Query 028622
Match_columns 206
No_of_seqs 15 out of 17
Neff 2.0
Searched_HMMs 46136
Date Fri Mar 29 14:23:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028622.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028622hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF11803 UXS1_N: UDP-glucurona 67.6 8.2 0.00018 29.8 3.6 37 53-89 25-65 (78)
2 PRK11367 hypothetical protein; 65.9 2.6 5.6E-05 39.9 0.8 34 116-149 7-40 (476)
3 PF12041 DELLA: Transcriptiona 64.2 8.2 0.00018 29.4 3.0 31 59-89 3-33 (73)
4 PF10439 Bacteriocin_IIc: Bact 59.4 7 0.00015 27.5 1.8 44 87-131 3-46 (65)
5 PF04930 FUN14: FUN14 family; 59.0 2.1 4.6E-05 31.9 -0.9 76 48-127 24-100 (100)
6 PF03902 Gal4_dimer: Gal4-like 51.7 14 0.00031 26.9 2.4 30 70-101 3-32 (57)
7 PF06295 DUF1043: Protein of u 51.2 5.9 0.00013 31.1 0.4 22 114-135 2-23 (128)
8 PF10779 XhlA: Haemolysin XhlA 51.1 18 0.00039 25.6 2.8 29 95-123 41-69 (71)
9 PF12072 DUF3552: Domain of un 50.6 9.3 0.0002 31.6 1.5 29 111-139 3-31 (201)
10 PF05957 DUF883: Bacterial pro 48.2 20 0.00044 26.1 2.8 51 74-126 35-89 (94)
11 PRK11677 hypothetical protein; 47.8 7.7 0.00017 31.6 0.6 23 113-136 5-27 (134)
12 PF08708 PriCT_1: Primase C te 44.4 35 0.00077 23.3 3.4 35 68-104 26-65 (71)
13 PF07566 DUF1543: Domain of Un 44.1 14 0.0003 25.4 1.3 18 42-59 3-20 (52)
14 PF10415 FumaraseC_C: Fumarase 44.0 32 0.00069 23.8 3.1 48 55-104 1-50 (55)
15 COG0341 SecF Preprotein transl 42.2 3.6 7.8E-05 37.2 -2.3 74 45-129 169-257 (305)
16 PRK15354 type III secretion sy 41.9 11 0.00024 33.6 0.8 14 51-64 117-130 (224)
17 PF09335 SNARE_assoc: SNARE as 41.1 33 0.00072 24.4 2.9 20 49-68 23-42 (123)
18 PRK04081 hypothetical protein; 40.7 21 0.00047 31.6 2.3 36 108-143 120-156 (207)
19 PRK05179 rpsM 30S ribosomal pr 37.5 32 0.00068 27.4 2.6 47 48-94 22-68 (122)
20 PF05542 DUF760: Protein of un 37.3 64 0.0014 23.8 4.0 33 49-87 51-86 (86)
21 KOG4404 Tandem pore domain K+ 35.6 37 0.0008 32.2 3.1 36 67-102 30-65 (350)
22 TIGR03631 bact_S13 30S ribosom 34.5 44 0.00095 26.2 2.9 47 48-94 20-66 (113)
23 PF14880 COX14: Cytochrome oxi 34.1 26 0.00056 24.4 1.4 27 114-140 22-48 (59)
24 CHL00137 rps13 ribosomal prote 33.9 39 0.00084 26.9 2.5 47 48-94 22-68 (122)
25 PF15628 RRM_DME: RRM in Demet 33.6 14 0.00031 29.7 0.0 38 22-59 8-63 (103)
26 PF04654 DUF599: Protein of un 32.3 36 0.00079 28.8 2.3 75 55-130 4-84 (216)
27 TIGR01710 typeII_sec_gspG gene 32.1 34 0.00075 26.4 2.0 22 67-88 30-51 (134)
28 PF02478 Pneumo_phosprot: Pneu 30.9 58 0.0013 30.1 3.4 48 73-140 164-211 (279)
29 PF13348 Y_phosphatase3C: Tyro 30.8 36 0.00077 23.0 1.7 28 74-101 37-64 (68)
30 PRK02898 cobalt transport prot 30.0 24 0.00053 28.0 0.8 25 106-130 68-92 (100)
31 cd02434 Nodulin-21_like_3 Nodu 29.5 1.1E+02 0.0023 26.1 4.6 22 45-66 31-55 (225)
32 PF11471 Sugarporin_N: Maltopo 29.0 48 0.0011 23.7 2.1 17 73-89 28-44 (60)
33 PF13213 DUF4021: Protein of u 27.8 22 0.00048 25.2 0.2 21 79-99 19-39 (46)
34 TIGR03160 cobT_DBIPRT nicotina 26.0 1.1E+02 0.0023 28.1 4.3 50 52-102 166-223 (333)
35 PF03672 UPF0154: Uncharacteri 25.8 28 0.00061 25.7 0.5 25 115-139 4-28 (64)
36 cd02439 DMB-PRT_CobT Nicotinat 25.6 1.1E+02 0.0023 27.4 4.1 40 52-91 150-197 (315)
37 PF08861 DUF1828: Domain of un 25.6 55 0.0012 23.8 1.9 50 64-115 28-84 (90)
38 PF14316 DUF4381: Domain of un 25.1 62 0.0013 25.3 2.3 56 95-150 3-63 (146)
39 PF13556 HTH_30: PucR C-termin 25.0 68 0.0015 21.6 2.2 21 68-88 22-42 (59)
40 PF08229 SHR3_chaperone: ER me 24.2 55 0.0012 28.4 2.0 35 114-148 138-172 (196)
41 TIGR01293 Kv_beta voltage-depe 24.2 55 0.0012 28.0 2.0 44 52-101 262-314 (317)
42 smart00786 SHR3_chaperone ER m 23.5 50 0.0011 28.9 1.6 29 118-146 142-170 (196)
43 TIGR01462 greA transcription e 22.9 92 0.002 24.7 2.9 35 63-97 42-76 (151)
44 PF10552 ORF6C: ORF6C domain; 22.5 1.1E+02 0.0025 23.2 3.2 30 73-102 11-43 (116)
45 PF08278 DnaG_DnaB_bind: DNA p 21.9 1.3E+02 0.0029 22.2 3.5 34 66-100 90-123 (127)
46 PRK13719 conjugal transfer tra 21.8 24 0.00053 30.9 -0.6 30 81-113 6-36 (217)
47 PF04882 Peroxin-3: Peroxin-3; 21.8 61 0.0013 30.1 2.0 35 35-69 1-35 (432)
48 PF15346 ARGLU: Arginine and g 21.7 67 0.0014 26.9 2.0 17 135-151 126-142 (149)
49 COG5478 Predicted small integr 21.5 46 0.001 28.0 1.0 25 72-96 77-101 (141)
50 PF08418 Pol_alpha_B_N: DNA po 21.2 82 0.0018 26.3 2.4 34 65-98 207-246 (253)
51 PRK00105 cobT nicotinate-nucle 20.8 1.9E+02 0.0042 26.5 4.9 47 52-98 166-220 (335)
52 KOG1444 Nucleotide-sugar trans 20.6 30 0.00065 32.1 -0.3 25 119-143 285-309 (314)
53 PF02355 SecD_SecF: Protein ex 20.2 1.1E+02 0.0023 25.5 2.8 68 53-129 85-154 (189)
No 1
>PF11803 UXS1_N: UDP-glucuronate decarboxylase N-terminal; InterPro: IPR021761 The N terminus of the UDP-glucuronate decarboxylases may be involved in localisation to the perinuclear Golgi membrane. ; GO: 0048040 UDP-glucuronate decarboxylase activity
Probab=67.60 E-value=8.2 Score=29.80 Aligned_cols=37 Identities=30% Similarity=0.612 Sum_probs=30.1
Q ss_pred hhhHHHHHHhhhhh-hhhhhH---hhHHHHHHHHHHHhhhh
Q 028622 53 TSLASIATAWIGYS-IRHLHQ---SKVDQRLESIESTLKEN 89 (206)
Q Consensus 53 TSiASv~tAWaGYs-lRhlhq---~kVd~RL~SIE~amk~~ 89 (206)
.++|-+++.|.-|. .|.+++ .|||++.++++.-++.+
T Consensus 25 al~ayiasvwg~~vnmrsIQEnGe~Kie~kiee~v~plrek 65 (78)
T PF11803_consen 25 ALIAYIASVWGNYVNMRSIQENGELKIEQKIEEAVAPLREK 65 (78)
T ss_pred HHHHHHHHHHHhhcCHHHHHhccchhHHHHHHHHHhHHHHH
Confidence 47888999999984 677765 79999999999888764
No 2
>PRK11367 hypothetical protein; Provisional
Probab=65.94 E-value=2.6 Score=39.93 Aligned_cols=34 Identities=24% Similarity=0.633 Sum_probs=27.6
Q ss_pred hhhhhhhccccccchhhhhhHHHHHHHHHhhccC
Q 028622 116 TTLIIGYGLGWRGGRWYATRKFRREQMKLLGQIK 149 (206)
Q Consensus 116 TtlviGY~LGwRGG~wya~rkfrreQ~kllgqik 149 (206)
...||..|..|-||.|||-++++.|=..++.+++
T Consensus 7 ~gVIVaLga~wtGgsWYTGk~iE~~~~~~v~~~N 40 (476)
T PRK11367 7 TGVIVALAVIWGGGTWYTGTQIQPGVEKFIKDFN 40 (476)
T ss_pred hhhhhhhhhhhccccceechHHHHHHHHHHHHHH
Confidence 5578888999999999999999998555555555
No 3
>PF12041 DELLA: Transcriptional regulator DELLA protein N terminal; InterPro: IPR021914 Gibberellins are plant hormones which have great impact on growth signalling. DELLA proteins are transcriptional regulators of growth related proteins which are downregulated when gibberellins bind to their receptor GID1. GID1 forms a complex with DELLA proteins and signals them towards 26S proteasome. The N-terminal of DELLA proteins contains conserved DELLA and VHYNP motifs which are important for GID1 binding and proteolysis of the DELLA proteins [].; PDB: 2ZSH_B 2ZSI_B.
Probab=64.18 E-value=8.2 Score=29.37 Aligned_cols=31 Identities=29% Similarity=0.482 Sum_probs=24.3
Q ss_pred HHHhhhhhhhhhhHhhHHHHHHHHHHHhhhh
Q 028622 59 ATAWIGYSIRHLHQSKVDQRLESIESTLKEN 89 (206)
Q Consensus 59 ~tAWaGYslRhlhq~kVd~RL~SIE~amk~~ 89 (206)
+.|=.||-.|-=-=..|-||||.+|..|-+.
T Consensus 3 llA~lGYkVrsSdmadVAQkLEqLE~vmg~~ 33 (73)
T PF12041_consen 3 LLAVLGYKVRSSDMADVAQKLEQLEMVMGNA 33 (73)
T ss_dssp HHHTTT-B-BGGGHHHHHHHHHHHHHHHTT-
T ss_pred hhhhhcccccchHHHHHHHHHHHHHHHHccc
Confidence 3567899999888889999999999999754
No 4
>PF10439 Bacteriocin_IIc: Bacteriocin class II with double-glycine leader peptide; InterPro: IPR019493 Bacteriocins are proteinaceous toxins produced by bacteria to inhibit the growth of similar or closely related strains. The producer bacteria are protected from the effects of their own bacteriocins by production of a specific immunity protein which is co-transcribed with the genes encoding the bacteriocins, e.g. IPR015046 from INTERPRO. The bacteriocins are structurally more specific than their immunity-protein counterparts. Typically, production of the bacteriocin gene is from within an operon carrying up to 6 genes including a typical two-component regulatory system (R and H), a small peptide pheromone (C), and a dedicated ABC transporter (A and -B) as well as an immunity protein []. The ABC transporter is thought to recognise the N termini of both the pheromone and the bacteriocins and to transport these peptides across the cytoplasmic membrane, concurrent with cleavage at the conserved double-glycine motif. Cleaved extracellular C can then bind to the sensor kinase, H, resulting in activation of R and up-regulation of the entire gene cluster via binding to consensus sequences within each promoter []. It seems likely that the whole regulon is carried on a transmissible plasmid which is passed between closely related Firmicute species since many clinical isolates from different Firmicutes can produce at least two bacteriocins, and the same bacteriocins can be produced by different species. The proteins in this entry include amylovorin-L, lactacin-F and salivaricin CRL 1328, all of them class IIb two-peptide bacteriocins.
Probab=59.42 E-value=7 Score=27.52 Aligned_cols=44 Identities=18% Similarity=0.176 Sum_probs=34.8
Q ss_pred hhhcccchhhhhhhccCCCchhhHHhhhhhhhhhhhccccccchh
Q 028622 87 KENYQVGHAEFKKLVDPGSSAATTMATAGTTLIIGYGLGWRGGRW 131 (206)
Q Consensus 87 k~~~~leh~Eikkiv~~~~s~~aC~ATagTtlviGY~LGwRGG~w 131 (206)
++-..|.+||+..|.. +++...|+..++...+.|...|-..|.|
T Consensus 3 ~~f~~L~~eeL~~I~G-G~~~~~~~~~~~~~~~~G~~~G~~~g~~ 46 (65)
T PF10439_consen 3 ENFEVLDEEELSSIEG-GNSWGNCVGGVGGGAAGGAAAGAAGGPP 46 (65)
T ss_pred HHHHhcCHHHHHHhcC-CccHHHHHHHHHHHHHHHHHHhhhccch
Confidence 5566788999999877 3688889988888888888887766654
No 5
>PF04930 FUN14: FUN14 family; InterPro: IPR007014 This is a family of short proteins found in eukaryotes and some archaea. Although the function of these proteins is not known they may contain transmembrane helices.
Probab=59.05 E-value=2.1 Score=31.94 Aligned_cols=76 Identities=16% Similarity=0.244 Sum_probs=40.2
Q ss_pred EEEechhhHHHHHH-hhhhhhhhhhHhhHHHHHHHHHHHhhhhcccchhhhhhhccCCCchhhHHhhhhhhhhhhhcccc
Q 028622 48 VFTIGTSLASIATA-WIGYSIRHLHQSKVDQRLESIESTLKENYQVGHAEFKKLVDPGSSAATTMATAGTTLIIGYGLGW 126 (206)
Q Consensus 48 VFTvGTSiASv~tA-WaGYslRhlhq~kVd~RL~SIE~amk~~~~leh~Eikkiv~~~~s~~aC~ATagTtlviGY~LGw 126 (206)
+|.+|.++..+-.| --||. .++-.|+++..++..+..+ .+.+..+++...++-..+-+--......++.|..||+
T Consensus 24 a~~~G~~~l~lq~l~~~G~i--~Vnw~kl~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~l~~~~~~~~gF~~Gf~lG~ 99 (100)
T PF04930_consen 24 AFLVGGGFLLLQYLASKGYI--KVNWDKLEKDVKKALDQNK--GKFDAPDIKSLWNKLMDFLKSNLPFSAGFLAGFLLGF 99 (100)
T ss_pred HHHHHHHHHHHHHHHHCCeE--EECHHHHHHHHHHHHHhhc--ccccchhHHHHHHHHHHHHHcCccHhHHHHHHHHHHc
Confidence 34556665555333 23444 6778889988887766665 3455555554433221100000122345667777777
Q ss_pred c
Q 028622 127 R 127 (206)
Q Consensus 127 R 127 (206)
|
T Consensus 100 ~ 100 (100)
T PF04930_consen 100 R 100 (100)
T ss_pred C
Confidence 5
No 6
>PF03902 Gal4_dimer: Gal4-like dimerisation domain; InterPro: IPR005600 The DNA binding domain (residues 1 to 147) of the yeast transcriptional activator GAL4 exists in solution in dimeric form, with the region responsible for dimerisation somewhere between residues 74 and 147. Experimental studies confirmed that the 'hydrophobic region' of the protein (residues 54-97, which contains a larger proportion of alpha-helix), is essential for dimerisation []. ; PDB: 1HBW_B 1D66_A 3COQ_A.
Probab=51.71 E-value=14 Score=26.93 Aligned_cols=30 Identities=30% Similarity=0.560 Sum_probs=21.3
Q ss_pred hhHhhHHHHHHHHHHHhhhhcccchhhhhhhc
Q 028622 70 LHQSKVDQRLESIESTLKENYQVGHAEFKKLV 101 (206)
Q Consensus 70 lhq~kVd~RL~SIE~amk~~~~leh~Eikkiv 101 (206)
-|=++||.||+..|+.+..-+ +..+|.+++
T Consensus 3 aHLTeVE~Rl~~lE~ll~~lf--P~~did~lL 32 (57)
T PF03902_consen 3 AHLTEVENRLEKLEQLLRELF--PGEDIDDLL 32 (57)
T ss_dssp HHHHHHHHHHHHHHHHHCCCS--SSSHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHHHHC--CCcCHHHHH
Confidence 367899999999999976543 244555544
No 7
>PF06295 DUF1043: Protein of unknown function (DUF1043); InterPro: IPR009386 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=51.15 E-value=5.9 Score=31.08 Aligned_cols=22 Identities=27% Similarity=0.401 Sum_probs=17.2
Q ss_pred hhhhhhhhhccccccchhhhhh
Q 028622 114 AGTTLIIGYGLGWRGGRWYATR 135 (206)
Q Consensus 114 agTtlviGY~LGwRGG~wya~r 135 (206)
|++.+|||.++||-.+|....+
T Consensus 2 ~~i~lvvG~iiG~~~~r~~~~~ 23 (128)
T PF06295_consen 2 AIIGLVVGLIIGFLIGRLTSSN 23 (128)
T ss_pred hHHHHHHHHHHHHHHHHHhccc
Confidence 5678999999999887776544
No 8
>PF10779 XhlA: Haemolysin XhlA; InterPro: IPR019715 Haemolysin XhlA is a cell-surface associated haemolysin that lyses the two most prevalent types of insect immune cells (granulocytes and plasmatocytes) as well as rabbit and horse erythrocytes [].
Probab=51.09 E-value=18 Score=25.64 Aligned_cols=29 Identities=21% Similarity=0.010 Sum_probs=19.6
Q ss_pred hhhhhhccCCCchhhHHhhhhhhhhhhhc
Q 028622 95 AEFKKLVDPGSSAATTMATAGTTLIIGYG 123 (206)
Q Consensus 95 ~Eikkiv~~~~s~~aC~ATagTtlviGY~ 123 (206)
++|++|.+.--=.-.++.+|+.+.++++.
T Consensus 41 ~~l~~I~~n~kW~~r~iiGaiI~~i~~~i 69 (71)
T PF10779_consen 41 KQLEKIKSNTKWIWRTIIGAIITAIIYLI 69 (71)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45666666443555688888888887764
No 9
>PF12072 DUF3552: Domain of unknown function (DUF3552); InterPro: IPR022711 This presumed domain is functionally uncharacterised. This domain is found in bacteria, archaea and eukaryotes. This domain is about 200 amino acids in length. This domain is found associated with PF00013 from PFAM, PF01966 from PFAM. This domain has a single completely conserved residue A that may be functionally important. ; GO: 0008663 2',3'-cyclic-nucleotide 2'-phosphodiesterase activity
Probab=50.56 E-value=9.3 Score=31.63 Aligned_cols=29 Identities=24% Similarity=0.438 Sum_probs=24.0
Q ss_pred HhhhhhhhhhhhccccccchhhhhhHHHH
Q 028622 111 MATAGTTLIIGYGLGWRGGRWYATRKFRR 139 (206)
Q Consensus 111 ~ATagTtlviGY~LGwRGG~wya~rkfrr 139 (206)
|..+...+|||+++||-..++...+++..
T Consensus 3 ii~~i~~~~vG~~~G~~~~~~~~~~~~~~ 31 (201)
T PF12072_consen 3 IIIAIVALIVGIGIGYLVRKKINRKKLEQ 31 (201)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 56778889999999999988888877754
No 10
>PF05957 DUF883: Bacterial protein of unknown function (DUF883); InterPro: IPR010279 This family consists of several bacterial proteins of unknown function that include the Escherichia coli genes for ElaB, YgaM and YqjD.
Probab=48.25 E-value=20 Score=26.06 Aligned_cols=51 Identities=10% Similarity=0.263 Sum_probs=26.8
Q ss_pred hHHHHHHHHHHHhhhhcccchhhhhhhccCCC----chhhHHhhhhhhhhhhhcccc
Q 028622 74 KVDQRLESIESTLKENYQVGHAEFKKLVDPGS----SAATTMATAGTTLIIGYGLGW 126 (206)
Q Consensus 74 kVd~RL~SIE~amk~~~~leh~Eikkiv~~~~----s~~aC~ATagTtlviGY~LGw 126 (206)
++++++++..+.+++..+-=.+..++.++.-. -.| +.+.|+++.||+.||+
T Consensus 35 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~V~e~P--~~svgiAagvG~llG~ 89 (94)
T PF05957_consen 35 RAEEALDDARDRAEDAADQAREQAREAAEQTEDYVRENP--WQSVGIAAGVGFLLGL 89 (94)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCh--HHHHHHHHHHHHHHHH
Confidence 56677777766666555444444444433221 222 2345556666666665
No 11
>PRK11677 hypothetical protein; Provisional
Probab=47.75 E-value=7.7 Score=31.59 Aligned_cols=23 Identities=30% Similarity=0.349 Sum_probs=18.0
Q ss_pred hhhhhhhhhhccccccchhhhhhH
Q 028622 113 TAGTTLIIGYGLGWRGGRWYATRK 136 (206)
Q Consensus 113 TagTtlviGY~LGwRGG~wya~rk 136 (206)
.|++.+|||.++||=.+|. .++.
T Consensus 5 ~a~i~livG~iiG~~~~R~-~~~~ 27 (134)
T PRK11677 5 YALIGLVVGIIIGAVAMRF-GNRK 27 (134)
T ss_pred HHHHHHHHHHHHHHHHHhh-ccch
Confidence 4668899999999999995 4433
No 12
>PF08708 PriCT_1: Primase C terminal 1 (PriCT-1); InterPro: IPR014820 This alpha helical domain is found at the C-terminal of primases.
Probab=44.41 E-value=35 Score=23.32 Aligned_cols=35 Identities=20% Similarity=0.224 Sum_probs=24.9
Q ss_pred hhhhHhh-----HHHHHHHHHHHhhhhcccchhhhhhhccCC
Q 028622 68 RHLHQSK-----VDQRLESIESTLKENYQVGHAEFKKLVDPG 104 (206)
Q Consensus 68 Rhlhq~k-----Vd~RL~SIE~amk~~~~leh~Eikkiv~~~ 104 (206)
+.+.+.. |.+.++.+-+.- ...|+++|++.|+++.
T Consensus 26 ~~v~~~~~~~~~v~~~~~~~N~~~--~~PL~~~Ev~~i~kSi 65 (71)
T PF08708_consen 26 RGVDQEEQFRQEVLSLAQAINSNF--SPPLPESEVKAIAKSI 65 (71)
T ss_pred hCCCHhHHHHHHHHHHHHHHHHHc--CCCCCHHHHHHHHHHH
Confidence 4555666 666666655442 7889999999999854
No 13
>PF07566 DUF1543: Domain of Unknown Function (DUF1543); InterPro: IPR011440 This domain is found as 1-2 copies in a small family of proteins of unknown function.; PDB: 2QSD_F.
Probab=44.11 E-value=14 Score=25.42 Aligned_cols=18 Identities=28% Similarity=0.514 Sum_probs=14.5
Q ss_pred hhhceeEEEechhhHHHH
Q 028622 42 FERHRVVFTIGTSLASIA 59 (206)
Q Consensus 42 FErHrVVFTvGTSiASv~ 59 (206)
-|.|.|.|.||.|+..+-
T Consensus 3 ~E~Hd~~fvVa~s~~ea~ 20 (52)
T PF07566_consen 3 IEQHDVRFVVAESIEEAK 20 (52)
T ss_dssp S-EECEEEEEESSCHHHH
T ss_pred cceeeeEEEEECCHHHHH
Confidence 489999999999987653
No 14
>PF10415 FumaraseC_C: Fumarase C C-terminus; InterPro: IPR018951 Fumarase C catalyses the stereo-specific interconversion of fumarate to L-malate as part of the Krebs cycle. The full-length protein forms a tetramer with visible globular shape. FumaraseC_C is the C-terminal 65 residues referred to as domain 3. The core of the molecule consists of a bundle of 20 alpha-helices from the five-helix bundle of domain 2. The projections from the core of the tetramer are generated from domains 1 and 3 of each subunit []. This entry does not appear to be part of either the active site or the activation site but is helical in structure forming a little bundle. ; GO: 0016829 lyase activity, 0006099 tricarboxylic acid cycle; PDB: 3RRP_A 3OCE_D 3OCF_D 3E04_B 3GTD_A 3R6V_F 3R6Q_F 1J3U_B 1FUR_A 1YFE_A ....
Probab=43.97 E-value=32 Score=23.85 Aligned_cols=48 Identities=23% Similarity=0.380 Sum_probs=30.7
Q ss_pred hHHHHHHhhhhhh--hhhhHhhHHHHHHHHHHHhhhhcccchhhhhhhccCC
Q 028622 55 LASIATAWIGYSI--RHLHQSKVDQRLESIESTLKENYQVGHAEFKKLVDPG 104 (206)
Q Consensus 55 iASv~tAWaGYsl--Rhlhq~kVd~RL~SIE~amk~~~~leh~Eikkiv~~~ 104 (206)
||.++...+||-- .-.++..-+ =.||.++....--+.++|+.+|+++-
T Consensus 1 laTaL~p~iGYe~aa~iAk~A~~~--g~svre~v~~~g~lt~ee~d~ll~p~ 50 (55)
T PF10415_consen 1 LATALNPYIGYEKAAEIAKEALAE--GRSVREVVLEEGLLTEEELDELLDPE 50 (55)
T ss_dssp GGGGGHHHHHHHHHHHHHHHHHHH--T--HHHHHHHTTSS-HHHHHHHTSHH
T ss_pred CeeeccchhccHHHHHHHHHHHHc--CCCHHHHHHHcCCCCHHHHHHHcCHH
Confidence 4567777888853 222222222 24788888888889999999999864
No 15
>COG0341 SecF Preprotein translocase subunit SecF [Intracellular trafficking and secretion]
Probab=42.15 E-value=3.6 Score=37.17 Aligned_cols=74 Identities=26% Similarity=0.498 Sum_probs=43.6
Q ss_pred ceeEEEec-----------hhhHHHHHHhhhhhhhh--hhHhhHHHHHHHHHHHhhhhcccchhhhhhhccCC-C-chhh
Q 028622 45 HRVVFTIG-----------TSLASIATAWIGYSIRH--LHQSKVDQRLESIESTLKENYQVGHAEFKKLVDPG-S-SAAT 109 (206)
Q Consensus 45 HrVVFTvG-----------TSiASv~tAWaGYslRh--lhq~kVd~RL~SIE~amk~~~~leh~Eikkiv~~~-~-s~~a 109 (206)
|-|++|+| |+||.++|- +|||+-- +==.||.|++.. ...+...++++.+ + ....
T Consensus 169 hDvii~~g~~slfgiE~~l~~IAAlLti-IGYSvNDtIVvfDRIREn~r~----------~~~~~~~~iin~si~qTlsR 237 (305)
T COG0341 169 HDVIITLGFFSLFGIEFNLATIAALLTI-IGYSVNDTIVVFDRIRENLRK----------YRRETLREIINTSINQTLTR 237 (305)
T ss_pred HHHHHHHHHHHHhheeecHHHHHHHHHH-eeeccCCeEEEEhHHHHHHhh----------hccCCHHHHHHHHHHHHHHH
Confidence 55666666 677777764 8999732 111245554432 1222233556655 5 8889
Q ss_pred HHhhhhhhhhhhhccccccc
Q 028622 110 TMATAGTTLIIGYGLGWRGG 129 (206)
Q Consensus 110 C~ATagTtlviGY~LGwRGG 129 (206)
|++|+.||++.-..|=.=||
T Consensus 238 ti~Ts~ttll~~~~l~~fgg 257 (305)
T COG0341 238 TINTSVTTLLVVVALLLFGG 257 (305)
T ss_pred HHHHHHHHHHHHHHHHHcCc
Confidence 99999999887444433333
No 16
>PRK15354 type III secretion system protein SsaK; Provisional
Probab=41.95 E-value=11 Score=33.64 Aligned_cols=14 Identities=29% Similarity=0.641 Sum_probs=13.4
Q ss_pred echhhHHHHHHhhh
Q 028622 51 IGTSLASIATAWIG 64 (206)
Q Consensus 51 vGTSiASv~tAWaG 64 (206)
|+++|.+|++||+|
T Consensus 117 I~~aI~~VltaW~g 130 (224)
T PRK15354 117 IKNSIEQVLLAWFD 130 (224)
T ss_pred HHHHHHHHHHHHhc
Confidence 78999999999998
No 17
>PF09335 SNARE_assoc: SNARE associated Golgi protein; InterPro: IPR015414 This is a entry contains SNARE associated Golgi proteins. The yeast member of this family (P36164 from SWISSPROT) localises with the t-SNARE Tlg2 [].
Probab=41.14 E-value=33 Score=24.38 Aligned_cols=20 Identities=25% Similarity=0.350 Sum_probs=12.6
Q ss_pred EEechhhHHHHHHhhhhhhh
Q 028622 49 FTIGTSLASIATAWIGYSIR 68 (206)
Q Consensus 49 FTvGTSiASv~tAWaGYslR 68 (206)
-++|+.+++...-|+|..+.
T Consensus 23 ~~~g~~~g~~~~y~lgr~~~ 42 (123)
T PF09335_consen 23 ATLGAVLGSLLAYLLGRYFG 42 (123)
T ss_pred HHHHHHHHHHHHHHHHHHHh
Confidence 34666777777767665553
No 18
>PRK04081 hypothetical protein; Provisional
Probab=40.66 E-value=21 Score=31.59 Aligned_cols=36 Identities=14% Similarity=0.403 Sum_probs=26.7
Q ss_pred hhHHhhhhhhhhhhhccc-cccchhhhhhHHHHHHHH
Q 028622 108 ATTMATAGTTLIIGYGLG-WRGGRWYATRKFRREQMK 143 (206)
Q Consensus 108 ~aC~ATagTtlviGY~LG-wRGG~wya~rkfrreQ~k 143 (206)
---.+.+......||.|| |-|-.-|-|.-|+.+|+-
T Consensus 120 G~gLg~~lLasaAGaiLGswIGnkLfNN~nyq~~~~~ 156 (207)
T PRK04081 120 GMGLGGTILASAAGAILGSWIGNKLFNNQNYQNQRQR 156 (207)
T ss_pred cccHHHHHHHHHHHHHHhhhhhHhhhcCHHHHHhhhc
Confidence 445677777888899998 777777777778776653
No 19
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=37.52 E-value=32 Score=27.35 Aligned_cols=47 Identities=23% Similarity=0.344 Sum_probs=31.8
Q ss_pred EEEechhhHHHHHHhhhhhhhhhhHhhHHHHHHHHHHHhhhhcccch
Q 028622 48 VFTIGTSLASIATAWIGYSIRHLHQSKVDQRLESIESTLKENYQVGH 94 (206)
Q Consensus 48 VFTvGTSiASv~tAWaGYslRhlhq~kVd~RL~SIE~amk~~~~leh 94 (206)
||-||-+.|-....=+|....--=..==|+-+++|++.+.++|.+|.
T Consensus 22 I~GIG~~~a~~i~~~lgi~~~~~~~~L~~~qi~~l~~~i~~~~~i~~ 68 (122)
T PRK05179 22 IYGIGRTRAKEILAAAGIDPDTRVKDLTDEELDKIREEIDKNYKVEG 68 (122)
T ss_pred cccccHHHHHHHHHHhCcCcccccccCCHHHHHHHHHHHHhhccchH
Confidence 56789999998888888763222122234567788888877776654
No 20
>PF05542 DUF760: Protein of unknown function (DUF760); InterPro: IPR008479 This entry contains uncharacterised proteins.
Probab=37.29 E-value=64 Score=23.83 Aligned_cols=33 Identities=36% Similarity=0.630 Sum_probs=19.0
Q ss_pred EEechhhHHHHHHh---hhhhhhhhhHhhHHHHHHHHHHHhh
Q 028622 49 FTIGTSLASIATAW---IGYSIRHLHQSKVDQRLESIESTLK 87 (206)
Q Consensus 49 FTvGTSiASv~tAW---aGYslRhlhq~kVd~RL~SIE~amk 87 (206)
.++-..=..=+.|| .||.||. +|+|++ +|+.||
T Consensus 51 i~~s~~~La~L~~~~mm~GYfLr~-----~E~R~~-Le~sL~ 86 (86)
T PF05542_consen 51 IQTSRENLAQLLAWSMMTGYFLRN-----AEQRLE-LERSLK 86 (86)
T ss_pred eEECHHHHHHHHHHHHHHhHHHHH-----HHHHHH-HHHhcC
Confidence 33333333334455 4999985 577775 566654
No 21
>KOG4404 consensus Tandem pore domain K+ channel TASK3/THIK-1 [Inorganic ion transport and metabolism]
Probab=35.62 E-value=37 Score=32.15 Aligned_cols=36 Identities=19% Similarity=0.445 Sum_probs=31.6
Q ss_pred hhhhhHhhHHHHHHHHHHHhhhhcccchhhhhhhcc
Q 028622 67 IRHLHQSKVDQRLESIESTLKENYQVGHAEFKKLVD 102 (206)
Q Consensus 67 lRhlhq~kVd~RL~SIE~amk~~~~leh~Eikkiv~ 102 (206)
|--=||.+..+||+.+++..+..||+.++|++.+..
T Consensus 30 LEse~E~~~r~~l~~~~~~~~~kyn~s~~d~r~~er 65 (350)
T KOG4404|consen 30 LESENEARERERLERRLANLKRKYNLSEEDYRELER 65 (350)
T ss_pred hcCcchHHHHHHHHHHHHHHHHhhCCCHHHHHHHHH
Confidence 455689999999999999999999999999987754
No 22
>TIGR03631 bact_S13 30S ribosomal protein S13. This model describes bacterial ribosomal protein S13, to the exclusion of the homologous archaeal S13P and eukaryotic ribosomal protein S18. This model identifies some (but not all) instances of chloroplast and mitochondrial S13, which is of bacterial type.
Probab=34.47 E-value=44 Score=26.17 Aligned_cols=47 Identities=17% Similarity=0.292 Sum_probs=31.5
Q ss_pred EEEechhhHHHHHHhhhhhhhhhhHhhHHHHHHHHHHHhhhhcccch
Q 028622 48 VFTIGTSLASIATAWIGYSIRHLHQSKVDQRLESIESTLKENYQVGH 94 (206)
Q Consensus 48 VFTvGTSiASv~tAWaGYslRhlhq~kVd~RL~SIE~amk~~~~leh 94 (206)
||-||-+.|-....=+|....-.=..==|+-+++|++.+.++|.+|.
T Consensus 20 i~GIG~~~a~~i~~~lgi~~~~~~~~L~~~qi~~l~~~l~~~~~i~~ 66 (113)
T TIGR03631 20 IYGIGRTRARKILEKAGIDPDKRVKDLTEEELNAIREEIEAKYKVEG 66 (113)
T ss_pred eecccHHHHHHHHHHhCcCcccccccCCHHHHHHHHHHHHhcCcchH
Confidence 56788888888888888764322222235567788888877776654
No 23
>PF14880 COX14: Cytochrome oxidase c assembly
Probab=34.12 E-value=26 Score=24.43 Aligned_cols=27 Identities=19% Similarity=0.111 Sum_probs=21.4
Q ss_pred hhhhhhhhhccccccchhhhhhHHHHH
Q 028622 114 AGTTLIIGYGLGWRGGRWYATRKFRRE 140 (206)
Q Consensus 114 agTtlviGY~LGwRGG~wya~rkfrre 140 (206)
.|.|++-||.++++...-+..++=+++
T Consensus 22 ig~T~~~g~~~~~~~y~~~~~~r~~~~ 48 (59)
T PF14880_consen 22 IGFTVYGGGLTVYTVYSYFKYNRRRRA 48 (59)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 568899999999998877776666655
No 24
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=33.92 E-value=39 Score=26.92 Aligned_cols=47 Identities=19% Similarity=0.283 Sum_probs=31.6
Q ss_pred EEEechhhHHHHHHhhhhhhhhhhHhhHHHHHHHHHHHhhhhcccch
Q 028622 48 VFTIGTSLASIATAWIGYSIRHLHQSKVDQRLESIESTLKENYQVGH 94 (206)
Q Consensus 48 VFTvGTSiASv~tAWaGYslRhlhq~kVd~RL~SIE~amk~~~~leh 94 (206)
+|-||-+.|-....=+|....--=..==|+.+++|++.+.++|.+|.
T Consensus 22 i~GIG~~~A~~ic~~lgi~~~~~~~~Lt~~qi~~l~~~i~~~~~i~~ 68 (122)
T CHL00137 22 IYGIGLTSAKEILEKANIDPDIRTKDLTDEQISALREIIEENYQVEG 68 (122)
T ss_pred cccccHHHHHHHHHHcCcCcCcCcccCCHHHHHHHHHHHHHhCcchH
Confidence 56789999998888888764432222234557778888877666543
No 25
>PF15628 RRM_DME: RRM in Demeter
Probab=33.61 E-value=14 Score=29.71 Aligned_cols=38 Identities=32% Similarity=0.547 Sum_probs=28.1
Q ss_pred HhhhhhhhhhhhhhhccHhhhhhc------------------eeEEEechhhHHHH
Q 028622 22 KKALNSWSAVQDTYFSTKDTFERH------------------RVVFTIGTSLASIA 59 (206)
Q Consensus 22 rka~nsw~AvqDTf~STKdvFErH------------------rVVFTvGTSiASv~ 59 (206)
|-|+...=-+.-|||.+.+||-.| |...=.||||.|+.
T Consensus 8 rtAmrg~FPLnGTYFQ~nEVFaD~~Ss~~Pi~vpr~~iw~L~rr~vYfGtsv~SIf 63 (103)
T PF15628_consen 8 RTAMRGSFPLNGTYFQVNEVFADHESSRNPIDVPRELIWNLPRRIVYFGTSVSSIF 63 (103)
T ss_pred hhhhCCccccCceEEEEEEEEeccccccCCeeccHHHhhcCCceEEEecCcHHHHh
Confidence 345555566778999999999877 23445799999974
No 26
>PF04654 DUF599: Protein of unknown function, DUF599; InterPro: IPR006747 This family includes several uncharacterised proteins.
Probab=32.25 E-value=36 Score=28.76 Aligned_cols=75 Identities=15% Similarity=0.223 Sum_probs=45.0
Q ss_pred hHHHHHHhhhhhhhhhhHhhHHHHHHHHHHH-----hhhhcccchhhhhhhccCCCchhhHHhhhhhhh-hhhhcccccc
Q 028622 55 LASIATAWIGYSIRHLHQSKVDQRLESIEST-----LKENYQVGHAEFKKLVDPGSSAATTMATAGTTL-IIGYGLGWRG 128 (206)
Q Consensus 55 iASv~tAWaGYslRhlhq~kVd~RL~SIE~a-----mk~~~~leh~Eikkiv~~~~s~~aC~ATagTtl-viGY~LGwRG 128 (206)
++..+..|+||.+-..|..+-+.-+..+.+. |++.. -++.+|-+.-.=.|..-+|.-.|-|++ ++|-.+++=|
T Consensus 4 v~~~l~~~~gY~~~l~~~~~~~pt~~~~~~~~R~~W~~~m~-~r~~~ildvq~Lrn~~~~~tffASTailli~g~~all~ 82 (216)
T PF04654_consen 4 VPLFLLCWVGYHLYLERRVRRRPTLSGIMNQYRRAWMRQMM-DRKNRILDVQTLRNLIMSATFFASTAILLIGGLLALLG 82 (216)
T ss_pred HHHHHHHHHHHHHHHhhhccCCChHHHHHHHHHHHHHHHHh-hcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 4566789999999888887766666655554 33333 344555555554565555555555544 4445556655
Q ss_pred ch
Q 028622 129 GR 130 (206)
Q Consensus 129 G~ 130 (206)
..
T Consensus 83 ~~ 84 (216)
T PF04654_consen 83 ST 84 (216)
T ss_pred Cc
Confidence 54
No 27
>TIGR01710 typeII_sec_gspG general secretion pathway protein G. This model represents GspG, protein G of the main terminal branch of the general secretion pathway, also called type II secretion. It transports folded proteins across the bacterial outer membrane and is widely distributed in Gram-negative pathogens.
Probab=32.05 E-value=34 Score=26.44 Aligned_cols=22 Identities=5% Similarity=0.187 Sum_probs=16.3
Q ss_pred hhhhhHhhHHHHHHHHHHHhhh
Q 028622 67 IRHLHQSKVDQRLESIESTLKE 88 (206)
Q Consensus 67 lRhlhq~kVd~RL~SIE~amk~ 88 (206)
+..-......+.|..|++||..
T Consensus 30 ~~~a~~~~~~~~l~~i~~al~~ 51 (134)
T TIGR01710 30 ADKAKAQVAKAQIKALKNALDM 51 (134)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 4455556778889999999874
No 28
>PF02478 Pneumo_phosprot: Pneumovirus phosphoprotein; InterPro: IPR003487 This family represents a phosphoprotein from Paramyxoviridae, which could be a putative RNA polymerase alpha subunit that may function in template binding [].; GO: 0003968 RNA-directed RNA polymerase activity
Probab=30.89 E-value=58 Score=30.07 Aligned_cols=48 Identities=33% Similarity=0.399 Sum_probs=34.1
Q ss_pred hhHHHHHHHHHHHhhhhcccchhhhhhhccCCCchhhHHhhhhhhhhhhhccccccchhhhhhHHHHH
Q 028622 73 SKVDQRLESIESTLKENYQVGHAEFKKLVDPGSSAATTMATAGTTLIIGYGLGWRGGRWYATRKFRRE 140 (206)
Q Consensus 73 ~kVd~RL~SIE~amk~~~~leh~Eikkiv~~~~s~~aC~ATagTtlviGY~LGwRGG~wya~rkfrre 140 (206)
.-|++||++||.-+- +|.-|.. .--|||||-|.. |.|+.=|.-..|.|
T Consensus 164 ~sieaRLe~IeEKLS--------mIlGmL~-----TL~vAtAGPTaA-------RDgIRDAMiG~REE 211 (279)
T PF02478_consen 164 LSIEARLERIEEKLS--------MILGMLR-----TLNVATAGPTAA-------RDGIRDAMIGLREE 211 (279)
T ss_pred hhHHHHHHHHHHHHH--------HHHHHHH-----HhhhcccCCchh-------hhhHHHHHHhHHHH
Confidence 468999999998764 3444443 345889998753 88888877777766
No 29
>PF13348 Y_phosphatase3C: Tyrosine phosphatase family C-terminal region; PDB: 1YWF_A 2OZ5_B.
Probab=30.85 E-value=36 Score=23.04 Aligned_cols=28 Identities=25% Similarity=0.516 Sum_probs=22.0
Q ss_pred hHHHHHHHHHHHhhhhcccchhhhhhhc
Q 028622 74 KVDQRLESIESTLKENYQVGHAEFKKLV 101 (206)
Q Consensus 74 kVd~RL~SIE~amk~~~~leh~Eikkiv 101 (206)
.|+++--|+|+=+++..+|+.++|.+|-
T Consensus 37 ~i~~~yGs~e~Yl~~~lgl~~~~i~~Lr 64 (68)
T PF13348_consen 37 AIDERYGSVENYLREELGLSEEDIERLR 64 (68)
T ss_dssp HHHHHHSSHHHHHHHT-T--HHHHHHHH
T ss_pred HHHHHcCCHHHHHHHcCCCCHHHHHHHH
Confidence 5788889999999999999999998874
No 30
>PRK02898 cobalt transport protein CbiN; Provisional
Probab=29.99 E-value=24 Score=27.99 Aligned_cols=25 Identities=40% Similarity=0.474 Sum_probs=21.5
Q ss_pred chhhHHhhhhhhhhhhhccccccch
Q 028622 106 SAATTMATAGTTLIIGYGLGWRGGR 130 (206)
Q Consensus 106 s~~aC~ATagTtlviGY~LGwRGG~ 130 (206)
|.=-|+=+|.-+.||||.||+--|+
T Consensus 68 SLLFaLQAAiGAgiIgY~lG~~~gr 92 (100)
T PRK02898 68 SLLFALQAALGAGIIGYILGYYKGR 92 (100)
T ss_pred HHHHHHHHHHhhhhhheeeeehhhh
Confidence 7777888999999999999987665
No 31
>cd02434 Nodulin-21_like_3 Nodulin-21 and CCC1-related protein family. Nodulin-21_like_3: This is a family of proteins closely related to nodulin-21, a plant nodule-specific protein that may be involved in symbiotic nitrogen fixation. This family is also related to CCC1, a yeast vacuole transmembrane protein that functions as an iron and manganese transporter.
Probab=29.48 E-value=1.1e+02 Score=26.13 Aligned_cols=22 Identities=27% Similarity=0.215 Sum_probs=11.1
Q ss_pred ceeEEEechhhH---HHHHHhhhhh
Q 028622 45 HRVVFTIGTSLA---SIATAWIGYS 66 (206)
Q Consensus 45 HrVVFTvGTSiA---Sv~tAWaGYs 66 (206)
+.+|+..|-+.. +.-.||..|.
T Consensus 31 ~~~ili~Gla~liAga~SMa~GeYl 55 (225)
T cd02434 31 PFVILIIGFANLLADGISMAAGEYV 55 (225)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345555554322 2345677776
No 32
>PF11471 Sugarporin_N: Maltoporin periplasmic N-terminal extension; InterPro: IPR021570 This N-terminal domain is found in members of the sugar porin family 1.B.3 from TC, They are related to LamB - the well characterised maltoporin of Escherichia coli for which the three-dimensional structures with and without its substrate have been obtained by X-ray diffraction. The protein consists of an 18 beta-stranded beta-barrel in contrast to proteins of the general bacterial porin family (GBP) and the Rhodobacter PorCa Porin (RPP) family which consist of 16 beta-stranded beta-barrels. Although maltoporin contains a wider beta-barrel than the porins of the GBP and RPP families (1.B.1 from TC and 1.B.7 from TC), it exhibits a narrower channel, showing only 5% of the ionic conductance of the latter porins.
Probab=28.99 E-value=48 Score=23.67 Aligned_cols=17 Identities=29% Similarity=0.548 Sum_probs=13.8
Q ss_pred hhHHHHHHHHHHHhhhh
Q 028622 73 SKVDQRLESIESTLKEN 89 (206)
Q Consensus 73 ~kVd~RL~SIE~amk~~ 89 (206)
.-|||||+.+|+-+..+
T Consensus 28 ltiEqRLa~LE~rL~~a 44 (60)
T PF11471_consen 28 LTIEQRLAALEQRLQAA 44 (60)
T ss_pred CCHHHHHHHHHHHHHHH
Confidence 35999999999987654
No 33
>PF13213 DUF4021: Protein of unknown function (DUF4021)
Probab=27.76 E-value=22 Score=25.18 Aligned_cols=21 Identities=14% Similarity=0.332 Sum_probs=18.5
Q ss_pred HHHHHHHhhhhcccchhhhhh
Q 028622 79 LESIESTLKENYQVGHAEFKK 99 (206)
Q Consensus 79 L~SIE~amk~~~~leh~Eikk 99 (206)
|+.-||||-.-|+.++.+|.+
T Consensus 19 L~~~EQaMNGlYGMPET~IED 39 (46)
T PF13213_consen 19 LQPEEQAMNGLYGMPETDIED 39 (46)
T ss_pred CCHHHHHhccccCCCcccccc
Confidence 667899999999999998865
No 34
>TIGR03160 cobT_DBIPRT nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase. Members of this family are nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase, an enzyme of cobalamin biosynthesis.
Probab=25.98 E-value=1.1e+02 Score=28.12 Aligned_cols=50 Identities=14% Similarity=0.164 Sum_probs=34.4
Q ss_pred chhhHHHHHHhh-hhhhh-------hhhHhhHHHHHHHHHHHhhhhcccchhhhhhhcc
Q 028622 52 GTSLASIATAWI-GYSIR-------HLHQSKVDQRLESIESTLKENYQVGHAEFKKLVD 102 (206)
Q Consensus 52 GTSiASv~tAWa-GYslR-------hlhq~kVd~RL~SIE~amk~~~~leh~Eikkiv~ 102 (206)
||+-||+.++-. ||... -+.+..++.+.+-||+||..+... .++-.+++.
T Consensus 166 nTTtAaAvl~aL~g~~~~~~vg~Gsg~~~~~~~~K~~vV~~al~~~~~~-~~dp~~vL~ 223 (333)
T TIGR03160 166 NTTPAAALLAALTGLPPEEVVGRGTGLDDEGLARKVAVIRRALARHRPN-AGDPLDVLA 223 (333)
T ss_pred hhHHHHHHHHHHhCcCHHHhcCCCCCCChHHHHHHHHHHHHHHHHcCCC-CCCHHHHHH
Confidence 466777666655 99884 457888999999999999975433 333334443
No 35
>PF03672 UPF0154: Uncharacterised protein family (UPF0154); InterPro: IPR005359 The proteins in this entry are functionally uncharacterised.
Probab=25.81 E-value=28 Score=25.69 Aligned_cols=25 Identities=24% Similarity=0.405 Sum_probs=19.0
Q ss_pred hhhhhhhhccccccchhhhhhHHHH
Q 028622 115 GTTLIIGYGLGWRGGRWYATRKFRR 139 (206)
Q Consensus 115 gTtlviGY~LGwRGG~wya~rkfrr 139 (206)
..++|+|..+||-.++||-.+-+++
T Consensus 4 ilali~G~~~Gff~ar~~~~k~l~~ 28 (64)
T PF03672_consen 4 ILALIVGAVIGFFIARKYMEKQLKE 28 (64)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4578888888888888887766653
No 36
>cd02439 DMB-PRT_CobT Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (DMB-PRT), also called CobT. Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (DMB-PRT/CobT, not to be confused with the CobT subunit of cobaltochelatase, which does not belong to this group) catalyzes the synthesis of alpha-ribazole-5'-phosphate, from nicotinate mononucleotide (NAMN) and 5,6-dimethylbenzimidazole (DMB). This function is essential to the anaerobic biosynthesis pathway of cobalamin (vitamin B12), which is the largest and most complex cofactor in a number of enzyme-catalyzed reactions in bacteria, archaea and eukaryotes. Only eubacteria and archaebacteria can synthesize vitamin B12; multicellular organisms have lost this ability during evolution. DMB-PRT/CobT works sequentially with CobC (a phosphatase) to couple the lower ligand of cobalamin to a ribosyl moiety. DMB is the most common lower ligand of cobamides; other lower ligands include adenine, 5-methoxyben
Probab=25.60 E-value=1.1e+02 Score=27.40 Aligned_cols=40 Identities=20% Similarity=0.233 Sum_probs=31.4
Q ss_pred chhhHHHHHHhhhhh--------hhhhhHhhHHHHHHHHHHHhhhhcc
Q 028622 52 GTSLASIATAWIGYS--------IRHLHQSKVDQRLESIESTLKENYQ 91 (206)
Q Consensus 52 GTSiASv~tAWaGYs--------lRhlhq~kVd~RL~SIE~amk~~~~ 91 (206)
||+-|++.++-.+|. ...+-+..++.+.+=||+||+.+..
T Consensus 150 nTTtAaavl~aL~~~~~~~v~g~g~g~~~~~~~~K~~vV~~al~~~~~ 197 (315)
T cd02439 150 NTTTAAAVLAALGGDPAEEVSGRGTGLPDEGLERKIAVVEEALARNGP 197 (315)
T ss_pred ccHHHHHHHHHHhCCCHHHeecCCCCCCHHHHHHHHHHHHHHHHHcCC
Confidence 577788777777774 5567888899999999999996544
No 37
>PF08861 DUF1828: Domain of unknown function DUF1828; InterPro: IPR014960 These proteins are functionally uncharacterised.
Probab=25.58 E-value=55 Score=23.76 Aligned_cols=50 Identities=22% Similarity=0.278 Sum_probs=33.9
Q ss_pred hhhhhhhhHhhH-----HHHHHHHHHHhhhhcccchhhhhhhccCCC--chhhHHhhhh
Q 028622 64 GYSIRHLHQSKV-----DQRLESIESTLKENYQVGHAEFKKLVDPGS--SAATTMATAG 115 (206)
Q Consensus 64 GYslRhlhq~kV-----d~RL~SIE~amk~~~~leh~Eikkiv~~~~--s~~aC~ATag 115 (206)
||.+-+|...-+ .+|.+.+++.+ +.|+++.+| ..|+-... .+|..+....
T Consensus 28 G~Tl~~L~~~G~~~~~s~~R~~~l~~il-~~~gv~~~~-~el~~~~~~~~~~~~~~~li 84 (90)
T PF08861_consen 28 GYTLMNLSSSGIDIDRSKKRKKILNSIL-NGFGVELDE-GELFIKTSEENFPQAKHRLI 84 (90)
T ss_pred HHHHHhHhHcCCccccchHHHHHHHHHH-HHcCccccC-CEEEEEeCHHHHHHHHHHHH
Confidence 788888877654 34777776655 458888877 66666554 6777665543
No 38
>PF14316 DUF4381: Domain of unknown function (DUF4381)
Probab=25.06 E-value=62 Score=25.31 Aligned_cols=56 Identities=23% Similarity=0.335 Sum_probs=35.2
Q ss_pred hhhhhhccCCC-c-hhhHHh---hhhhhhhhhhccccccchhhhhhHHHHHHHHHhhccCC
Q 028622 95 AEFKKLVDPGS-S-AATTMA---TAGTTLIIGYGLGWRGGRWYATRKFRREQMKLLGQIKP 150 (206)
Q Consensus 95 ~Eikkiv~~~~-s-~~aC~A---TagTtlviGY~LGwRGG~wya~rkfrreQ~kllgqikp 150 (206)
+++++|.-|.. | .|-..+ -++.-+++...+.|+-.+.|-.++.|||=.+.|.+++.
T Consensus 3 ~~L~DI~~P~~vswwP~a~GWwll~~lll~~~~~~~~~~~r~~~~~~yrr~Al~~L~~l~~ 63 (146)
T PF14316_consen 3 AQLRDIHLPPPVSWWPLAPGWWLLLALLLLLLILLLWRLWRRWRRNRYRREALRELAQLES 63 (146)
T ss_pred cccCCCCCCCCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHccc
Confidence 57788888875 4 343222 12222222335567777888888899998888888753
No 39
>PF13556 HTH_30: PucR C-terminal helix-turn-helix domain; PDB: 3ONQ_B.
Probab=24.97 E-value=68 Score=21.60 Aligned_cols=21 Identities=33% Similarity=0.501 Sum_probs=16.6
Q ss_pred hhhhHhhHHHHHHHHHHHhhh
Q 028622 68 RHLHQSKVDQRLESIESTLKE 88 (206)
Q Consensus 68 Rhlhq~kVd~RL~SIE~amk~ 88 (206)
=|+|..-|..||+.||+-+--
T Consensus 22 L~iHrNTl~yRl~ki~~l~g~ 42 (59)
T PF13556_consen 22 LHIHRNTLRYRLKKIEELLGL 42 (59)
T ss_dssp HTS-HHHHHHHHHHHHHHHS-
T ss_pred HCCCHHHHHHHHHHHHHHHCc
Confidence 378999999999999987643
No 40
>PF08229 SHR3_chaperone: ER membrane protein SH3 ; InterPro: IPR013248 This family of proteins are membrane localised chaperones that are required for correct plasma membrane localisation of amino acid permeases (AAPs) []. Shr3 prevents AAPs proteins from aggregating and assists in their correct folding. In the absence of Shr3, AAPs are retained in the ER.
Probab=24.17 E-value=55 Score=28.36 Aligned_cols=35 Identities=26% Similarity=0.322 Sum_probs=25.4
Q ss_pred hhhhhhhhhccccccchhhhhhHHHHHHHHHhhcc
Q 028622 114 AGTTLIIGYGLGWRGGRWYATRKFRREQMKLLGQI 148 (206)
Q Consensus 114 agTtlviGY~LGwRGG~wya~rkfrreQ~kllgqi 148 (206)
....+++.=.|.--+|.|||.|.-++++.+.....
T Consensus 138 ~Ii~~~LvGVLvLQaG~~YAe~~~~~~~~~~~~~e 172 (196)
T PF08229_consen 138 TIIALVLVGVLVLQAGQWYAERKDAKELEEFEKEE 172 (196)
T ss_pred HHHHHHHHHHHHHHhhHHHHhhhhHHHHHHHHHHH
Confidence 34455555567789999999999888877665543
No 41
>TIGR01293 Kv_beta voltage-dependent potassium channel beta subunit, animal. Plant beta subunits and their closely related bacterial homologs (in Deinococcus radiudurans, Xylella fastidiosa, etc.) appear more closely related to each other than to animal forms. However, the bacterial species lack convincing counterparts the Kv alpha subunit and the Kv beta homolog may serve as an enzyme. Cutoffs are set for this model such that yeast and plant forms and bacterial close homologs score between trusted and noise cutoffs.
Probab=24.15 E-value=55 Score=27.96 Aligned_cols=44 Identities=18% Similarity=0.293 Sum_probs=27.0
Q ss_pred chhhHHHHHHhhhhhhhhhhHhhH------HHHHHHHHHHhhhhc---ccchhhhhhhc
Q 028622 52 GTSLASIATAWIGYSIRHLHQSKV------DQRLESIESTLKENY---QVGHAEFKKLV 101 (206)
Q Consensus 52 GTSiASv~tAWaGYslRhlhq~kV------d~RL~SIE~amk~~~---~leh~Eikkiv 101 (206)
|.|+|.++.+|+- ++..| -...+.+|+.++.-. .|+.+|+++|-
T Consensus 262 g~s~aqlal~w~l------~~~~v~~~i~G~~~~~ql~en~~a~~~~~~Ls~e~~~~l~ 314 (317)
T TIGR01293 262 GCTLPQLAIAWCL------RNEGVSSVLLGASSAEQLMENLGSLQVLPKLSSSIIHEID 314 (317)
T ss_pred CcCHHHHHHHHHh------cCCCCeEEEeCCCCHHHHHHHHHHhhccCCCCHHHHHHHH
Confidence 6799999999963 22111 123333455554432 69999998873
No 42
>smart00786 SHR3_chaperone ER membrane protein SH3. This family of proteins are membrane localised chaperones that are required for correct plasma membrane localisation of amino acid permeases (AAPs) PUBMED:15623581. Shr3 prevents AAPs proteins from aggregating and assists in their correct folding. In the absence of Shr3, AAPs are retained in the ER.
Probab=23.46 E-value=50 Score=28.91 Aligned_cols=29 Identities=24% Similarity=0.429 Sum_probs=20.9
Q ss_pred hhhhhccccccchhhhhhHHHHHHHHHhh
Q 028622 118 LIIGYGLGWRGGRWYATRKFRREQMKLLG 146 (206)
Q Consensus 118 lviGY~LGwRGG~wya~rkfrreQ~kllg 146 (206)
++..=-|.-.+|.|||.|+=++|+.+...
T Consensus 142 ~vLvGVL~LQaG~wYAer~~~~~~~~~~~ 170 (196)
T smart00786 142 FVLVGVLVLQAGLWYAERKDAKQKEEFAA 170 (196)
T ss_pred HHHHHHHHHHhhHHHHHHhHHHHHHHHHH
Confidence 33334456789999999988888776653
No 43
>TIGR01462 greA transcription elongation factor GreA. In the Chlamydias and some spirochetes, the region described by this model is found as the C-terminal region of a much larger protein.
Probab=22.94 E-value=92 Score=24.69 Aligned_cols=35 Identities=14% Similarity=0.233 Sum_probs=29.1
Q ss_pred hhhhhhhhhHhhHHHHHHHHHHHhhhhcccchhhh
Q 028622 63 IGYSIRHLHQSKVDQRLESIESTLKENYQVGHAEF 97 (206)
Q Consensus 63 aGYslRhlhq~kVd~RL~SIE~amk~~~~leh~Ei 97 (206)
++|...---|..+|.|++.||+.|.+-.-++..++
T Consensus 42 a~y~aak~~~~~~e~ri~~L~~~L~~a~iv~~~~~ 76 (151)
T TIGR01462 42 AEYHAAKEEQGFNEGRIAELEDLLANAQVIDDSKL 76 (151)
T ss_pred cchHHHHHHHHHHHHHHHHHHHHHHhCcccCcccC
Confidence 46888888999999999999999998777765544
No 44
>PF10552 ORF6C: ORF6C domain; InterPro: IPR018878 This entry represents the carboxy-terminal domain from ORF6 (Q9B012 from SWISSPROT), an antirepressor protein from Lactococcus phage bIL285 [].
Probab=22.46 E-value=1.1e+02 Score=23.22 Aligned_cols=30 Identities=20% Similarity=0.445 Sum_probs=22.4
Q ss_pred hhHHHHHHHHH---HHhhhhcccchhhhhhhcc
Q 028622 73 SKVDQRLESIE---STLKENYQVGHAEFKKLVD 102 (206)
Q Consensus 73 ~kVd~RL~SIE---~amk~~~~leh~Eikkiv~ 102 (206)
..+++|++.|| +-++++..|...|-+.|-.
T Consensus 11 ~~~~~ki~~ve~~V~~l~~~~~i~~~q~~~i~~ 43 (116)
T PF10552_consen 11 EEHNEKIEEVENRVDDLEENMPIDPGQQKEIQK 43 (116)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHH
Confidence 46788888888 4457888888877666654
No 45
>PF08278 DnaG_DnaB_bind: DNA primase DnaG DnaB-binding ; InterPro: IPR013173 Eubacterial DnaG primases interact with several factors to form the replisome. One of these factors is DnaB, a helicase. This domain has been demonstrated to be responsible for the interaction between DnaG and DnaB []. This domain has a multi-helical structure that forms an orthogonal bundle [].; GO: 0003896 DNA primase activity, 0006269 DNA replication, synthesis of RNA primer; PDB: 2HAJ_A 1T3W_B.
Probab=21.90 E-value=1.3e+02 Score=22.18 Aligned_cols=34 Identities=15% Similarity=0.364 Sum_probs=25.1
Q ss_pred hhhhhhHhhHHHHHHHHHHHhhhhcccchhhhhhh
Q 028622 66 SIRHLHQSKVDQRLESIESTLKENYQVGHAEFKKL 100 (206)
Q Consensus 66 slRhlhq~kVd~RL~SIE~amk~~~~leh~Eikki 100 (206)
++++|++..+++|++.+.+.... .+|+.+|-+.+
T Consensus 90 ~l~~L~~~~~~~~i~~L~~k~~~-~~Lt~eEk~el 123 (127)
T PF08278_consen 90 ALARLQEQALERRIEELKAKPRR-GGLTDEEKQEL 123 (127)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHTT-T---HHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHhhcc-CCcCHHHHHHH
Confidence 67889999999999999887776 67888885543
No 46
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=21.82 E-value=24 Score=30.93 Aligned_cols=30 Identities=10% Similarity=0.167 Sum_probs=23.8
Q ss_pred HHHHHhhhhcccchhhhhhhccCCC-chhhHHhh
Q 028622 81 SIESTLKENYQVGHAEFKKLVDPGS-SAATTMAT 113 (206)
Q Consensus 81 SIE~amk~~~~leh~Eikkiv~~~~-s~~aC~AT 113 (206)
-+|++.-++-+|++ ++..+++ . ++|+||=.
T Consensus 6 r~e~~~~~Q~~~~~-~~~~~i~--~~~~P~CiR~ 36 (217)
T PRK13719 6 RRERATIRQIDLPE-SLTAFID--DYSYPACIRN 36 (217)
T ss_pred hhhhcchhhhhhHH-HHHHHHH--cCCCCeEEEC
Confidence 46888888888887 7888887 5 99999853
No 47
>PF04882 Peroxin-3: Peroxin-3; InterPro: IPR006966 Peroxin 3 (Pex3p), also known as Peroxisomal biogenesis factor 3, has been identified and characterised as a peroxisomal membrane protein in yeasts and mammals []. Two putative peroxisomal membrane-bound Pex3p homologues have also been found in Arabidopsis thaliana []. They possess a membrane peroxisomal targeting signal. Pex3p is an integral membrane protein of peroxisomes, exposing its N- and C-terminal parts to the cytosol []. Peroxin is involved in peroxisome biosynthesis and integrity; it assembles membrane vesicles before the matrix proteins are translocated. In humans, defects in PEX3 are the cause of peroxisome biogenesis disorders [], which include Zellweger syndrome (ZWS), neonatal adrenoleukodystrophy (NALD), infantile Refsum disease (IRD), and classical rhizomelic chondrodysplasia punctata (RCDP). These are peroxisomal disorders that are the result of proteins failing to be imported into the peroxisome.; GO: 0007031 peroxisome organization, 0005779 integral to peroxisomal membrane; PDB: 3MK4_A 3AJB_A.
Probab=21.76 E-value=61 Score=30.09 Aligned_cols=35 Identities=17% Similarity=0.269 Sum_probs=0.0
Q ss_pred hhccHhhhhhceeEEEechhhHHHHHHhhhhhhhh
Q 028622 35 YFSTKDTFERHRVVFTIGTSLASIATAWIGYSIRH 69 (206)
Q Consensus 35 f~STKdvFErHrVVFTvGTSiASv~tAWaGYslRh 69 (206)
|-|+++-|.|||==|.||.-|++.+-+-.-|..+.
T Consensus 1 ~~~~~~f~~Rhr~k~~~~~~v~g~~y~~~~y~~~k 35 (432)
T PF04882_consen 1 FSSLRSFFRRHRRKIIVTGGVVGGGYLLYQYAQKK 35 (432)
T ss_dssp -----------------------------------
T ss_pred CCccccccccccccccccccccccccccccccccc
Confidence 45788999999988888766655554444455543
No 48
>PF15346 ARGLU: Arginine and glutamate-rich 1
Probab=21.74 E-value=67 Score=26.95 Aligned_cols=17 Identities=47% Similarity=0.749 Sum_probs=13.2
Q ss_pred hHHHHHHHHHhhccCCc
Q 028622 135 RKFRREQMKLLGQIKPR 151 (206)
Q Consensus 135 rkfrreQ~kllgqikp~ 151 (206)
++.+.|||++||.++++
T Consensus 126 kk~k~EQ~~iLgK~~sR 142 (149)
T PF15346_consen 126 KKQKEEQMKILGKNNSR 142 (149)
T ss_pred HHHHHHHHHHhCCCCCC
Confidence 56677899999997753
No 49
>COG5478 Predicted small integral membrane protein [Function unknown]
Probab=21.50 E-value=46 Score=28.01 Aligned_cols=25 Identities=20% Similarity=0.371 Sum_probs=20.7
Q ss_pred HhhHHHHHHHHHHHhhhhcccchhh
Q 028622 72 QSKVDQRLESIESTLKENYQVGHAE 96 (206)
Q Consensus 72 q~kVd~RL~SIE~amk~~~~leh~E 96 (206)
|.|+|++|-|.+.+=-+.-++||.+
T Consensus 77 ~aKLDElir~~~e~~n~~VgIEh~~ 101 (141)
T COG5478 77 QAKLDELIRSLREARNDVVGIEHLK 101 (141)
T ss_pred HHHHHHHHHHhccccCceeeeccCC
Confidence 6899999999888877777888754
No 50
>PF08418 Pol_alpha_B_N: DNA polymerase alpha subunit B N-terminal; InterPro: IPR013627 This is the eukaryotic DNA polymerase alpha subunit B N-terminal domain which is involved in complex formation []. ; PDB: 4E2I_9 2KEB_A 3FLO_G.
Probab=21.22 E-value=82 Score=26.30 Aligned_cols=34 Identities=26% Similarity=0.604 Sum_probs=20.5
Q ss_pred hhhhhhhHh------hHHHHHHHHHHHhhhhcccchhhhh
Q 028622 65 YSIRHLHQS------KVDQRLESIESTLKENYQVGHAEFK 98 (206)
Q Consensus 65 YslRhlhq~------kVd~RL~SIE~amk~~~~leh~Eik 98 (206)
|..|+|.|. -+|+|++.+-+..+..|+++..||-
T Consensus 207 ~~yr~M~~kL~e~sevLDdrId~f~~~iq~~~~~~~~~fg 246 (253)
T PF08418_consen 207 YKYRYMFQKLSERSEVLDDRIDEFAELIQEHYKLEDSEFG 246 (253)
T ss_dssp -----S---HHHHHHHHHHHHHHHHHHHHHHHT--GGGB-
T ss_pred cCchHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccccC
Confidence 788988874 3688999999999999999998874
No 51
>PRK00105 cobT nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase; Reviewed
Probab=20.77 E-value=1.9e+02 Score=26.51 Aligned_cols=47 Identities=11% Similarity=0.147 Sum_probs=32.5
Q ss_pred chhhHHHHHHh-hhhhhhh-------hhHhhHHHHHHHHHHHhhhhcccchhhhh
Q 028622 52 GTSLASIATAW-IGYSIRH-------LHQSKVDQRLESIESTLKENYQVGHAEFK 98 (206)
Q Consensus 52 GTSiASv~tAW-aGYslRh-------lhq~kVd~RL~SIE~amk~~~~leh~Eik 98 (206)
||+-||+.++- .||.... +.+..++.+.+-||+||+.+.....+-+.
T Consensus 166 nTTtAaAvl~aL~g~~~~~~vg~Gsg~~~~~~~~K~~vV~~al~~~~~~~~dp~~ 220 (335)
T PRK00105 166 NTTPAAALVAALTGGDPEEVVGRGTGIDDAGLARKIAVVRRALARHRPALQDPLD 220 (335)
T ss_pred hhHHHHHHHHHHhCcCHHHhcCCCCCCCcHHHHHHHHHHHHHHHhcCCCCCCHHH
Confidence 46666655544 4998853 57888999999999999976544434333
No 52
>KOG1444 consensus Nucleotide-sugar transporter VRG4/SQV-7 [Carbohydrate transport and metabolism; Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=20.61 E-value=30 Score=32.06 Aligned_cols=25 Identities=32% Similarity=0.675 Sum_probs=20.3
Q ss_pred hhhhccccccchhhhhhHHHHHHHH
Q 028622 119 IIGYGLGWRGGRWYATRKFRREQMK 143 (206)
Q Consensus 119 viGY~LGwRGG~wya~rkfrreQ~k 143 (206)
++|.-+|+=||.||+--++|++|++
T Consensus 285 ~~gll~~~~ggv~Y~~~~~~~k~~~ 309 (314)
T KOG1444|consen 285 VIGLLVGFFGGVLYSYATFRKKKQP 309 (314)
T ss_pred hHHHHHHhhhhhHHhhhhhhhccCC
Confidence 3455678999999999999998654
No 53
>PF02355 SecD_SecF: Protein export membrane protein; InterPro: IPR022813 Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component []. From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins. The translocase protein subunits are encoded on the bacterial chromosome. The translocase itself comprises 7 proteins, including a chaperone protein (SecB), an ATPase (SecA), an integral membrane complex (SecCY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) []. The chaperone protein SecB [] is a highly acidic homotetrameric protein that exists as a "dimer of dimers" in the bacterial cytoplasm. SecB maintains preproteins in an unfolded state after translation, and targets these to the peripheral membrane protein ATPase SecA for secretion []. Together with SecY and SecG, SecE forms a multimeric channel through which preproteins are translocated, using both proton motive forces and ATP-driven secretion. The latter is mediated by SecA. The structure of the Escherichia coli SecYEG assembly revealed a sandwich of two membranes interacting through the extensive cytoplasmic domains []. Each membrane is composed of dimers of SecYEG. The monomeric complex contains 15 transmembrane helices. The SecD and SecF equivalents of the Gram-positive bacterium Bacillus subtilis are jointly present in one polypeptide, denoted SecDF, that is required to maintain a high capacity for protein secretion. Unlike the SecD subunit of the pre-protein translocase of E. coli, SecDF of B. subtilis was not required for the release of a mature secretory protein from the membrane, indicating that SecDF is involved in earlier translocation steps []. Comparison with SecD and SecF proteins from other organisms revealed the presence of 10 conserved regions in SecDF, some of which appear to be important for SecDF function. Interestingly, the SecDF protein of B. subtilis has 12 putative transmembrane domains. Thus, SecDF does not only show sequence similarity but also structural similarity to secondary solute transporters []. This entry represents bacterial SecD and SecF protein export membrane proteins and their archaeal homologues []. It is found in association with PF07549 from PFAM SecD and SecF proteins are part of the multimeric protein export complex comprising SecA, D, E, F, G, Y, and YajC []. SecD and SecF are required to maintain a proton motive force []. ; PDB: 3AQP_A 2RRN_A 3AQO_B.
Probab=20.16 E-value=1.1e+02 Score=25.49 Aligned_cols=68 Identities=25% Similarity=0.339 Sum_probs=38.9
Q ss_pred hhhHHHHHHhhhhhhhhhhHhhHHHHHHHHHHHhhhhcccchhhhhhhccCC-C-chhhHHhhhhhhhhhhhccccccc
Q 028622 53 TSLASIATAWIGYSIRHLHQSKVDQRLESIESTLKENYQVGHAEFKKLVDPG-S-SAATTMATAGTTLIIGYGLGWRGG 129 (206)
Q Consensus 53 TSiASv~tAWaGYslRhlhq~kVd~RL~SIE~amk~~~~leh~Eikkiv~~~-~-s~~aC~ATagTtlviGY~LGwRGG 129 (206)
.+||..++ =+|||+ |.-.=-.|.-.++-+..+.+.+++.++.+ + .....+.|..||+++.-.|=+=||
T Consensus 85 ~~iaall~-~iG~sV--------d~~IVifdRIre~~~~~~~~~~~~~~~~s~~~tl~r~i~t~~ttll~~~~L~~~g~ 154 (189)
T PF02355_consen 85 PSIAALLT-IIGYSV--------DDNIVIFDRIREELRASRGKSLREAINISIKQTLSRTIDTSLTTLLAALILFFFGG 154 (189)
T ss_dssp HHHHHHHH-HHHHHH--------HHHHHHHHHHHHHHCC-STS-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC--
T ss_pred HHHHHHHH-HHHHHH--------hcceeehHHHHHHhhhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 34555544 489985 32222233333333344667777777766 3 777788888888877766655554
Done!