=22.02 Aligned_cols=20 Identities=25% Similarity=0.365 Sum_probs=17.5
Q ss_pred CCCHHHHHHHHHHHHHHHhh
Q 030908 102 PVTHQAAERWLHHMQIALDS 121 (169)
Q Consensus 102 ~It~~~fd~Wl~~~~~aLd~ 121 (169)
.=++++.+.|++.++.+|+.
T Consensus 83 a~s~~e~~~Wi~ai~~v~~~ 102 (103)
T cd01251 83 CETEQDRREWIAAFQNVLSR 102 (103)
T ss_pred CCCHHHHHHHHHHHHHHhcC
Confidence 36899999999999999864
No 43
>cd01264 PH_melted Melted pleckstrin homology (PH) domain. Melted pleckstrin homology (PH) domain. The melted protein has a C-terminal PH domain. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinsases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes.
Probab=22.23 E-value=65 Score=23.15 Aligned_cols=18 Identities=33% Similarity=0.674 Sum_probs=15.5
Q ss_pred CCCHHHHHHHHHHHHHHH
Q 030908 102 PVTHQAAERWLHHMQIAL 119 (169)
Q Consensus 102 ~It~~~fd~Wl~~~~~aL 119 (169)
.=++++.+.|+.++..|+
T Consensus 84 A~se~e~e~WI~~i~~a~ 101 (101)
T cd01264 84 AKDEKNAEEWLQCLNIAV 101 (101)
T ss_pred eCCHHHHHHHHHHHHhhC
Confidence 468999999999998874
No 44
>PRK15114 tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ; Provisional
Probab=21.52 E-value=1.7e+02 Score=24.24 Aligned_cols=39 Identities=23% Similarity=0.209 Sum_probs=30.6
Q ss_pred CCHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHH
Q 030908 103 VTHQAAERWLHHMQIALDSTPEIDADSKIKMMNFFRHTA 141 (169)
Q Consensus 103 It~~~fd~Wl~~~~~aLd~~~~~~~~~~~~l~~~~~~~a 141 (169)
-+.++.+..+++|.+.|+++|-++++..+.++..++++=
T Consensus 179 a~~~~l~~l~~~l~~~l~~i~f~~~~~~~~~~~~lrrll 217 (245)
T PRK15114 179 PLVDDLERFYGHLEQTLLATGFIRENHPGQVMNKLRRLF 217 (245)
T ss_pred CCHHHHHHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHH
Confidence 378999999999999999994245677777777766654
No 45
>TIGR00050 rRNA_methyl_1 RNA methyltransferase, TrmH family, group 1. This is part of the trmH (spoU) family of S-adenosyl-L-methionine (AdoMet)-dependent methyltransferases, and is now characterized, in E. coli, as a tRNA:Cm32/Um32 methyltransferase. It may be named TrMet(Xm32), or TrmJ, according to the nomenclature style chosen
Probab=20.73 E-value=1.9e+02 Score=23.64 Aligned_cols=39 Identities=26% Similarity=0.198 Sum_probs=30.9
Q ss_pred CCHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHH
Q 030908 103 VTHQAAERWLHHMQIALDSTPEIDADSKIKMMNFFRHTA 141 (169)
Q Consensus 103 It~~~fd~Wl~~~~~aLd~~~~~~~~~~~~l~~~~~~~a 141 (169)
.+.++.+..++++.+.|++.|-++++..+.++..++++=
T Consensus 170 a~~~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~~lr~l~ 208 (233)
T TIGR00050 170 ATTDQLELLLEHLEEILLSLGFIPEHKIRRVMRKFRRLY 208 (233)
T ss_pred CCHHHHHHHHHHHHHHHHHcCCCCccCHHHHHHHHHHHH
Confidence 588999999999999999984357777777776665554
No 46
>PF02881 SRP54_N: SRP54-type protein, helical bundle domain; InterPro: IPR013822 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]. SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. This entry represents the N-terminal helical bundle domain of the 54 kDa SRP54 component, a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 of the signal recognition particle has a three-domain structure: an N-terminal helical bundle domain, a GTPase domain, and the M-domain that binds the 7s RNA and also binds the signal sequence. The extreme C-terminal region is glycine-rich and lower in complexity and poorly conserved between species. These proteins include Escherichia coli and Bacillus subtilis ffh protein (P48), which seems to be the prokaryotic counterpart of SRP54; signal recognition particle receptor alpha subunit (docking protein), an integral membrane GTP-binding protein which ensures, in conjunction with SRP, the correct targeting of nascent secretory proteins to the endoplasmic reticulum membrane; bacterial FtsY protein, which is believed to play a similar role to that of the docking protein in eukaryotes; the pilA protein from Neisseria gonorrhoeae, the homologue of ftsY; and bacterial flagellar biosynthesis protein flhF.; GO: 0005525 GTP binding, 0006614 SRP-dependent cotranslational protein targeting to membrane; PDB: 1J8M_F 1J8Y_F 2J37_W 2OG2_A 3B9Q_A 2V3C_C 3NDB_B 1ZU5_B 1ZU4_A 1WGW_A ....
Probab=20.27 E-value=2.5e+02 Score=18.05 Aligned_cols=37 Identities=16% Similarity=0.306 Sum_probs=33.1
Q ss_pred CCCHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHH
Q 030908 102 PVTHQAAERWLHHMQIALDSTPEIDADSKIKMMNFFRH 139 (169)
Q Consensus 102 ~It~~~fd~Wl~~~~~aLd~~~~~~~~~~~~l~~~~~~ 139 (169)
-+++...+.+++-+..+|=+. +|..+.+.++.+.+..
T Consensus 17 ~~~~~~i~~~l~ele~~Li~a-DVg~~~a~~i~~~ik~ 53 (75)
T PF02881_consen 17 FLTEKDIEEFLEELEEALIEA-DVGVEVAEKIIENIKK 53 (75)
T ss_dssp SCTHHHHHHHHHHHHHHHHHT-TTSHHHHHHHHHHHHH
T ss_pred cccHHhHHHHHHHHHHHHHHc-CcCHHHHHHHHHHHHH
Confidence 467888899999999999999 7999999999988776
No 47
>PF15409 PH_8: Pleckstrin homology domain
Probab=20.00 E-value=85 Score=22.14 Aligned_cols=17 Identities=24% Similarity=0.542 Sum_probs=14.3
Q ss_pred CCCHHHHHHHHHHHHHH
Q 030908 102 PVTHQAAERWLHHMQIA 118 (169)
Q Consensus 102 ~It~~~fd~Wl~~~~~a 118 (169)
..++++|+.|+..++.|
T Consensus 72 a~s~~~f~~Wv~aL~~a 88 (89)
T PF15409_consen 72 AKSQEDFQRWVSALQKA 88 (89)
T ss_pred cCCHHHHHHHHHHHHhc
Confidence 36899999999988764
Done!