Query 031957
Match_columns 150
No_of_seqs 128 out of 380
Neff 2.9
Searched_HMMs 46136
Date Fri Mar 29 07:41:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031957.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031957hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 CHL00075 rpl21 ribosomal prote 99.4 1.5E-13 3.3E-18 103.1 6.1 39 101-140 1-40 (108)
2 PF00829 Ribosomal_L21p: Ribos 99.4 3.2E-13 6.9E-18 98.6 5.5 37 103-140 1-38 (96)
3 PRK05573 rplU 50S ribosomal pr 99.4 3.7E-13 8E-18 99.8 5.8 37 103-140 1-38 (103)
4 COG0261 RplU Ribosomal protein 99.4 5.6E-13 1.2E-17 100.5 5.6 38 103-141 1-39 (103)
5 TIGR00061 L21 ribosomal protei 99.3 6.8E-12 1.5E-16 93.1 5.4 36 104-140 1-37 (101)
6 KOG1686 Mitochondrial/chloropl 98.9 2.3E-09 4.9E-14 85.7 5.1 54 96-149 19-75 (151)
7 PF02311 AraC_binding: AraC-li 87.2 1 2.3E-05 30.4 3.8 21 105-125 34-54 (136)
8 COG0662 {ManC} Mannose-6-phosp 85.0 1.4 3.1E-05 32.5 3.8 21 105-125 68-88 (127)
9 PF11356 Pilus_PilP: Type IV p 84.3 1.2 2.6E-05 30.4 3.0 25 99-123 37-62 (87)
10 PF07883 Cupin_2: Cupin domain 80.8 2.9 6.3E-05 26.4 3.5 22 105-126 30-51 (71)
11 PF12791 RsgI_N: Anti-sigma fa 79.7 3.5 7.7E-05 26.5 3.7 30 101-137 4-33 (56)
12 PF04351 PilP: Pilus assembly 78.7 2.8 6.1E-05 32.3 3.5 25 100-124 88-113 (149)
13 PRK09943 DNA-binding transcrip 78.0 3.4 7.3E-05 31.9 3.8 22 105-126 139-160 (185)
14 COG3168 PilP Tfp pilus assembl 72.0 4.1 8.9E-05 33.7 3.0 25 101-125 108-132 (170)
15 cd04867 TGS_YchF_C TGS_YchF_C: 69.6 2.2 4.7E-05 31.5 0.8 20 105-124 62-81 (83)
16 PF01050 MannoseP_isomer: Mann 63.5 12 0.00025 29.4 3.9 23 104-126 94-116 (151)
17 PRK13290 ectC L-ectoine syntha 63.3 16 0.00034 27.7 4.5 41 106-147 67-112 (125)
18 TIGR03214 ura-cupin putative a 62.5 11 0.00023 31.5 3.7 23 104-126 210-232 (260)
19 PF06249 EutQ: Ethanolamine ut 62.1 9.8 0.00021 30.5 3.3 20 107-126 108-127 (152)
20 PF06071 YchF-GTPase_C: Protei 59.1 1.9 4.2E-05 31.8 -1.1 20 105-124 62-81 (84)
21 KOG4317 Predicted Zn-finger pr 58.7 0.29 6.3E-06 44.3 -6.5 75 51-137 240-314 (383)
22 PRK11171 hypothetical protein; 57.2 15 0.00033 30.7 3.7 21 105-125 216-236 (266)
23 PRK15457 ethanolamine utilizat 56.1 16 0.00035 31.4 3.8 22 106-127 187-208 (233)
24 TIGR02988 YaaA_near_RecF S4 do 55.9 8.7 0.00019 24.9 1.7 19 107-125 36-59 (59)
25 PRK13501 transcriptional activ 55.2 15 0.00033 29.6 3.4 24 104-127 48-71 (290)
26 cd04092 mtEFG2_II_like mtEFG2_ 54.7 16 0.00034 24.7 2.9 23 115-137 60-82 (83)
27 PRK10296 DNA-binding transcrip 51.3 23 0.0005 28.3 3.8 22 105-126 54-75 (278)
28 PF10949 DUF2777: Protein of u 51.3 17 0.00037 30.2 3.1 22 106-127 67-88 (185)
29 PRK10371 DNA-binding transcrip 50.6 22 0.00048 29.6 3.7 22 105-126 57-78 (302)
30 PRK13500 transcriptional activ 50.6 20 0.00044 29.7 3.5 23 105-127 79-101 (312)
31 TIGR03021 pilP_fam type IV pil 49.2 21 0.00046 27.2 3.1 24 99-122 77-101 (119)
32 PF13510 Fer2_4: 2Fe-2S iron-s 47.4 9.8 0.00021 26.6 1.0 17 107-123 6-22 (82)
33 cd04088 EFG_mtEFG_II EFG_mtEFG 47.1 25 0.00054 23.5 2.9 23 115-137 60-82 (83)
34 TIGR00092 GTP-binding protein 46.4 12 0.00026 33.5 1.6 20 105-124 345-364 (368)
35 PF00842 Ala_racemase_C: Alani 46.0 56 0.0012 24.8 5.0 34 105-139 53-93 (129)
36 PF14525 AraC_binding_2: AraC- 45.5 35 0.00075 24.3 3.6 22 105-126 66-87 (172)
37 PRK13502 transcriptional activ 45.3 31 0.00066 27.5 3.6 23 105-127 49-71 (282)
38 PRK09685 DNA-binding transcrip 43.9 33 0.00073 27.5 3.7 22 105-126 82-103 (302)
39 TIGR02297 HpaA 4-hydroxyphenyl 43.8 31 0.00067 27.4 3.4 23 105-127 55-77 (287)
40 PF11699 CENP-C_C: Mif2/CENP-C 43.2 34 0.00075 24.7 3.3 23 106-128 45-67 (85)
41 PF01455 HupF_HypC: HupF/HypC 43.0 52 0.0011 22.8 4.0 31 101-137 15-45 (68)
42 TIGR01479 GMP_PMI mannose-1-ph 42.0 35 0.00076 30.7 3.8 41 104-144 407-451 (468)
43 cd03691 BipA_TypA_II BipA_TypA 42.0 30 0.00065 23.3 2.7 22 115-136 63-84 (86)
44 PRK15460 cpsB mannose-1-phosph 41.7 35 0.00075 31.4 3.8 36 105-140 417-456 (478)
45 PRK09601 GTP-binding protein Y 41.4 19 0.00042 32.2 2.1 18 107-124 343-360 (364)
46 smart00835 Cupin_1 Cupin. This 40.9 32 0.00068 25.5 2.9 21 106-126 63-89 (146)
47 PRK10572 DNA-binding transcrip 39.6 36 0.00077 27.4 3.2 22 105-126 60-81 (290)
48 PRK11171 hypothetical protein; 36.3 52 0.0011 27.5 3.8 22 105-126 94-115 (266)
49 PHA02885 putative interleukin 36.0 22 0.00047 28.3 1.4 21 117-137 72-92 (135)
50 KOG2925 Predicted translation 35.7 35 0.00076 28.3 2.6 44 101-144 34-92 (167)
51 PF05899 Cupin_3: Protein of u 35.5 64 0.0014 21.9 3.5 17 110-126 42-58 (74)
52 PF11213 DUF3006: Protein of u 35.0 61 0.0013 22.2 3.4 12 102-113 9-20 (71)
53 PF04347 FliO: Flagellar biosy 34.6 42 0.00091 22.8 2.5 26 102-127 30-57 (84)
54 PRK13503 transcriptional activ 34.4 29 0.00062 27.4 1.9 22 105-126 46-67 (278)
55 TIGR01222 minC septum site-det 34.3 58 0.0013 26.4 3.7 25 110-137 121-145 (217)
56 COG1917 Uncharacterized conser 34.0 52 0.0011 23.7 3.1 21 106-126 76-96 (131)
57 PF00717 Peptidase_S24: Peptid 32.8 56 0.0012 20.7 2.8 10 115-124 24-33 (70)
58 PF08838 DUF1811: Protein of u 32.6 35 0.00077 26.2 2.1 19 111-129 58-78 (102)
59 cd03689 RF3_II RF3_II: this su 31.8 58 0.0013 22.6 2.9 22 116-137 62-83 (85)
60 smart00363 S4 S4 RNA-binding d 31.4 85 0.0018 18.1 3.2 21 106-126 27-52 (60)
61 KOG2757 Mannose-6-phosphate is 30.8 74 0.0016 29.7 4.1 44 104-147 363-410 (411)
62 TIGR01713 typeII_sec_gspC gene 30.4 50 0.0011 27.9 2.8 24 100-123 94-117 (259)
63 PF10618 Tail_tube: Phage tail 30.1 53 0.0011 24.8 2.6 24 104-127 8-31 (119)
64 PRK13415 flagella biosynthesis 30.0 29 0.00063 29.6 1.3 33 103-137 115-147 (219)
65 TIGR00074 hypC_hupF hydrogenas 29.9 84 0.0018 22.4 3.5 31 103-139 15-45 (76)
66 TIGR03214 ura-cupin putative a 29.8 78 0.0017 26.4 3.8 22 105-126 91-112 (260)
67 PF01479 S4: S4 domain; Inter 29.1 45 0.00097 20.3 1.8 17 106-122 27-48 (48)
68 PTZ00305 NADH:ubiquinone oxido 27.9 53 0.0012 29.2 2.6 23 101-123 65-88 (297)
69 PF05164 ZapA: Cell division p 27.8 54 0.0012 22.0 2.1 18 107-124 4-23 (89)
70 PTZ00258 GTP-binding protein; 27.7 65 0.0014 29.1 3.2 17 108-124 368-384 (390)
71 KOG0126 Predicted RNA-binding 27.6 46 0.001 28.6 2.1 29 105-137 36-64 (219)
72 cd06530 S26_SPase_I The S26 Ty 26.8 1.3E+02 0.0029 19.8 3.9 24 116-139 14-41 (85)
73 cd03690 Tet_II Tet_II: This su 26.5 68 0.0015 22.1 2.5 22 115-136 62-83 (85)
74 KOG1491 Predicted GTP-binding 26.4 42 0.0009 31.1 1.8 16 109-124 372-387 (391)
75 PF12969 DUF3857: Domain of Un 25.7 84 0.0018 23.0 3.0 32 106-137 48-97 (177)
76 PF03473 MOSC: MOSC domain; I 25.6 1E+02 0.0022 22.3 3.4 24 98-124 110-133 (133)
77 PRK10413 hydrogenase 2 accesso 25.3 1.3E+02 0.0028 21.8 3.8 16 102-117 17-32 (82)
78 PF05726 Pirin_C: Pirin C-term 24.1 90 0.0019 22.2 2.8 37 107-149 31-67 (104)
79 PF03823 Neurokinin_B: Neuroki 24.1 50 0.0011 23.3 1.4 27 7-33 10-36 (59)
80 PRK05177 minC septum formation 24.1 1.1E+02 0.0024 25.5 3.7 25 110-137 142-166 (239)
81 COG0298 HypC Hydrogenase matur 23.5 1.1E+02 0.0024 22.8 3.2 28 104-137 18-46 (82)
82 TIGR03404 bicupin_oxalic bicup 23.5 1.3E+02 0.0029 26.6 4.3 32 110-143 287-324 (367)
83 PRK04804 minC septum formation 23.1 1.2E+02 0.0027 24.8 3.8 25 110-137 123-147 (221)
84 cd03699 lepA_II lepA_II: This 22.7 97 0.0021 21.1 2.7 23 115-137 59-85 (86)
85 cd04091 mtEFG1_II_like mtEFG1_ 22.2 1E+02 0.0023 20.7 2.7 21 115-136 59-79 (81)
86 PF02563 Poly_export: Polysacc 21.7 53 0.0011 22.5 1.2 17 112-128 9-25 (82)
87 cd08379 C2D_MCTP_PRT_plant C2 20.2 1.3E+02 0.0028 22.5 3.1 18 98-115 21-38 (126)
No 1
>CHL00075 rpl21 ribosomal protein L21
Probab=99.45 E-value=1.5e-13 Score=103.14 Aligned_cols=39 Identities=26% Similarity=0.382 Sum_probs=35.9
Q ss_pred CceEEEEEeCCEEEEEcCCCEEEecccCCCCCCCeEE-eee
Q 031957 101 EEIFAVVMIGSRQYIVFPGRFIYTQRLKGANVNDKVC-NFC 140 (150)
Q Consensus 101 ~~MYAIVeiGGKQYKVe~GdvI~VerLkgaEvGD~V~-~~~ 140 (150)
++|||||++|||||||++||+|.||+|+ +++||+|+ +.+
T Consensus 1 ~~myAIi~~gGkQykV~~Gd~i~vekl~-~~~G~~i~l~~V 40 (108)
T CHL00075 1 MMTYAIIEAGGKQLWVEPGRFYDINHFP-LEPGTKILLNRV 40 (108)
T ss_pred CcEEEEEEECCEEEEEeCCCEEEEEEcC-CCCCCEEEEEEE
Confidence 3699999999999999999999999996 89999999 555
No 2
>PF00829 Ribosomal_L21p: Ribosomal prokaryotic L21 protein; InterPro: IPR001787 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L21 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L21 is known to bind to the 23S rRNA in the presence of L20. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities, groups: Bacterial L21. Marchantia polymorpha chloroplast L21. Cyanelle L21. Plant chloroplast L21 (nuclear-encoded). Bacterial L21 is a protein of about 100 amino-acid residues, the mature form of the spinach chloroplast L21 has 200 residues.; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2XG0_V 2X9S_V 2XG2_V 3UZ1_2 2Y19_V 2WDL_V 3V23_V 2WRO_V 2WRL_V 2Y11_V ....
Probab=99.41 E-value=3.2e-13 Score=98.62 Aligned_cols=37 Identities=38% Similarity=0.608 Sum_probs=33.7
Q ss_pred eEEEEEeCCEEEEEcCCCEEEecccCCCCCCCeEE-eee
Q 031957 103 IFAVVMIGSRQYIVFPGRFIYTQRLKGANVNDKVC-NFC 140 (150)
Q Consensus 103 MYAIVeiGGKQYKVe~GdvI~VerLkgaEvGD~V~-~~~ 140 (150)
|||||++|||||||++||+|+||+| ++++||+|+ +.+
T Consensus 1 myAIi~~ggkQykV~~gd~i~v~~l-~~~~G~~i~l~~V 38 (96)
T PF00829_consen 1 MYAIIEIGGKQYKVEEGDVIDVERL-DAEVGDKIELDKV 38 (96)
T ss_dssp -EEEEESSSEEEEESSSEEEEEEST-SSSTTSEEEETTE
T ss_pred CEEEEEECCEEEEEeCCCEEEECCc-CcCCCCEEEEEEE
Confidence 9999999999999999999999999 599999999 444
No 3
>PRK05573 rplU 50S ribosomal protein L21; Validated
Probab=99.41 E-value=3.7e-13 Score=99.76 Aligned_cols=37 Identities=32% Similarity=0.533 Sum_probs=34.9
Q ss_pred eEEEEEeCCEEEEEcCCCEEEecccCCCCCCCeEE-eee
Q 031957 103 IFAVVMIGSRQYIVFPGRFIYTQRLKGANVNDKVC-NFC 140 (150)
Q Consensus 103 MYAIVeiGGKQYKVe~GdvI~VerLkgaEvGD~V~-~~~ 140 (150)
|||||++|||||||++||+|+||+|+ +++||+|+ +.+
T Consensus 1 MyAIi~~gGkQykV~~Gd~i~v~~l~-~~~G~~i~l~~V 38 (103)
T PRK05573 1 MYAIIKTGGKQYKVEEGDVIKVEKLD-AEVGDTVEFDEV 38 (103)
T ss_pred CEEEEEECCEEEEEeCCCEEEEcccC-CCCCCEEEEeEE
Confidence 99999999999999999999999996 89999999 555
No 4
>COG0261 RplU Ribosomal protein L21 [Translation, ribosomal structure and biogenesis]
Probab=99.39 E-value=5.6e-13 Score=100.53 Aligned_cols=38 Identities=32% Similarity=0.490 Sum_probs=35.5
Q ss_pred eEEEEEeCCEEEEEcCCCEEEecccCCCCCCCeEE-eeec
Q 031957 103 IFAVVMIGSRQYIVFPGRFIYTQRLKGANVNDKVC-NFCA 141 (150)
Q Consensus 103 MYAIVeiGGKQYKVe~GdvI~VerLkgaEvGD~V~-~~~~ 141 (150)
|||||++|||||||++||+|+||+|+ +++||+|+ +.++
T Consensus 1 mYAii~tGGKQykV~~G~~i~vEkl~-~e~g~~v~f~~VL 39 (103)
T COG0261 1 MYAIIKTGGKQYKVEEGDVIKVEKLD-AEPGDKVEFDEVL 39 (103)
T ss_pred CeEEEEECCEEEEEecCCEEEEEEcC-CCCCCEEEEEEEE
Confidence 99999999999999999999999996 89999999 6653
No 5
>TIGR00061 L21 ribosomal protein L21. Eubacterial and chloroplast.
Probab=99.27 E-value=6.8e-12 Score=93.15 Aligned_cols=36 Identities=33% Similarity=0.495 Sum_probs=33.9
Q ss_pred EEEEEeCCEEEEEcCCCEEEecccCCCCCCCeEE-eee
Q 031957 104 FAVVMIGSRQYIVFPGRFIYTQRLKGANVNDKVC-NFC 140 (150)
Q Consensus 104 YAIVeiGGKQYKVe~GdvI~VerLkgaEvGD~V~-~~~ 140 (150)
||||++|||||||++||+|.||+|+ +++||.|+ +.+
T Consensus 1 yAIi~~gGkQykV~~Gd~i~Ve~l~-~~~G~~i~l~~V 37 (101)
T TIGR00061 1 YAIVEIGGKQYKVEEGQTVRIEKLD-AAPGDTVEFDKV 37 (101)
T ss_pred CEEEEECCEEEEEeCCCEEEEcccC-CCCCCEEEEEEE
Confidence 8999999999999999999999996 89999999 555
No 6
>KOG1686 consensus Mitochondrial/chloroplast ribosomal L21 protein [Translation, ribosomal structure and biogenesis]
Probab=98.89 E-value=2.3e-09 Score=85.66 Aligned_cols=54 Identities=39% Similarity=0.331 Sum_probs=48.8
Q ss_pred cCCCCCceEEEEEeCCEEEEEcCCCEEEecccCCCCCCCeEE-eee--ccCCcceec
Q 031957 96 EEPKREEIFAVVMIGSRQYIVFPGRFIYTQRLKGANVNDKVC-NFC--AFSPLQFLI 149 (150)
Q Consensus 96 ~~~~r~~MYAIVeiGGKQYKVe~GdvI~VerLkgaEvGD~V~-~~~--~~~~~~~~~ 149 (150)
...+|+..||||.+||+||||..||.||.++++.+++||++. +++ .|+-.|++|
T Consensus 19 ~~~kr~~~favv~v~srq~kvs~gd~iy~eg~~p~nv~d~i~l~kVlLvg~~~~T~~ 75 (151)
T KOG1686|consen 19 HSIKRPSGFAVVSVGSRQRKVSSGDTIYTEGLKPKNVLDSIPLPKVLLVGPVEETRI 75 (151)
T ss_pred hccccCCccEEEEEcceeEEecCCCeeeecCccccccccccccceEEEecCcceeEe
Confidence 568899999999999999999999999999999999999999 776 677777765
No 7
>PF02311 AraC_binding: AraC-like ligand binding domain; InterPro: IPR003313 This entry defines the arabinose-binding and dimerisation domain of the bacterial gene regulatory protein AraC. The crystal structure of the arabinose-binding and dimerization domain of the Escherichia coli gene regulatory protein AraC was determined in the presence and absence of L-arabinose. The arabinose-bound molecule shows that the protein adopts an unusual fold, binding sugar within a beta barrel and completely burying the arabinose with the amino-terminal arm of the protein. Dimer contacts in the presence of arabinose are mediated by an antiparallel coiled-coil. In the uncomplexed protein, the amino-terminal arm is disordered, uncovering the sugar-binding pocket and allowing it to serve as an oligomerization interface [].; GO: 0006355 regulation of transcription, DNA-dependent; PDB: 1XJA_B 2ARA_A 2AAC_B 2ARC_A.
Probab=87.22 E-value=1 Score=30.35 Aligned_cols=21 Identities=19% Similarity=0.453 Sum_probs=16.3
Q ss_pred EEEEeCCEEEEEcCCCEEEec
Q 031957 105 AVVMIGSRQYIVFPGRFIYTQ 125 (150)
Q Consensus 105 AIVeiGGKQYKVe~GdvI~Ve 125 (150)
+.+.++|++|.|.+||++.+.
T Consensus 34 ~~~~~~~~~~~l~~g~~~li~ 54 (136)
T PF02311_consen 34 GTLHIDGQEYPLKPGDLFLIP 54 (136)
T ss_dssp EEEEETTEEEEE-TT-EEEE-
T ss_pred EEEEECCEEEEEECCEEEEec
Confidence 457899999999999999976
No 8
>COG0662 {ManC} Mannose-6-phosphate isomerase [Carbohydrate transport and metabolism]
Probab=84.97 E-value=1.4 Score=32.53 Aligned_cols=21 Identities=29% Similarity=0.396 Sum_probs=19.5
Q ss_pred EEEEeCCEEEEEcCCCEEEec
Q 031957 105 AVVMIGSRQYIVFPGRFIYTQ 125 (150)
Q Consensus 105 AIVeiGGKQYKVe~GdvI~Ve 125 (150)
|+|.+||+++-|.+||.++|+
T Consensus 68 g~v~~~~~~~~v~~gd~~~iP 88 (127)
T COG0662 68 GKVTIGGEEVEVKAGDSVYIP 88 (127)
T ss_pred EEEEECCEEEEecCCCEEEEC
Confidence 567899999999999999997
No 9
>PF11356 Pilus_PilP: Type IV pilus biogenesis; InterPro: IPR022753 Type IV pili are required for auto-agglutination, twitching motility, biofilm formation, adherence and DNA uptake during transformation []. PilP is an inner membrane protein, required for pilus expression and transformation []. PilP interacts with PilQ which suggests that the two proteins may have coordinated activity in functions such as pilus extrusion/retraction []. ; PDB: 3OSS_C 2LNV_A.
Probab=84.35 E-value=1.2 Score=30.44 Aligned_cols=25 Identities=20% Similarity=0.064 Sum_probs=19.5
Q ss_pred CCCceEEEEE-eCCEEEEEcCCCEEE
Q 031957 99 KREEIFAVVM-IGSRQYIVFPGRFIY 123 (150)
Q Consensus 99 ~r~~MYAIVe-iGGKQYKVe~GdvI~ 123 (150)
.....+|||+ .+|+|+.+..||.|.
T Consensus 37 ~~~~~~Aii~~~~~~~~~~~~Gd~i~ 62 (87)
T PF11356_consen 37 GGGRSSAIIRPSGGEQRTYRVGDTIP 62 (87)
T ss_dssp CSSS-EEEEE-CTTEEEEE-TTEE-S
T ss_pred CCCceEEEEEeCCCcEEEEECcCEeC
Confidence 4556899999 999999999999987
No 10
>PF07883 Cupin_2: Cupin domain; InterPro: IPR013096 This family represents the conserved barrel domain of the cupin superfamily [] (cupa is the Latin term for a small barrel). ; PDB: 2OPK_C 3BU7_B 2PHD_D 3NVC_A 3NKT_A 3NJZ_A 3NW4_A 3NST_A 3NL1_A 2H0V_A ....
Probab=80.81 E-value=2.9 Score=26.35 Aligned_cols=22 Identities=18% Similarity=0.359 Sum_probs=18.8
Q ss_pred EEEEeCCEEEEEcCCCEEEecc
Q 031957 105 AVVMIGSRQYIVFPGRFIYTQR 126 (150)
Q Consensus 105 AIVeiGGKQYKVe~GdvI~Ver 126 (150)
+.+.++|+.|.+++||.++++.
T Consensus 30 ~~~~~~~~~~~l~~Gd~~~i~~ 51 (71)
T PF07883_consen 30 GTLTVDGERVELKPGDAIYIPP 51 (71)
T ss_dssp EEEEETTEEEEEETTEEEEEET
T ss_pred EEEEEccEEeEccCCEEEEECC
Confidence 3456999999999999999874
No 11
>PF12791 RsgI_N: Anti-sigma factor N-terminus; InterPro: IPR024449 The heat shock genes in Bacillus subtilis can be classified into several groups according to their regulation [], and the sigma gene, sigI, of Bacillus subtilis belongs to the group IV heat-shock response genes and has many orthologues in the bacterial phylum Firmicutes []. Regulation of sigma factor I is carried out by RsgI from the same operon. This entry represents the N-terminal cytoplasmic portion of RsgI ('upstream' of the single transmembrane helix) which has been shown to interact directly with Sigma-I [].
Probab=79.70 E-value=3.5 Score=26.55 Aligned_cols=30 Identities=27% Similarity=0.510 Sum_probs=25.5
Q ss_pred CceEEEEEeCCEEEEEcCCCEEEecccCCCCCCCeEE
Q 031957 101 EEIFAVVMIGSRQYIVFPGRFIYTQRLKGANVNDKVC 137 (150)
Q Consensus 101 ~~MYAIVeiGGKQYKVe~GdvI~VerLkgaEvGD~V~ 137 (150)
..-||||.+. .|+.+.|.+-.+.++||+|+
T Consensus 4 ~~~~aiVlT~-------dGeF~~ik~~~~~~vG~eI~ 33 (56)
T PF12791_consen 4 KKKYAIVLTP-------DGEFIKIKRKPGMEVGQEIE 33 (56)
T ss_pred cCCEEEEEcC-------CCcEEEEeCCCCCcccCEEE
Confidence 4568888886 68889999888899999998
No 12
>PF04351 PilP: Pilus assembly protein, PilP; InterPro: IPR007446 The PilP family are periplasmic proteins involved in the biogenesis of type IV pili [].; PDB: 2Y4Y_B 2Y4X_A 2IVW_A 2LC4_A.
Probab=78.72 E-value=2.8 Score=32.33 Aligned_cols=25 Identities=24% Similarity=0.275 Sum_probs=21.5
Q ss_pred CCceEEEEEe-CCEEEEEcCCCEEEe
Q 031957 100 REEIFAVVMI-GSRQYIVFPGRFIYT 124 (150)
Q Consensus 100 r~~MYAIVei-GGKQYKVe~GdvI~V 124 (150)
...++|+|+. +|+=|+|.+||+|=-
T Consensus 88 ~~~~~ALv~~pdg~v~~V~~G~yiG~ 113 (149)
T PF04351_consen 88 GGQPWALVQDPDGKVYRVKVGDYIGQ 113 (149)
T ss_dssp TTEEEEEEEE-TTEEEEEETTEEETT
T ss_pred CCEEEEEEEeCCCCEEEecCCCEecc
Confidence 3458999999 999999999998743
No 13
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=78.05 E-value=3.4 Score=31.93 Aligned_cols=22 Identities=18% Similarity=0.321 Sum_probs=19.6
Q ss_pred EEEEeCCEEEEEcCCCEEEecc
Q 031957 105 AVVMIGSRQYIVFPGRFIYTQR 126 (150)
Q Consensus 105 AIVeiGGKQYKVe~GdvI~Ver 126 (150)
+.++++|+.|.+.+||.++++.
T Consensus 139 ~~~~~~~~~~~l~~Gd~~~~~~ 160 (185)
T PRK09943 139 IVLTINGQDYHLVAGQSYAINT 160 (185)
T ss_pred EEEEECCEEEEecCCCEEEEcC
Confidence 4578999999999999999874
No 14
>COG3168 PilP Tfp pilus assembly protein PilP [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=71.98 E-value=4.1 Score=33.74 Aligned_cols=25 Identities=16% Similarity=0.248 Sum_probs=21.9
Q ss_pred CceEEEEEeCCEEEEEcCCCEEEec
Q 031957 101 EEIFAVVMIGSRQYIVFPGRFIYTQ 125 (150)
Q Consensus 101 ~~MYAIVeiGGKQYKVe~GdvI~Ve 125 (150)
...+|+|+.+|+-|+|..|++|=.+
T Consensus 108 ~~~~A~i~~~~~v~~V~vG~YlGqN 132 (170)
T COG3168 108 QGVSALIEAPGGVYRVRVGQYLGQN 132 (170)
T ss_pred CceEEEEEcCCceEEEeeccEeecc
Confidence 3479999999999999999999644
No 15
>cd04867 TGS_YchF_C TGS_YchF_C: This subfamily represents TGS domain-containing YchF GTP-binding protein, a universally conserved GTPase whose function is unknown. The N-terminal domain of the YchF protein belongs to the Obg-like family of GTPases, and some members of the family contain a C-terminal TGS domain. TGS is a small domain of about 50 amino acid residues with a predominantly beta-sheet structure. There is no direct information on the function of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role.
Probab=69.59 E-value=2.2 Score=31.55 Aligned_cols=20 Identities=20% Similarity=0.376 Sum_probs=17.8
Q ss_pred EEEEeCCEEEEEcCCCEEEe
Q 031957 105 AVVMIGSRQYIVFPGRFIYT 124 (150)
Q Consensus 105 AIVeiGGKQYKVe~GdvI~V 124 (150)
..++.-||+|.|+.||+|.+
T Consensus 62 Gkir~eGK~Yiv~DGDi~~f 81 (83)
T cd04867 62 GKYRQEGKDYVVQDGDIIFF 81 (83)
T ss_pred ChhhhhCCceEeeCCeEEEE
Confidence 46788999999999999986
No 16
>PF01050 MannoseP_isomer: Mannose-6-phosphate isomerase; InterPro: IPR001538 Mannose-6-phosphate isomerase or phosphomannose isomerase (5.3.1.8 from EC) (PMI) is the enzyme that catalyses the interconversion of mannose-6-phosphate and fructose-6-phosphate. In eukaryotes PMI is involved in the synthesis of GDP-mannose, a constituent of N- and O-linked glycans and GPI anchors and in prokaryotes it participates in a variety of pathways, including capsular polysaccharide biosynthesis and D-mannose metabolism. PMI's belong to the cupin superfamily whose functions range from isomerase and epimerase activities involved in the modification of cell wall carbohydrates in bacteria and plants, to non-enzymatic storage proteins in plant seeds, and transcription factors linked to congenital baldness in mammals []. Three classes of PMI have been defined []. The type II phosphomannose isomerases are bifunctional enzymes 5.3.1.8 from EC. This entry covers the isomerase region of the protein []. The guanosine diphospho-D-mannose pyrophosphorylase region is described in another InterPro entry (see IPR005836 from INTERPRO).; GO: 0016779 nucleotidyltransferase activity, 0005976 polysaccharide metabolic process
Probab=63.51 E-value=12 Score=29.45 Aligned_cols=23 Identities=22% Similarity=0.398 Sum_probs=20.5
Q ss_pred EEEEEeCCEEEEEcCCCEEEecc
Q 031957 104 FAVVMIGSRQYIVFPGRFIYTQR 126 (150)
Q Consensus 104 YAIVeiGGKQYKVe~GdvI~Ver 126 (150)
-|.|.++|+.+.|.+||.++|.+
T Consensus 94 ~a~v~~~~~~~~~~~g~sv~Ip~ 116 (151)
T PF01050_consen 94 TAEVTLDDEEFTLKEGDSVYIPR 116 (151)
T ss_pred eEEEEECCEEEEEcCCCEEEECC
Confidence 47788999999999999999863
No 17
>PRK13290 ectC L-ectoine synthase; Reviewed
Probab=63.33 E-value=16 Score=27.66 Aligned_cols=41 Identities=15% Similarity=0.203 Sum_probs=27.3
Q ss_pred EEE-e-CCEEEEEcCCCEEEecccCC---CCCCCeEEeeeccCCcce
Q 031957 106 VVM-I-GSRQYIVFPGRFIYTQRLKG---ANVNDKVCNFCAFSPLQF 147 (150)
Q Consensus 106 IVe-i-GGKQYKVe~GdvI~VerLkg---aEvGD~V~~~~~~~~~~~ 147 (150)
.+. + +|+.|.+.+||.++++.-.. .+. +..+..|.++|-+|
T Consensus 67 ~~~~i~~g~~~~L~aGD~i~~~~~~~H~~~N~-e~~~~l~v~tP~~~ 112 (125)
T PRK13290 67 EVEDLATGEVHPIRPGTMYALDKHDRHYLRAG-EDMRLVCVFNPPLT 112 (125)
T ss_pred EEEEcCCCEEEEeCCCeEEEECCCCcEEEEcC-CCEEEEEEECCCCC
Confidence 345 6 59999999999999874321 122 44456777777654
No 18
>TIGR03214 ura-cupin putative allantoin catabolism protein. This model represents a protein containing a tandem arrangement of cupin domains (N-terminal part of pfam07883 and C-terminal more distantly related to pfam00190). This protein is found in the vicinity of genes involved in the catabolism of allantoin, a breakdown product of urate and sometimes of urate iteslf. The distribution of pathway components in the genomes in which this family is observed suggests that the function is linked to the allantoate catabolism to glyoxylate pathway (GenProp0686) since it is sometimes found in genomes lacking any elements of the xanthine-to-allantoin pathways (e.g. in Enterococcus faecalis).
Probab=62.49 E-value=11 Score=31.48 Aligned_cols=23 Identities=17% Similarity=0.177 Sum_probs=20.1
Q ss_pred EEEEEeCCEEEEEcCCCEEEecc
Q 031957 104 FAVVMIGSRQYIVFPGRFIYTQR 126 (150)
Q Consensus 104 YAIVeiGGKQYKVe~GdvI~Ver 126 (150)
-+++.++|+-+.|++||+|++.-
T Consensus 210 ~G~~~~~g~~~~V~~GD~i~i~~ 232 (260)
T TIGR03214 210 KGVYNLDNNWVPVEAGDYIWMGA 232 (260)
T ss_pred eEEEEECCEEEEecCCCEEEECC
Confidence 46788999999999999999863
No 19
>PF06249 EutQ: Ethanolamine utilisation protein EutQ; InterPro: IPR010424 The eut operon of Salmonella typhimurium encodes proteins involved in the cobalamin-dependent degradation of ethanolamine. The role of EutQ in this process is unclear [].; PDB: 2PYT_B 3LWC_A.
Probab=62.13 E-value=9.8 Score=30.51 Aligned_cols=20 Identities=20% Similarity=0.464 Sum_probs=16.2
Q ss_pred EEeCCEEEEEcCCCEEEecc
Q 031957 107 VMIGSRQYIVFPGRFIYTQR 126 (150)
Q Consensus 107 VeiGGKQYKVe~GdvI~Ver 126 (150)
|.++|+-|...+||+|++.+
T Consensus 108 i~~~G~~~~A~~GDvi~iPk 127 (152)
T PF06249_consen 108 ISIDGQTVTAKPGDVIFIPK 127 (152)
T ss_dssp EEETTEEEEEETT-EEEE-T
T ss_pred EEECCEEEEEcCCcEEEECC
Confidence 45899999999999999875
No 20
>PF06071 YchF-GTPase_C: Protein of unknown function (DUF933); InterPro: IPR013029 This domain is found at the C terminus of family of conserved hypothetical proteins found in both prokaryotes and eukaryotes. While the function of these proteins is not known, the crystal structure of P44681 from SWISSPROT from Haemophilus influenzae has been determined []. This protein consists of three domains: an N-terminal domain which has a mononucleotide binding fold typical for the P-loop NTPases, a central domain which forms an alpha-helical coiled coil, and this C-terminal domain which is composed of a six-stranded half-barrel curved around an alpha helix. The central domain and this domain are topologically similar to RNA-binding proteins, while the N-terminal region contains the features typical of GTP-dependent molecular switches. The purified protein was capable of binding both double-stranded nucleic acid and GTP. It was suggested, therefore, that this protein might be part of a nucleoprotein complex and could function as a GTP-dependent translation factor.; PDB: 1NI3_A 1JAL_A 2DWQ_B 2DBY_A 2OHF_A.
Probab=59.08 E-value=1.9 Score=31.77 Aligned_cols=20 Identities=25% Similarity=0.396 Sum_probs=13.9
Q ss_pred EEEEeCCEEEEEcCCCEEEe
Q 031957 105 AVVMIGSRQYIVFPGRFIYT 124 (150)
Q Consensus 105 AIVeiGGKQYKVe~GdvI~V 124 (150)
..++.-||.|.|+.||+|.+
T Consensus 62 Gk~r~eGK~YivqDGDIi~f 81 (84)
T PF06071_consen 62 GKLRLEGKDYIVQDGDIIHF 81 (84)
T ss_dssp T-SEEEETT-B--TTEEEEE
T ss_pred CCccccCCceeEeCCCEEEE
Confidence 34678899999999999986
No 21
>KOG4317 consensus Predicted Zn-finger protein [Function unknown]
Probab=58.72 E-value=0.29 Score=44.32 Aligned_cols=75 Identities=4% Similarity=-0.155 Sum_probs=57.8
Q ss_pred CCCcccccccCCCCCCCCCCCCCchhhhhhcccCCchHHHhhhhccCCCCCceEEEEEeCCEEEEEcCCCEEEecccCCC
Q 031957 51 RPTFSFTHKFSQTEPPPVSEPEVEPEAALEAEAEPTTEVVESAAKEEPKREEIFAVVMIGSRQYIVFPGRFIYTQRLKGA 130 (150)
Q Consensus 51 r~~~~~~~~~s~se~~~v~~~~~~~e~~~epe~~~~~~i~e~v~~~~~~r~~MYAIVeiGGKQYKVe~GdvI~VerLkga 130 (150)
|+.|..+....+++++|+++.+++++. ...+...+ .+..+...++++ +|.|.++--|+.+.+.+--.-
T Consensus 240 ~~~~~Sa~e~ls~~a~v~~t~~~~~~~--------~g~~~~~~--~v~~v~~~~~~~--~G~~~~~lgdl~~~i~ga~k~ 307 (383)
T KOG4317|consen 240 RRSIQSASEGLSSEAQVIDTEQVKNLG--------GGLKFGLN--LVDDVICFLSLG--SGAMVCLLGDLQRLILGAIKE 307 (383)
T ss_pred ccCchhHHHHHHHHHHHHhhhhcCCCC--------ccccchhh--hhhhHhhhhccc--CceeEEecccHHHHHhhhhhh
Confidence 999999999999999999999998774 55555433 445677788998 999999999888887654323
Q ss_pred CCCCeEE
Q 031957 131 NVNDKVC 137 (150)
Q Consensus 131 EvGD~V~ 137 (150)
.+++++.
T Consensus 308 ~v~~e~r 314 (383)
T KOG4317|consen 308 VKSSSGR 314 (383)
T ss_pred hhchhHH
Confidence 4565544
No 22
>PRK11171 hypothetical protein; Provisional
Probab=57.24 E-value=15 Score=30.66 Aligned_cols=21 Identities=24% Similarity=0.327 Sum_probs=19.0
Q ss_pred EEEEeCCEEEEEcCCCEEEec
Q 031957 105 AVVMIGSRQYIVFPGRFIYTQ 125 (150)
Q Consensus 105 AIVeiGGKQYKVe~GdvI~Ve 125 (150)
.++.++|+-|.|++||.|++.
T Consensus 216 ~~~~~~~~~~~l~~GD~i~~~ 236 (266)
T PRK11171 216 GVYRLNNDWVEVEAGDFIWMR 236 (266)
T ss_pred EEEEECCEEEEeCCCCEEEEC
Confidence 567899999999999999985
No 23
>PRK15457 ethanolamine utilization protein EutQ; Provisional
Probab=56.11 E-value=16 Score=31.41 Aligned_cols=22 Identities=14% Similarity=0.152 Sum_probs=19.3
Q ss_pred EEEeCCEEEEEcCCCEEEeccc
Q 031957 106 VVMIGSRQYIVFPGRFIYTQRL 127 (150)
Q Consensus 106 IVeiGGKQYKVe~GdvI~VerL 127 (150)
.+.++|+.|.+.+||+|++.+=
T Consensus 187 ~l~IdG~t~~l~pGDvlfIPkG 208 (233)
T PRK15457 187 HVRHEGETMIAKAGDVMFIPKG 208 (233)
T ss_pred EEEECCEEEEeCCCcEEEECCC
Confidence 3678999999999999999763
No 24
>TIGR02988 YaaA_near_RecF S4 domain protein YaaA. This small protein has a single S4 domain (pfam01479), as do bacterial ribosomal protein S4, some pseudouridine synthases, tyrosyl-tRNA synthetases. The S4 domain may bind RNA. Members of this protein family are found almost exclusively in the Firmicutes, and almost invariably just a few nucleotides upstream of the gene for the DNA replication and repair protein RecF. The few members of this family that are not near recF are found instead near dnaA and/or dnaN, the usual neighbors of recF, near the origin of replication. The conserved location suggests a possible role in replication in the Firmicutes lineage.
Probab=55.88 E-value=8.7 Score=24.88 Aligned_cols=19 Identities=21% Similarity=0.469 Sum_probs=13.0
Q ss_pred EEeCCE-----EEEEcCCCEEEec
Q 031957 107 VMIGSR-----QYIVFPGRFIYTQ 125 (150)
Q Consensus 107 VeiGGK-----QYKVe~GdvI~Ve 125 (150)
|.++|+ .|+|..||.|.|+
T Consensus 36 V~VNg~~~~~~~~~l~~Gd~v~i~ 59 (59)
T TIGR02988 36 VLVNGELENRRGKKLYPGDVIEIP 59 (59)
T ss_pred EEECCEEccCCCCCCCCCCEEEeC
Confidence 455564 5678888888764
No 25
>PRK13501 transcriptional activator RhaR; Provisional
Probab=55.16 E-value=15 Score=29.64 Aligned_cols=24 Identities=17% Similarity=0.301 Sum_probs=20.5
Q ss_pred EEEEEeCCEEEEEcCCCEEEeccc
Q 031957 104 FAVVMIGSRQYIVFPGRFIYTQRL 127 (150)
Q Consensus 104 YAIVeiGGKQYKVe~GdvI~VerL 127 (150)
-+.+.++|+.|.+.+||.+.|..-
T Consensus 48 ~~~~~i~~~~~~l~~g~~~~I~p~ 71 (290)
T PRK13501 48 NGLHVLNDHPYRITCGDVFYIQAA 71 (290)
T ss_pred ceEEEECCeeeeecCCeEEEEcCC
Confidence 456889999999999999999643
No 26
>cd04092 mtEFG2_II_like mtEFG2_C: C-terminus of mitochondrial Elongation factor G2 (mtEFG2)-like proteins found in eukaryotes. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than that in prokaryotes, with both cytoplasmic and mitochondrial elongation factors and multiple isoforms being expressed in certain species. Eukaryotic EF-2 operates in the cytosolic protein synthesis machinery of eukaryotes, EF-Gs in protein synthesis in bacteria. Eukaryotic mtEFG1 proteins show significant homology to bacterial EF-Gs. No clear phenotype has been found for mutants in the yeast homologue of mtEFG2, MEF2. There are two forms of mtEFG present in mammals (designated mtEFG1s and mtEFG2s) mtEFG1s are n
Probab=54.68 E-value=16 Score=24.71 Aligned_cols=23 Identities=17% Similarity=0.180 Sum_probs=19.8
Q ss_pred EEcCCCEEEecccCCCCCCCeEE
Q 031957 115 IVFPGRFIYTQRLKGANVNDKVC 137 (150)
Q Consensus 115 KVe~GdvI~VerLkgaEvGD~V~ 137 (150)
.+..||++.+-.++++..||.+.
T Consensus 60 ~~~aGdI~~i~gl~~~~~Gdtl~ 82 (83)
T cd04092 60 SLSAGNIGVITGLKQTRTGDTLV 82 (83)
T ss_pred eeCCCCEEEEECCCCcccCCEEe
Confidence 57889999999998888999875
No 27
>PRK10296 DNA-binding transcriptional regulator ChbR; Provisional
Probab=51.30 E-value=23 Score=28.26 Aligned_cols=22 Identities=14% Similarity=0.295 Sum_probs=19.4
Q ss_pred EEEEeCCEEEEEcCCCEEEecc
Q 031957 105 AVVMIGSRQYIVFPGRFIYTQR 126 (150)
Q Consensus 105 AIVeiGGKQYKVe~GdvI~Ver 126 (150)
+.+.++|+.|.+.+||.+.|+.
T Consensus 54 ~~~~i~~~~~~l~~g~l~~i~p 75 (278)
T PRK10296 54 YYQEINGKRVLLERGDFVFIPL 75 (278)
T ss_pred EEEEECCEEEEECCCcEEEeCC
Confidence 5688999999999999999864
No 28
>PF10949 DUF2777: Protein of unknown function (DUF2777); InterPro: IPR024488 This family of proteins with unknown function appears to be restricted to Bacillaceae.
Probab=51.26 E-value=17 Score=30.21 Aligned_cols=22 Identities=23% Similarity=0.235 Sum_probs=20.0
Q ss_pred EEEeCCEEEEEcCCCEEEeccc
Q 031957 106 VVMIGSRQYIVFPGRFIYTQRL 127 (150)
Q Consensus 106 IVeiGGKQYKVe~GdvI~VerL 127 (150)
+|.++|++|.++.|+.|.+++-
T Consensus 67 ~v~~~~e~~~L~~ge~IRi~K~ 88 (185)
T PF10949_consen 67 IVSIDGEQIPLSNGESIRIRKK 88 (185)
T ss_pred eEEeCCeEEecCCCCEEEEeec
Confidence 7799999999999999998763
No 29
>PRK10371 DNA-binding transcriptional regulator MelR; Provisional
Probab=50.64 E-value=22 Score=29.58 Aligned_cols=22 Identities=9% Similarity=0.093 Sum_probs=19.7
Q ss_pred EEEEeCCEEEEEcCCCEEEecc
Q 031957 105 AVVMIGSRQYIVFPGRFIYTQR 126 (150)
Q Consensus 105 AIVeiGGKQYKVe~GdvI~Ver 126 (150)
+.+.++|++|.+.+||.+.++-
T Consensus 57 ~~~~i~g~~~~l~~Gd~ili~s 78 (302)
T PRK10371 57 VEYLINNEKVQINQGHITLFWA 78 (302)
T ss_pred EEEEECCEEEEEcCCcEEEEec
Confidence 5789999999999999999863
No 30
>PRK13500 transcriptional activator RhaR; Provisional
Probab=50.56 E-value=20 Score=29.71 Aligned_cols=23 Identities=17% Similarity=0.416 Sum_probs=20.0
Q ss_pred EEEEeCCEEEEEcCCCEEEeccc
Q 031957 105 AVVMIGSRQYIVFPGRFIYTQRL 127 (150)
Q Consensus 105 AIVeiGGKQYKVe~GdvI~VerL 127 (150)
+.+.++|+.|.+.+||+++|+.-
T Consensus 79 g~~~v~~~~~~l~~Gdl~~I~~~ 101 (312)
T PRK13500 79 GLHVLNDRPYRITRGDLFYIHAD 101 (312)
T ss_pred EEEEECCEEEeecCCeEEEECCC
Confidence 56788999999999999999753
No 31
>TIGR03021 pilP_fam type IV pilus biogenesis protein PilP. Members of this protein family are found in type IV pilus biogenesis loci and include proteins designated PilP.
Probab=49.19 E-value=21 Score=27.20 Aligned_cols=24 Identities=21% Similarity=0.293 Sum_probs=21.3
Q ss_pred CCCceEEEEEe-CCEEEEEcCCCEE
Q 031957 99 KREEIFAVVMI-GSRQYIVFPGRFI 122 (150)
Q Consensus 99 ~r~~MYAIVei-GGKQYKVe~GdvI 122 (150)
....|.|.++. ||++..|..||.|
T Consensus 77 ~~~~l~A~l~l~~G~~~~v~~G~~l 101 (119)
T TIGR03021 77 RGGRLTATLRLPGGREVDVQVGDSL 101 (119)
T ss_pred cCCCeEEEEEeCCCcEEEecCCCcc
Confidence 34669999999 9999999999987
No 32
>PF13510 Fer2_4: 2Fe-2S iron-sulfur cluster binding domain; PDB: 1Y56_A 3ADA_A 1VRQ_A 1X31_A 3AD9_A 3AD8_A 3AD7_A 2GAG_A 2GAH_A.
Probab=47.42 E-value=9.8 Score=26.55 Aligned_cols=17 Identities=29% Similarity=0.426 Sum_probs=14.5
Q ss_pred EEeCCEEEEEcCCCEEE
Q 031957 107 VMIGSRQYIVFPGRFIY 123 (150)
Q Consensus 107 VeiGGKQYKVe~GdvI~ 123 (150)
|.++||.|.|.+|+.|.
T Consensus 6 i~idG~~v~~~~G~til 22 (82)
T PF13510_consen 6 ITIDGKPVEVPPGETIL 22 (82)
T ss_dssp EEETTEEEEEEET-BHH
T ss_pred EEECCEEEEEcCCCHHH
Confidence 78999999999999875
No 33
>cd04088 EFG_mtEFG_II EFG_mtEFG_II: this subfamily represents the domain II of elongation factor G (EF-G) in bacteria and, the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2)_like proteins found in eukaryotes. During the process of peptide synthesis and tRNA site changes, the ribosome is moved along the mRNA a distance equal to one codon with the addition of each amino acid. In bacteria this translocation step is catalyzed by EF-G_GTP, which is hydrolyzed to provide the required energy. Thus, this action releases the uncharged tRNA from the P site and transfers the newly formed peptidyl-tRNA from the A site to the P site. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more compl
Probab=47.13 E-value=25 Score=23.49 Aligned_cols=23 Identities=22% Similarity=0.263 Sum_probs=19.2
Q ss_pred EEcCCCEEEecccCCCCCCCeEE
Q 031957 115 IVFPGRFIYTQRLKGANVNDKVC 137 (150)
Q Consensus 115 KVe~GdvI~VerLkgaEvGD~V~ 137 (150)
.+..||++.+..++++.+||.+.
T Consensus 60 ~~~aGdI~~i~g~~~~~~Gdtl~ 82 (83)
T cd04088 60 EAGAGDIGAVAGLKDTATGDTLC 82 (83)
T ss_pred EeCCCCEEEEECCCCCccCCEee
Confidence 46789999999988888999874
No 34
>TIGR00092 GTP-binding protein YchF. This predicted GTP-binding protein is found in a single copy in every complete bacterial genome, and is found in Eukaryotes. A more distantly related protein, separated from this model, is found in the archaea. It is known to bind GTP and double-stranded nucleic acid. It is suggested to belong to a nucleoprotein complex and act as a translation factor.
Probab=46.43 E-value=12 Score=33.55 Aligned_cols=20 Identities=15% Similarity=0.448 Sum_probs=17.9
Q ss_pred EEEEeCCEEEEEcCCCEEEe
Q 031957 105 AVVMIGSRQYIVFPGRFIYT 124 (150)
Q Consensus 105 AIVeiGGKQYKVe~GdvI~V 124 (150)
..++..||.|.|+.||+|++
T Consensus 345 Gk~r~eGK~YivqDGDIi~f 364 (368)
T TIGR00092 345 GLMRLEGKYYVVDDGDVLFF 364 (368)
T ss_pred CchhhcCCeEEeeCCeEEEE
Confidence 46788999999999999986
No 35
>PF00842 Ala_racemase_C: Alanine racemase, C-terminal domain; InterPro: IPR011079 Alanine racemase (5.1.1.1 from EC) plays a role in providing the D-alanine required for cell wall biosynthesis by isomerising L-alanine to D-alanine. Proteins contains this domain are found in both prokaryotic and eukaryotic proteins [,]. The molecular structure of alanine racemase from Bacillus stearothermophilus (Geobacillus stearothermophilus) was determined by X-ray crystallography to a resolution of 1.9 A []. The alanine racemase monomer is composed of two domains, an eight-stranded alpha/beta barrel at the N terminus, and a C-terminal domain essentially composed of beta-strand. The pyridoxal 5'-phosphate (PLP) cofactor lies in and above the mouth of the alpha/beta barrel and is covalently linked via an aldimine linkage to a lysine residue, which is at the C terminus of the first beta-strand of the alpha/beta barrel.; GO: 0008784 alanine racemase activity, 0006522 alanine metabolic process; PDB: 3HUR_A 4A3Q_B 3S46_A 1RCQ_A 3CO8_A 1VFT_B 1VFH_A 1VFS_B 2DY3_B 4ECL_C ....
Probab=46.00 E-value=56 Score=24.76 Aligned_cols=34 Identities=24% Similarity=0.451 Sum_probs=21.9
Q ss_pred EEEEeCCEEEEEcCCCE------EEeccc-CCCCCCCeEEee
Q 031957 105 AVVMIGSRQYIVFPGRF------IYTQRL-KGANVNDKVCNF 139 (150)
Q Consensus 105 AIVeiGGKQYKVe~Gdv------I~VerL-kgaEvGD~V~~~ 139 (150)
+-|.++|+.+.|- |++ |.+..+ .++++||+|+.+
T Consensus 53 ~~v~i~G~~~piv-G~v~MD~~~vdvt~~~~~v~~GD~V~l~ 93 (129)
T PF00842_consen 53 GYVLINGKRCPIV-GRVCMDMTMVDVTDIEPDVKVGDEVTLF 93 (129)
T ss_dssp EEEEETTEEEEEE-S---SS-EEEEESTSTST--TT-EEEEE
T ss_pred cEEEECCEEEEEE-EEEEeeEEEEEcCCCCCCCCCCCEEEEE
Confidence 4677899999875 443 667766 568999999844
No 36
>PF14525 AraC_binding_2: AraC-binding-like domain
Probab=45.51 E-value=35 Score=24.30 Aligned_cols=22 Identities=23% Similarity=0.373 Sum_probs=18.8
Q ss_pred EEEEeCCEEEEEcCCCEEEecc
Q 031957 105 AVVMIGSRQYIVFPGRFIYTQR 126 (150)
Q Consensus 105 AIVeiGGKQYKVe~GdvI~Ver 126 (150)
+.++.||+.+.+.+||.+.++-
T Consensus 66 ~~~~~~g~~~~~~pg~~~l~d~ 87 (172)
T PF14525_consen 66 ARIEQGGREVELAPGDVVLLDP 87 (172)
T ss_pred EEEEECCEEEEEcCCeEEEEcC
Confidence 4688999999999999888763
No 37
>PRK13502 transcriptional activator RhaR; Provisional
Probab=45.25 E-value=31 Score=27.53 Aligned_cols=23 Identities=17% Similarity=0.433 Sum_probs=20.1
Q ss_pred EEEEeCCEEEEEcCCCEEEeccc
Q 031957 105 AVVMIGSRQYIVFPGRFIYTQRL 127 (150)
Q Consensus 105 AIVeiGGKQYKVe~GdvI~VerL 127 (150)
..+.++|+.|.+.+||++.|+.-
T Consensus 49 ~~~~i~~~~~~l~~g~l~li~~~ 71 (282)
T PRK13502 49 GLHVLNERPYRITRGDLFYIRAE 71 (282)
T ss_pred EEEEECCEEEeecCCcEEEECCC
Confidence 56888999999999999998753
No 38
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=43.88 E-value=33 Score=27.51 Aligned_cols=22 Identities=18% Similarity=0.243 Sum_probs=19.2
Q ss_pred EEEEeCCEEEEEcCCCEEEecc
Q 031957 105 AVVMIGSRQYIVFPGRFIYTQR 126 (150)
Q Consensus 105 AIVeiGGKQYKVe~GdvI~Ver 126 (150)
+.++.+|+.|.|.+||.+.++.
T Consensus 82 ~~~~~~g~~~~l~~G~~~l~~~ 103 (302)
T PRK09685 82 AIIEQDDRQVQLAAGDITLIDA 103 (302)
T ss_pred EEEEECCeEEEEcCCCEEEEEC
Confidence 4578899999999999999864
No 39
>TIGR02297 HpaA 4-hydroxyphenylacetate catabolism regulatory protein HpaA. This putative transcriptional regulator, which contains both the substrate-binding, dimerization domain (pfam02311) and the helix-turn-helix DNA-binding domain (pfam00165) of the AraC famil, is located proximal to genes of the 4-hydroxyphenylacetate catabolism pathway.
Probab=43.79 E-value=31 Score=27.42 Aligned_cols=23 Identities=13% Similarity=0.270 Sum_probs=19.9
Q ss_pred EEEEeCCEEEEEcCCCEEEeccc
Q 031957 105 AVVMIGSRQYIVFPGRFIYTQRL 127 (150)
Q Consensus 105 AIVeiGGKQYKVe~GdvI~VerL 127 (150)
+.+.++|+.|.+.+||.+.++.-
T Consensus 55 ~~~~~~~~~~~l~~g~~~ii~~~ 77 (287)
T TIGR02297 55 IALQLDEHEYSEYAPCFFLTPPS 77 (287)
T ss_pred eEEEECCEEEEecCCeEEEeCCC
Confidence 56889999999999999998743
No 40
>PF11699 CENP-C_C: Mif2/CENP-C like; PDB: 2VPV_B.
Probab=43.17 E-value=34 Score=24.69 Aligned_cols=23 Identities=22% Similarity=0.226 Sum_probs=17.7
Q ss_pred EEEeCCEEEEEcCCCEEEecccC
Q 031957 106 VVMIGSRQYIVFPGRFIYTQRLK 128 (150)
Q Consensus 106 IVeiGGKQYKVe~GdvI~VerLk 128 (150)
-|.+++.+|.|..|+..+|++=.
T Consensus 45 ~Vti~~~~f~v~~G~~F~VP~gN 67 (85)
T PF11699_consen 45 EVTIHETSFVVTKGGSFQVPRGN 67 (85)
T ss_dssp EEEETTEEEEEETT-EEEE-TT-
T ss_pred EEEEcCcEEEEeCCCEEEECCCC
Confidence 36789999999999999998743
No 41
>PF01455 HupF_HypC: HupF/HypC family; InterPro: IPR001109 The large subunit of [NiFe]-hydrogenase, as well as other nickel metalloenzymes, is synthesised as a precursor devoid of the metalloenzyme active site. This precursor then undergoes a complex post-translational maturation process that requires a number of accessory proteins. The hydrogenase expression/formation proteins (HupF/HypC) form a family of small proteins that are hydrogenase precursor-specific chaperones required for this maturation process []. They are believed to keep the hydrogenase precursor in a conformation accessible for metal incorporation [, ].; PDB: 3D3R_A 2Z1C_C 2OT2_A.
Probab=42.95 E-value=52 Score=22.80 Aligned_cols=31 Identities=26% Similarity=0.179 Sum_probs=18.8
Q ss_pred CceEEEEEeCCEEEEEcCCCEEEecccCCCCCCCeEE
Q 031957 101 EEIFAVVMIGSRQYIVFPGRFIYTQRLKGANVNDKVC 137 (150)
Q Consensus 101 ~~MYAIVeiGGKQYKVe~GdvI~VerLkgaEvGD~V~ 137 (150)
.+..|+|+.+|.+-+| .+..+.++.+||-|.
T Consensus 15 ~~~~A~v~~~G~~~~V------~~~lv~~v~~Gd~VL 45 (68)
T PF01455_consen 15 DGGMAVVDFGGVRREV------SLALVPDVKVGDYVL 45 (68)
T ss_dssp TTTEEEEEETTEEEEE------EGTTCTSB-TT-EEE
T ss_pred CCCEEEEEcCCcEEEE------EEEEeCCCCCCCEEE
Confidence 4689999999988765 233343344555444
No 42
>TIGR01479 GMP_PMI mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase. This enzyme is known to be bifunctional, as both mannose-6-phosphate isomerase (EC 5.3.1.8) (PMI) and mannose-1-phosphate guanylyltransferase (EC 2.7.7.22) in Pseudomonas aeruginosa, Xanthomonas campestris, and Gluconacetobacter xylinus. The literature on the enzyme from E. coli attributes mannose-6-phosphate isomerase activity to an adjacent gene, but the present sequence has not been shown to lack the activity. The PMI domain is C-terminal.
Probab=42.02 E-value=35 Score=30.69 Aligned_cols=41 Identities=17% Similarity=-0.024 Sum_probs=28.0
Q ss_pred EEEEEeCCEEEEEcCCCEEEecccC---CCCCCCeEE-eeeccCC
Q 031957 104 FAVVMIGSRQYIVFPGRFIYTQRLK---GANVNDKVC-NFCAFSP 144 (150)
Q Consensus 104 YAIVeiGGKQYKVe~GdvI~VerLk---gaEvGD~V~-~~~~~~~ 144 (150)
-+.|.++|+.|.+.+||.++++.-. =.+.|++-. ..+...|
T Consensus 407 ~~~v~~dg~~~~l~~GDsi~ip~~~~H~~~N~g~~~~~~i~v~~~ 451 (468)
T TIGR01479 407 TARVTIGDETLLLTENESTYIPLGVIHRLENPGKIPLELIEVQSG 451 (468)
T ss_pred EEEEEECCEEEEecCCCEEEECCCCcEEEEcCCCCCEEEEEEEcC
Confidence 3568999999999999999987532 125665444 4444443
No 43
>cd03691 BipA_TypA_II BipA_TypA_II: domain II of BipA (also called TypA) having homology to domain II of the elongation factors (EFs) EF-G and EF-Tu. BipA is a highly conserved protein with global regulatory properties in Escherichia coli. BipA is phosphorylated on a tyrosine residue under some cellular conditions. Mutants show altered regulation of some pathways. BipA functions as a translation factor that is required specifically for the expression of the transcriptional modulator Fis. BipA binds to ribosomes at a site that coincides with that of EF-G and has a GTPase activity that is sensitive to high GDP:GTP ratios and, is stimulated by 70S ribosomes programmed with mRNA and aminoacylated tRNAs. The growth rate-dependent induction of BipA allows the efficient expression of Fis, thereby modulating a range of downstream processes, including DNA metabolism and type III secretion.
Probab=41.97 E-value=30 Score=23.30 Aligned_cols=22 Identities=9% Similarity=0.235 Sum_probs=19.1
Q ss_pred EEcCCCEEEecccCCCCCCCeE
Q 031957 115 IVFPGRFIYTQRLKGANVNDKV 136 (150)
Q Consensus 115 KVe~GdvI~VerLkgaEvGD~V 136 (150)
.+..||++.+.+++++.+||.+
T Consensus 63 ~~~aG~I~~i~gl~~~~~Gdtl 84 (86)
T cd03691 63 EAEAGDIVAIAGIEDITIGDTI 84 (86)
T ss_pred EECCCCEEEEECCCCCccccee
Confidence 3688999999999888899986
No 44
>PRK15460 cpsB mannose-1-phosphate guanyltransferase; Provisional
Probab=41.72 E-value=35 Score=31.43 Aligned_cols=36 Identities=17% Similarity=-0.065 Sum_probs=25.4
Q ss_pred EEEEeCCEEEEEcCCCEEEecccC---CCCCCCeEE-eee
Q 031957 105 AVVMIGSRQYIVFPGRFIYTQRLK---GANVNDKVC-NFC 140 (150)
Q Consensus 105 AIVeiGGKQYKVe~GdvI~VerLk---gaEvGD~V~-~~~ 140 (150)
+.|.++|+.|.+.+||.|+++.-. -.|.|++-. ..|
T Consensus 417 ~~v~idg~~~~L~~GDSi~ip~g~~H~~~N~g~~~l~iI~ 456 (478)
T PRK15460 417 AKVTIDGDIKLLGENESIYIPLGATHCLENPGKIPLDLIE 456 (478)
T ss_pred EEEEECCEEEEecCCCEEEECCCCcEEEEcCCCCCEEEEE
Confidence 567899999999999999986431 025666443 444
No 45
>PRK09601 GTP-binding protein YchF; Reviewed
Probab=41.40 E-value=19 Score=32.19 Aligned_cols=18 Identities=28% Similarity=0.447 Sum_probs=15.8
Q ss_pred EEeCCEEEEEcCCCEEEe
Q 031957 107 VMIGSRQYIVFPGRFIYT 124 (150)
Q Consensus 107 VeiGGKQYKVe~GdvI~V 124 (150)
+++-||.|.|+.||+|.+
T Consensus 343 ~rleGkdY~v~DGDIi~f 360 (364)
T PRK09601 343 VRLEGKDYIVQDGDVMHF 360 (364)
T ss_pred eeccCCceEecCCCEEEE
Confidence 357799999999999987
No 46
>smart00835 Cupin_1 Cupin. This family represents the conserved barrel domain of the 'cupin' superfamily ('cupa' is the Latin term for a small barrel). This family contains 11S and 7S plant seed storage proteins, and germins. Plant seed storage proteins provide the major nitrogen source for the developing plant.
Probab=40.92 E-value=32 Score=25.54 Aligned_cols=21 Identities=10% Similarity=-0.009 Sum_probs=16.4
Q ss_pred EEEeCCE------EEEEcCCCEEEecc
Q 031957 106 VVMIGSR------QYIVFPGRFIYTQR 126 (150)
Q Consensus 106 IVeiGGK------QYKVe~GdvI~Ver 126 (150)
.+.++++ .+++++||.++++.
T Consensus 63 ~~~~~~~~~~~~~~~~l~~GD~~~ip~ 89 (146)
T smart00835 63 RVGVVDPNGNKVYDARLREGDVFVVPQ 89 (146)
T ss_pred EEEEEeCCCCeEEEEEecCCCEEEECC
Confidence 3446555 89999999999975
No 47
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=39.56 E-value=36 Score=27.35 Aligned_cols=22 Identities=23% Similarity=0.572 Sum_probs=19.1
Q ss_pred EEEEeCCEEEEEcCCCEEEecc
Q 031957 105 AVVMIGSRQYIVFPGRFIYTQR 126 (150)
Q Consensus 105 AIVeiGGKQYKVe~GdvI~Ver 126 (150)
+.+.+||+.|.+++||.+.+..
T Consensus 60 ~~~~~~~~~~~~~~g~~i~i~p 81 (290)
T PRK10572 60 GVIFNGGRAFVCRPGDLLLFPP 81 (290)
T ss_pred EEEecCCeeEecCCCCEEEECC
Confidence 4477999999999999999874
No 48
>PRK11171 hypothetical protein; Provisional
Probab=36.33 E-value=52 Score=27.47 Aligned_cols=22 Identities=9% Similarity=0.249 Sum_probs=19.6
Q ss_pred EEEEeCCEEEEEcCCCEEEecc
Q 031957 105 AVVMIGSRQYIVFPGRFIYTQR 126 (150)
Q Consensus 105 AIVeiGGKQYKVe~GdvI~Ver 126 (150)
..|+++|+.|.+.+||.++++.
T Consensus 94 l~v~~~g~~~~L~~GDsi~~p~ 115 (266)
T PRK11171 94 ITLTLEGKTHALSEGGYAYLPP 115 (266)
T ss_pred EEEEECCEEEEECCCCEEEECC
Confidence 5678999999999999999874
No 49
>PHA02885 putative interleukin binding protein; Provisional
Probab=35.95 E-value=22 Score=28.28 Aligned_cols=21 Identities=33% Similarity=0.676 Sum_probs=18.9
Q ss_pred cCCCEEEecccCCCCCCCeEE
Q 031957 117 FPGRFIYTQRLKGANVNDKVC 137 (150)
Q Consensus 117 e~GdvI~VerLkgaEvGD~V~ 137 (150)
++|.+|+++.+.|+++|+.++
T Consensus 72 spgeyif~enl~g~~egqd~t 92 (135)
T PHA02885 72 SPGEYIFIENLEGANEGQDNT 92 (135)
T ss_pred CCcceeeeecccccccCccch
Confidence 689999999999999998775
No 50
>KOG2925 consensus Predicted translation initiation factor related to eIF-1A [Translation, ribosomal structure and biogenesis]
Probab=35.68 E-value=35 Score=28.29 Aligned_cols=44 Identities=14% Similarity=0.244 Sum_probs=34.0
Q ss_pred CceEEEEEeCCEEE------------EEcCCCEEEecccCCCCCCCeEE---eeeccCC
Q 031957 101 EEIFAVVMIGSRQY------------IVFPGRFIYTQRLKGANVNDKVC---NFCAFSP 144 (150)
Q Consensus 101 ~~MYAIVeiGGKQY------------KVe~GdvI~VerLkgaEvGD~V~---~~~~~~~ 144 (150)
...+-|+..+|+-| |+.-|+++.|+.+...+-|++|. -|+++.+
T Consensus 34 snlheV~danGq~~lvsmP~KfRksiWiRRg~FvvVdpiee~~~g~KVkgeI~yVl~~d 92 (167)
T KOG2925|consen 34 SNLHEVMDANGQNSLVSMPAKFRKSIWIRRGSFVVVDPIEEEKSGSKVKGEICYVLFFD 92 (167)
T ss_pred cchhhhhhcCCceeeeeCCHhhhhceEEeeCCEEEEccccccccCCccceEEEEEEccH
Confidence 34667777788776 56689999999997556799999 5667776
No 51
>PF05899 Cupin_3: Protein of unknown function (DUF861); InterPro: IPR008579 The function of the proteins in this entry are unknown. They contain the conserved barrel domain of the 'cupin' superfamily and members are specific to plants and bacteria.; PDB: 1RC6_A 3MYX_A 1O5U_A 2K9Z_A 1LKN_A 3ES4_A 1SFN_B 3BCW_A.
Probab=35.46 E-value=64 Score=21.88 Aligned_cols=17 Identities=6% Similarity=0.151 Sum_probs=14.7
Q ss_pred CCEEEEEcCCCEEEecc
Q 031957 110 GSRQYIVFPGRFIYTQR 126 (150)
Q Consensus 110 GGKQYKVe~GdvI~Ver 126 (150)
+|..+.+.+||.+++.+
T Consensus 42 ~G~~~~~~aGD~~~~p~ 58 (74)
T PF05899_consen 42 DGETVTFKAGDAFFLPK 58 (74)
T ss_dssp TTEEEEEETTEEEEE-T
T ss_pred CCCEEEEcCCcEEEECC
Confidence 99999999999999753
No 52
>PF11213 DUF3006: Protein of unknown function (DUF3006); InterPro: IPR021377 This family of proteins has no known function.
Probab=34.96 E-value=61 Score=22.17 Aligned_cols=12 Identities=17% Similarity=0.260 Sum_probs=10.2
Q ss_pred ceEEEEEeCCEE
Q 031957 102 EIFAVVMIGSRQ 113 (150)
Q Consensus 102 ~MYAIVeiGGKQ 113 (150)
+=|||++.++.+
T Consensus 9 ~~~AVl~~~~~~ 20 (71)
T PF11213_consen 9 GDYAVLELEDGE 20 (71)
T ss_pred CCEEEEEECCCe
Confidence 569999999877
No 53
>PF04347 FliO: Flagellar biosynthesis protein, FliO; InterPro: IPR022781 FliO is an essential component of the flagellum-specific protein export apparatus []. It is an integral membrane protein. Its precise molecular function is unknown. FliO is a short protein found in flagellar biosynthesis operons, and which contains a highly hydrophobic N-terminal sequence followed generally by two basic amino acids. This region is reminiscent of but distinct from the twin-arginine translocation signal sequence. Some instances of this gene have been names "FliZ" but phylogenetic tree building supports a single FliO family.; GO: 0043064 flagellum organization, 0016021 integral to membrane, 0019861 flagellum
Probab=34.57 E-value=42 Score=22.77 Aligned_cols=26 Identities=15% Similarity=0.224 Sum_probs=18.8
Q ss_pred ceEEEEEeCCEEEEEcCCC--EEEeccc
Q 031957 102 EIFAVVMIGSRQYIVFPGR--FIYTQRL 127 (150)
Q Consensus 102 ~MYAIVeiGGKQYKVe~Gd--vI~VerL 127 (150)
..-.||++||++|-+-.|+ +-.+..+
T Consensus 30 ~~l~lV~v~~~~~Llgvt~~~i~~L~~l 57 (84)
T PF04347_consen 30 KSLVLVEVGGRYLLLGVTDGGITLLAEL 57 (84)
T ss_pred CEEEEEEECCEEEEEEECCCCCEEEEEe
Confidence 3567999999999986664 4445555
No 54
>PRK13503 transcriptional activator RhaS; Provisional
Probab=34.44 E-value=29 Score=27.37 Aligned_cols=22 Identities=9% Similarity=0.344 Sum_probs=19.4
Q ss_pred EEEEeCCEEEEEcCCCEEEecc
Q 031957 105 AVVMIGSRQYIVFPGRFIYTQR 126 (150)
Q Consensus 105 AIVeiGGKQYKVe~GdvI~Ver 126 (150)
+.+.++|++|.+.+||.+.|..
T Consensus 46 ~~~~i~~~~~~l~~g~~~~i~~ 67 (278)
T PRK13503 46 GIHVFNGQPYTLSGGTVCFVRD 67 (278)
T ss_pred eeeEecCCcccccCCcEEEECC
Confidence 5678999999999999999954
No 55
>TIGR01222 minC septum site-determining protein MinC. The minC protein assists in correct placement of the septum for cell division by inhibiting septum formation at other sites. Homologs from Deinocoocus, Synechocystis PCC 6803, and Helicobacter pylori do not hit the full length of the model and score between the trusted and noise cutoffs.
Probab=34.25 E-value=58 Score=26.45 Aligned_cols=25 Identities=20% Similarity=0.211 Sum_probs=20.1
Q ss_pred CCEEEEEcCCCEEEecccCCCCCCCeEE
Q 031957 110 GSRQYIVFPGRFIYTQRLKGANVNDKVC 137 (150)
Q Consensus 110 GGKQYKVe~GdvI~VerLkgaEvGD~V~ 137 (150)
.|+|.....||+|.+ .++++|.+|.
T Consensus 121 SGQ~i~~~~gDliil---G~Vn~GAeVi 145 (217)
T TIGR01222 121 SGQQIYAKHGDLIVL---GNVNAGAEVL 145 (217)
T ss_pred CCCEEEecCCCEEEE---CCCCCCCEEE
Confidence 468888877999984 5678999988
No 56
>COG1917 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]
Probab=34.02 E-value=52 Score=23.73 Aligned_cols=21 Identities=14% Similarity=0.140 Sum_probs=17.7
Q ss_pred EEEeCCEEEEEcCCCEEEecc
Q 031957 106 VVMIGSRQYIVFPGRFIYTQR 126 (150)
Q Consensus 106 IVeiGGKQYKVe~GdvI~Ver 126 (150)
.+.++|.=+.+.+||+|+++.
T Consensus 76 ~~~~~g~~~~l~~Gd~i~ip~ 96 (131)
T COG1917 76 TVQLEGEKKELKAGDVIIIPP 96 (131)
T ss_pred EEEecCCceEecCCCEEEECC
Confidence 356778999999999999875
No 57
>PF00717 Peptidase_S24: Peptidase S24-like peptidase classification. ; InterPro: IPR019759 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ].; PDB: 1KCA_H 3BDN_A 1F39_A 1JHH_A 1JHE_B 3JSP_A 1JHF_B 1JHC_A 3JSO_B 1B12_D ....
Probab=32.82 E-value=56 Score=20.66 Aligned_cols=10 Identities=10% Similarity=0.029 Sum_probs=3.4
Q ss_pred EEcCCCEEEe
Q 031957 115 IVFPGRFIYT 124 (150)
Q Consensus 115 KVe~GdvI~V 124 (150)
++..||.+.+
T Consensus 24 ~~~~gdivv~ 33 (70)
T PF00717_consen 24 EPKDGDIVVV 33 (70)
T ss_dssp ---TTSEEEE
T ss_pred CCccCeEEEE
Confidence 4445554444
No 58
>PF08838 DUF1811: Protein of unknown function (DUF1811); InterPro: IPR014938 This entry consists uncharacterised bacterial proteins. Some of the proteins are annotated as being transcriptional regulators (see Q4MQL7 from SWISSPROT, Q65MA2 from SWISSPROT). The structure of one of the proteins has revealed a beta-barrel like structure with helix-turn-helix like motif. ; PDB: 2YXY_A 1SF9_A.
Probab=32.58 E-value=35 Score=26.16 Aligned_cols=19 Identities=21% Similarity=0.443 Sum_probs=15.1
Q ss_pred CEEEEEc--CCCEEEecccCC
Q 031957 111 SRQYIVF--PGRFIYTQRLKG 129 (150)
Q Consensus 111 GKQYKVe--~GdvI~VerLkg 129 (150)
|+.|+|. +|+...|++|+|
T Consensus 58 G~~Y~i~~~~~~~F~V~ylnG 78 (102)
T PF08838_consen 58 GEIYRIEGDPEEYFKVDYLNG 78 (102)
T ss_dssp T-EEEETTCCCEEEEEEEEET
T ss_pred CCEEEecCCCCceEEEEEEee
Confidence 6888887 778888999987
No 59
>cd03689 RF3_II RF3_II: this subfamily represents the domain II of bacterial Release Factor 3 (RF3). Termination of protein synthesis by the ribosome requires two release factor (RF) classes. The class II RF3 is a GTPase that removes class I RFs (RF1 or RF2) from the ribosome after release of the nascent polypeptide. RF3 in the GDP state binds to the ribosomal class I RF complex, followed by an exchange of GDP for GTP and release of the class I RF. Sequence comparison of class II release factors with elongation factors shows that prokaryotic RF3 is more similar to EF-G whereas eukaryotic eRF3 is more similar to eEF1A, implying that their precise function may differ.
Probab=31.77 E-value=58 Score=22.59 Aligned_cols=22 Identities=18% Similarity=0.344 Sum_probs=19.0
Q ss_pred EcCCCEEEecccCCCCCCCeEE
Q 031957 116 VFPGRFIYTQRLKGANVNDKVC 137 (150)
Q Consensus 116 Ve~GdvI~VerLkgaEvGD~V~ 137 (150)
+..||.+.+-+++++..||.+.
T Consensus 62 a~aGdIv~v~gl~~~~~Gdtl~ 83 (85)
T cd03689 62 AYPGDIIGLVNPGNFQIGDTLT 83 (85)
T ss_pred ECCCCEEEEECCCCccccCEee
Confidence 6789999999998888999874
No 60
>smart00363 S4 S4 RNA-binding domain.
Probab=31.36 E-value=85 Score=18.12 Aligned_cols=21 Identities=29% Similarity=0.441 Sum_probs=13.3
Q ss_pred EEEeCCEEE-----EEcCCCEEEecc
Q 031957 106 VVMIGSRQY-----IVFPGRFIYTQR 126 (150)
Q Consensus 106 IVeiGGKQY-----KVe~GdvI~Ver 126 (150)
-|.++|+.- ++..||.|.+..
T Consensus 27 ~i~vng~~~~~~~~~l~~gd~i~~~~ 52 (60)
T smart00363 27 RVKVNGKKVTKPSYIVKPGDVISVRG 52 (60)
T ss_pred CEEECCEEecCCCeEeCCCCEEEEcc
Confidence 355666543 677777777654
No 61
>KOG2757 consensus Mannose-6-phosphate isomerase [Carbohydrate transport and metabolism]
Probab=30.79 E-value=74 Score=29.66 Aligned_cols=44 Identities=16% Similarity=0.271 Sum_probs=30.7
Q ss_pred EEEEEeC-CEEEEEcCCCEEEecccCC--CCC-CCeEEeeeccCCcce
Q 031957 104 FAVVMIG-SRQYIVFPGRFIYTQRLKG--ANV-NDKVCNFCAFSPLQF 147 (150)
Q Consensus 104 YAIVeiG-GKQYKVe~GdvI~VerLkg--aEv-GD~V~~~~~~~~~~~ 147 (150)
-++++.+ +.++.|..||+++|.--.. .+. .|.+..|-+|+++-+
T Consensus 363 ~g~l~~~t~~~~~v~rG~V~fI~a~~~i~~~~~sd~~~~yrAf~~~r~ 410 (411)
T KOG2757|consen 363 SGILKTDTDSKILVNRGDVLFIPANHPIHLSSSSDPFLGYRAFSNSRF 410 (411)
T ss_pred ceEEecCCCCceeeccCcEEEEcCCCCceeeccCcceeeeeccccccC
Confidence 3677888 9999999999999863221 222 333558888887754
No 62
>TIGR01713 typeII_sec_gspC general secretion pathway protein C. This model represents GspC, protein C of the main terminal branch of the general secretion pathway, also called type II secretion. This system transports folded proteins across the bacterial outer membrane and is widely distributed in Gram-negative pathogens.
Probab=30.40 E-value=50 Score=27.85 Aligned_cols=24 Identities=21% Similarity=0.069 Sum_probs=21.0
Q ss_pred CCceEEEEEeCCEEEEEcCCCEEE
Q 031957 100 REEIFAVVMIGSRQYIVFPGRFIY 123 (150)
Q Consensus 100 r~~MYAIVeiGGKQYKVe~GdvI~ 123 (150)
...-+|||+.+|+|.....||.|.
T Consensus 94 ~~~s~AiI~~~~~q~~y~iGd~i~ 117 (259)
T TIGR01713 94 RIRSIAIIEEGSEQVSLGINESFE 117 (259)
T ss_pred CcceEEEEEeCCeEEEEeCCCCcC
Confidence 355789999999999999999875
No 63
>PF10618 Tail_tube: Phage tail tube protein; InterPro: IPR019596 This entry is represented by Bacteriophage Mu, GpM tail tube protein. Bacteriophage Mu has an eicosahedral head and contractile tail. The tail is composed of an outer sheath and an inner tube.
Probab=30.07 E-value=53 Score=24.85 Aligned_cols=24 Identities=17% Similarity=0.083 Sum_probs=19.3
Q ss_pred EEEEEeCCEEEEEcCCCEEEeccc
Q 031957 104 FAVVMIGSRQYIVFPGRFIYTQRL 127 (150)
Q Consensus 104 YAIVeiGGKQYKVe~GdvI~VerL 127 (150)
-|.|+++|+||.+..|=.+..-..
T Consensus 8 ~a~i~vdG~~l~~~~g~~~~~gg~ 31 (119)
T PF10618_consen 8 TAYIRVDGQQLPVKGGATYNPGGV 31 (119)
T ss_pred EEEEEECCEEEEccCCeEECCCCe
Confidence 589999999999999866664433
No 64
>PRK13415 flagella biosynthesis protein FliZ; Provisional
Probab=30.00 E-value=29 Score=29.63 Aligned_cols=33 Identities=21% Similarity=0.257 Sum_probs=22.7
Q ss_pred eEEEEEeCCEEEEEcCCCEEEecccCCCCCCCeEE
Q 031957 103 IFAVVMIGSRQYIVFPGRFIYTQRLKGANVNDKVC 137 (150)
Q Consensus 103 MYAIVeiGGKQYKVe~GdvI~VerLkgaEvGD~V~ 137 (150)
--.||++|+++|-|-.||- |..|...+..++|+
T Consensus 115 ~VvlVeVG~k~LVvGV~ds--I~lL~Ei~d~~eve 147 (219)
T PRK13415 115 SVQLIKVGNRVLVVGVGES--IQLLKEIEDEKEIE 147 (219)
T ss_pred EEEEEEECCEEEEEEecCc--eeEeeecCCHHHHH
Confidence 3468999999999999984 55665334443443
No 65
>TIGR00074 hypC_hupF hydrogenase assembly chaperone HypC/HupF. An additional proposed function is to shuttle the iron atom that has been liganded at the HypC/HypD complex to the precursor of the large hydrogenase (HycE) subunit. PubMed:12441107.
Probab=29.90 E-value=84 Score=22.45 Aligned_cols=31 Identities=19% Similarity=0.019 Sum_probs=20.4
Q ss_pred eEEEEEeCCEEEEEcCCCEEEecccCCCCCCCeEEee
Q 031957 103 IFAVVMIGSRQYIVFPGRFIYTQRLKGANVNDKVCNF 139 (150)
Q Consensus 103 MYAIVeiGGKQYKVe~GdvI~VerLkgaEvGD~V~~~ 139 (150)
.+|+|+.+|-+-.|. +..+..+.+||-|.++
T Consensus 15 ~~A~v~~~G~~~~v~------l~lv~~~~vGD~VLVH 45 (76)
T TIGR00074 15 NIALVEFCGIKRDVS------LDLVGEVKVGDYVLVH 45 (76)
T ss_pred CEEEEEcCCeEEEEE------EEeeCCCCCCCEEEEe
Confidence 469999999876643 3334446677766643
No 66
>TIGR03214 ura-cupin putative allantoin catabolism protein. This model represents a protein containing a tandem arrangement of cupin domains (N-terminal part of pfam07883 and C-terminal more distantly related to pfam00190). This protein is found in the vicinity of genes involved in the catabolism of allantoin, a breakdown product of urate and sometimes of urate iteslf. The distribution of pathway components in the genomes in which this family is observed suggests that the function is linked to the allantoate catabolism to glyoxylate pathway (GenProp0686) since it is sometimes found in genomes lacking any elements of the xanthine-to-allantoin pathways (e.g. in Enterococcus faecalis).
Probab=29.81 E-value=78 Score=26.42 Aligned_cols=22 Identities=14% Similarity=0.129 Sum_probs=19.2
Q ss_pred EEEEeCCEEEEEcCCCEEEecc
Q 031957 105 AVVMIGSRQYIVFPGRFIYTQR 126 (150)
Q Consensus 105 AIVeiGGKQYKVe~GdvI~Ver 126 (150)
..|.++|+-|.+.+||.++++.
T Consensus 91 l~v~~~g~~~~L~~Gd~~y~pa 112 (260)
T TIGR03214 91 VNVTAEGETHELREGGYAYLPP 112 (260)
T ss_pred EEEEECCEEEEECCCCEEEECC
Confidence 4578999999999999999863
No 67
>PF01479 S4: S4 domain; InterPro: IPR002942 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterised, small proteins that may be involved in translation regulation []. The S4 domain probably mediates binding to RNA.; GO: 0003723 RNA binding; PDB: 3BBU_A 1DM9_B 2K6P_A 3U5G_E 3U5C_E 3IZB_D 2XZM_D 2XZN_D 3O30_E 3O2Z_E ....
Probab=29.09 E-value=45 Score=20.28 Aligned_cols=17 Identities=29% Similarity=0.393 Sum_probs=11.2
Q ss_pred EEEeCCEEEE-----EcCCCEE
Q 031957 106 VVMIGSRQYI-----VFPGRFI 122 (150)
Q Consensus 106 IVeiGGKQYK-----Ve~GdvI 122 (150)
-|.++|+.-+ |.+||+|
T Consensus 27 ~V~VNg~~v~~~~~~v~~~d~I 48 (48)
T PF01479_consen 27 RVKVNGKVVKDPSYIVKPGDVI 48 (48)
T ss_dssp TEEETTEEESSTTSBESTTEEE
T ss_pred EEEECCEEEcCCCCCCCCcCCC
Confidence 4677777643 7777765
No 68
>PTZ00305 NADH:ubiquinone oxidoreductase; Provisional
Probab=27.86 E-value=53 Score=29.19 Aligned_cols=23 Identities=9% Similarity=0.107 Sum_probs=19.0
Q ss_pred CceEEEEEeCCEEEEE-cCCCEEE
Q 031957 101 EEIFAVVMIGSRQYIV-FPGRFIY 123 (150)
Q Consensus 101 ~~MYAIVeiGGKQYKV-e~GdvI~ 123 (150)
..--++|.|+||++.| .+|..|.
T Consensus 65 ~~~~~~I~IDGk~VeV~~~G~TIL 88 (297)
T PTZ00305 65 HKPRAIMFVNKRPVEIIPQEENLL 88 (297)
T ss_pred cCCceEEEECCEEEEecCCCChHH
Confidence 3456899999999999 8998763
No 69
>PF05164 ZapA: Cell division protein ZapA; InterPro: IPR007838 This entry a structural domain found in the cell division protein ZapA, as well as in related proteins. This domain has a core structure consisting of two layers alpha/beta, and has a long C-terminal helix that forms dimeric parallel and tetrameric antiparallel coiled coils []. ZapA interacts with FtsZ, where FtsZ is part of a mid-cell cytokinetic structure termed the Z-ring that recruits a hierarchy of fission related proteins early in the bacterial cell cycle. ZapA drives the polymerisation and filament bundling of FtsZ, thereby contributing to the spatio-temporal tuning of the Z-ring.; PDB: 1T3U_B 1W2E_B 3HNW_A.
Probab=27.77 E-value=54 Score=22.04 Aligned_cols=18 Identities=28% Similarity=0.233 Sum_probs=13.6
Q ss_pred EEeCCEEEEEc--CCCEEEe
Q 031957 107 VMIGSRQYIVF--PGRFIYT 124 (150)
Q Consensus 107 VeiGGKQYKVe--~GdvI~V 124 (150)
|.|+|+.|.+. .||.=++
T Consensus 4 v~I~G~~y~i~~~~~~ee~l 23 (89)
T PF05164_consen 4 VTILGREYRIKCPDEDEEYL 23 (89)
T ss_dssp EEETTEEEEECETGCGHHHH
T ss_pred EEECCEEEEeecCCCCHHHH
Confidence 78999999998 5554333
No 70
>PTZ00258 GTP-binding protein; Provisional
Probab=27.66 E-value=65 Score=29.07 Aligned_cols=17 Identities=24% Similarity=0.487 Sum_probs=14.9
Q ss_pred EeCCEEEEEcCCCEEEe
Q 031957 108 MIGSRQYIVFPGRFIYT 124 (150)
Q Consensus 108 eiGGKQYKVe~GdvI~V 124 (150)
+.-||.|.|+.||+|.+
T Consensus 368 r~eGkdYiv~DGDIi~f 384 (390)
T PTZ00258 368 RQEGKDYVVQDGDIIFF 384 (390)
T ss_pred eeeCCceEecCCCEEEE
Confidence 45599999999999987
No 71
>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=27.63 E-value=46 Score=28.60 Aligned_cols=29 Identities=21% Similarity=0.284 Sum_probs=23.2
Q ss_pred EEEEeCCEEEEEcCCCEEEecccCCCCCCCeEE
Q 031957 105 AVVMIGSRQYIVFPGRFIYTQRLKGANVNDKVC 137 (150)
Q Consensus 105 AIVeiGGKQYKVe~GdvI~VerLkgaEvGD~V~ 137 (150)
|.|.+||--|-+.+||+|-|=. +=|..|.
T Consensus 36 A~Iyiggl~~~LtEgDil~VFS----qyGe~vd 64 (219)
T KOG0126|consen 36 AYIYIGGLPYELTEGDILCVFS----QYGEIVD 64 (219)
T ss_pred eEEEECCCcccccCCcEEEEee----ccCceEE
Confidence 8999999999999999998732 3444454
No 72
>cd06530 S26_SPase_I The S26 Type I signal peptidase (SPase; LepB; leader peptidase B; leader peptidase I; EC 3.4.21.89) family members are essential membrane-bound serine proteases that function to cleave the amino-terminal signal peptide extension from proteins that are translocated across biological membranes. The bacterial signal peptidase I, which is the most intensively studied, has two N-terminal transmembrane segments inserted in the plasma membrane and a hydrophilic, C-terminal catalytic region that is located in the periplasmic space. Although the bacterial signal peptidase I is monomeric, signal peptidases of eukaryotic cells commonly function as oligomeric complexes containing two divergent copies of the catalytic monomer. These are the IMP1 and IMP2 signal peptidases of the mitochondrial inner membrane that remove leader peptides from nuclear- and mitochondrial-encoded proteins. Also, two components of the endoplasmic reticulum signal peptidase in mammals (18-kDa and 21-kDa
Probab=26.78 E-value=1.3e+02 Score=19.84 Aligned_cols=24 Identities=21% Similarity=0.296 Sum_probs=14.3
Q ss_pred EcCCCEEEecccCC----CCCCCeEEee
Q 031957 116 VFPGRFIYTQRLKG----ANVNDKVCNF 139 (150)
Q Consensus 116 Ve~GdvI~VerLkg----aEvGD~V~~~ 139 (150)
...||+|.|++... .+.||.|..+
T Consensus 14 i~~gd~v~v~~~~~~~~~~~~GDiv~~~ 41 (85)
T cd06530 14 LQPGDLVLVNKLSYGFREPKRGDVVVFK 41 (85)
T ss_pred ccCCCEEEEEEeecccCCCCCCCEEEEe
Confidence 45677777776542 4566665533
No 73
>cd03690 Tet_II Tet_II: This subfamily represents domain II of ribosomal protection proteins Tet(M) and Tet(O). This domain has homology to domain II of the elongation factors EF-G and EF-2. Tet(M) and Tet(O) catalyze the release of tetracycline (Tc) from the ribosome in a GTP-dependent manner thereby mediating Tc resistance. Tcs are broad-spectrum antibiotics. Typical Tcs bind to the ribosome and inhibit the elongation phase of protein synthesis, by inhibiting the occupation of site A by aminoacyl-tRNA.
Probab=26.50 E-value=68 Score=22.06 Aligned_cols=22 Identities=32% Similarity=0.394 Sum_probs=18.0
Q ss_pred EEcCCCEEEecccCCCCCCCeE
Q 031957 115 IVFPGRFIYTQRLKGANVNDKV 136 (150)
Q Consensus 115 KVe~GdvI~VerLkgaEvGD~V 136 (150)
.|..||++-+-.++++..||.+
T Consensus 62 ~~~aGdI~ai~gl~~~~~Gdtl 83 (85)
T cd03690 62 TVTAGDIAILTGLKGLRVGDVL 83 (85)
T ss_pred EECCCCEEEEECCCCCcCcccc
Confidence 4778999998888878888875
No 74
>KOG1491 consensus Predicted GTP-binding protein (ODN superfamily) [General function prediction only]
Probab=26.42 E-value=42 Score=31.08 Aligned_cols=16 Identities=31% Similarity=0.509 Sum_probs=14.5
Q ss_pred eCCEEEEEcCCCEEEe
Q 031957 109 IGSRQYIVFPGRFIYT 124 (150)
Q Consensus 109 iGGKQYKVe~GdvI~V 124 (150)
..||+|.|++||+|+.
T Consensus 372 ~~Gk~yiVedGDIi~F 387 (391)
T KOG1491|consen 372 QVGKEYIVEDGDIIFF 387 (391)
T ss_pred hcCceeeecCCCEEEE
Confidence 7799999999999975
No 75
>PF12969 DUF3857: Domain of Unknown Function with PDB structure (DUF3857); InterPro: IPR024618 This domain is based on the first domain of the PDB structure 3KD4 (residues 1-228). It is structurally similar to domains in other hydrolases, eg. M1 family aminopeptidase, despite lack of any significant sequence similarity. The domain is N-terminal to a transglutaminase domain, which is found in many proteins known to have transglutaminase activity. The function of this domain is unknown. ; PDB: 3KD4_A.
Probab=25.75 E-value=84 Score=23.05 Aligned_cols=32 Identities=9% Similarity=-0.005 Sum_probs=13.3
Q ss_pred EEEeCCEEEEEcCCCEEEec------------------ccCCCCCCCeEE
Q 031957 106 VVMIGSRQYIVFPGRFIYTQ------------------RLKGANVNDKVC 137 (150)
Q Consensus 106 IVeiGGKQYKVe~GdvI~Ve------------------rLkgaEvGD~V~ 137 (150)
|+.-+|+..++...+.-..+ .+.++++||.|+
T Consensus 48 v~~~dg~i~~~~~~~i~~~~~~~~~~~~~y~~~~~~~~~~p~v~~GdiIe 97 (177)
T PF12969_consen 48 VIRPDGKIDKLDKSDIKDRSAESASEAPIYSDSRTKVFAFPDVRVGDIIE 97 (177)
T ss_dssp EE-TTS-EEE--GGGEEEE--GGGTT-GGGTT-EEEEEE--S--TT-EEE
T ss_pred EEcCCCeEEecChHHeEEeecccccccccccCcEEEEEEcCCCCCCcEEE
Confidence 45556666776666532222 245688899888
No 76
>PF03473 MOSC: MOSC domain; InterPro: IPR005302 Molybdenum cofactor (MOCO) sulphurases [] catalyse the insertion of a terminal sulphur ligand into the molybdenum cofactor, thereby converting the oxo form of MOCO to a sulphurylated form. Suphurylated MOCO is required by several enzymes, including: aldehyde oxidase (1.2.3.1 from EC), which function in the last step of abscisic acid biosynthesis in plants []; and xanthine dehydrogenase (1.17.1.4 from EC), which synthesis uric acid from xanthine during nitrogen metabolism []. This entry represents the beta-barrel C-terminal domain of MOCO sulphurase (MOSC domain), which has a beta-barrel structure similar to that of the beta-barrel domain in pyruvate kinase and contains a highly conserved cysteine residue required for activity. MOSC domains are found in several diverse metal-sulphur cluster biosynthesis proteins from both eukaryotes and prokaryotes. MOSC domains occu as either stand-alone forms, such as the YiiM protein from Escherichia coli, or fused to other domains, such as a NifS-like catalytic domain in MOCO sulphurase. The MOSC domain is predicted to be a sulphur-carrier domain that receives sulphur abstracted from pyridoxal phosphate-dependent NifS-like enzymes, on its conserved cysteine, and delivers it for the formation of diverse sulphur-metal clusters []. The MOSC domain contains several patches of hydrophobic residues and an absolutely conserved cysteine residue situated closer to the C-terminal end of the domain. The absolutely conserved cysteine in the MOSC domain is reminiscent of the analogous conservation of a cysteine in the active site of the thioredoxin and rhodanese superfamilies. Members of both these superfamilies, especially of the latter one, have been implicated in the synthesis of Fe-S clusters, through mobilisation of sulphur with their active cysteine. ; GO: 0003824 catalytic activity, 0030151 molybdenum ion binding, 0030170 pyridoxal phosphate binding; PDB: 1ORU_B 1O67_C 1O65_C.
Probab=25.61 E-value=1e+02 Score=22.27 Aligned_cols=24 Identities=25% Similarity=0.425 Sum_probs=17.3
Q ss_pred CCCCceEEEEEeCCEEEEEcCCCEEEe
Q 031957 98 PKREEIFAVVMIGSRQYIVFPGRFIYT 124 (150)
Q Consensus 98 ~~r~~MYAIVeiGGKQYKVe~GdvI~V 124 (150)
.....+||.|..+| .|+.||.|+|
T Consensus 110 ~~~~G~~~~V~~~G---~I~vGD~V~V 133 (133)
T PF03473_consen 110 PGRRGVYARVIKGG---TIRVGDEVEV 133 (133)
T ss_dssp CTSS-EEEEEEE-E---EEETTSEEEE
T ss_pred cCCceEEEEeccCC---EEccCCeEEC
Confidence 34667899887665 6899999986
No 77
>PRK10413 hydrogenase 2 accessory protein HypG; Provisional
Probab=25.33 E-value=1.3e+02 Score=21.83 Aligned_cols=16 Identities=19% Similarity=-0.037 Sum_probs=13.1
Q ss_pred ceEEEEEeCCEEEEEc
Q 031957 102 EIFAVVMIGSRQYIVF 117 (150)
Q Consensus 102 ~MYAIVeiGGKQYKVe 117 (150)
.+.|+|+.+|-.-+|.
T Consensus 17 ~~~A~vd~~Gv~r~V~ 32 (82)
T PRK10413 17 HQLAQVEVCGIKRDVN 32 (82)
T ss_pred CcEEEEEcCCeEEEEE
Confidence 4689999999887764
No 78
>PF05726 Pirin_C: Pirin C-terminal cupin domain; InterPro: IPR008778 This entry represents C-terminal domain of Pirin proteins from both eukaryotes and prokaryotes. The function of Pirin is unknown but the gene coding for this protein is known to be expressed in all tissues in the human body although it is expressed most strongly in the liver and heart. Pirin is known to be a nuclear protein, exclusively localised within the nucleoplasma and predominantly concentrated within dot-like subnuclear structures []. Pirin is composed of two structurally similar domains arranged face to face. The N-terminal domain additionally features four beta-strands, and the C-terminal domain also includes four additional -strands and a short alpha-helix. Although the two domains are similar, the C-terminal domain of Pirin differs from the N-terminal domain as it does not contain a metal binding site and its sequence does not contain the conserved metal-coordinating residues []. Pirin is confirmed to be a member of the cupin superfamily on the basis of primary sequence and structural similarity. The presence of a metal binding site in the N-terminal beta-barrel of Pirin, may be significant in its role in regulating NFI DNA replication and NF-kappaB transcription factor activity []. Pirin structure has been found to closely resemble members of the cupin superfamily. Pirin contains the two characteristic sequences of the cupin superfamily, namely PG-(X)5-HXH-(X)4-E-(X)6-G and G-(X)5-PXG-(X)2-H-(X)3-N separated by a variable stretch of 15-50 amino acids. These motifs are best conserved in the N-terminal where the conserved histidine and glutamic acid residues correspond to the metal-coordinating residues. The C-terminal domain motifs lack the metal binding residues normally associated with the cupin fold []. Pirin was identified to be a metal-binding protein [], and was found that the metal-binding residues of Pirins are highly conserved across mammals, plants, fungi, and prokaryotic organisms. Pirin acts as a cofactor for the transcription factor NFI, the regulatory mechanism of which is generally believed to require the assistance of a metal ion []. Structural data supports the hypothesis that the bound iron of Pirin may participate in this transcriptional regulation by enhancing and stabilising the formation of the p50,Bcl3,DNA complex []. Metals have been implicated directly or indirectly in the NF-kappaB family of transcription factors that control expression of a number of early response genes associated with inflammatory responses, cell growth, cell cycle progression, and neoplastic transformation []. However, most metal-dependent transcription factors are DNA-binding proteins that bind to specific sequences when the metal binds to the protein. Pirin, on the other hand, appears to function differently and bind to the transcription factor DNA complex [].; PDB: 1J1L_A 3ACL_A 2P17_A.
Probab=24.12 E-value=90 Score=22.24 Aligned_cols=37 Identities=16% Similarity=0.245 Sum_probs=21.6
Q ss_pred EEeCCEEEEEcCCCEEEecccCCCCCCCeEEeeeccCCcceec
Q 031957 107 VMIGSRQYIVFPGRFIYTQRLKGANVNDKVCNFCAFSPLQFLI 149 (150)
Q Consensus 107 VeiGGKQYKVe~GdvI~VerLkgaEvGD~V~~~~~~~~~~~~~ 149 (150)
++++|..-.+.+|+.+..+ .|+.|.+......+++|+
T Consensus 31 ~~v~~~~~~~~~~~~~~l~------~g~~i~~~a~~~~a~~ll 67 (104)
T PF05726_consen 31 VEVGGEEDPLEAGQLVVLE------DGDEIELTAGEEGARFLL 67 (104)
T ss_dssp EEETTTTEEEETTEEEEE-------SECEEEEEESSSSEEEEE
T ss_pred EEECCCcceECCCcEEEEC------CCceEEEEECCCCcEEEE
Confidence 4566777778888888865 344555433334444443
No 79
>PF03823 Neurokinin_B: Neurokinin B; InterPro: IPR003635 Tachykinins [, , ] are a group of biologically active peptides which excite neurons, evoke behavioral responses, are potent vasodilatators and contract (directly or indirectly) many smooth muscles. This family includes neurokinins, as well as many other peptides. Like other tachykinins, neurokinins are synthesized as larger protein precursors that are enzymatically converted to their mature forms.; GO: 0007217 tachykinin receptor signaling pathway
Probab=24.12 E-value=50 Score=23.34 Aligned_cols=27 Identities=22% Similarity=0.246 Sum_probs=20.9
Q ss_pred hHHHHHhhhcccceeecCCCCCCCCCC
Q 031957 7 CATLALCSSLTSHCKISCQNPNPHPQL 33 (150)
Q Consensus 7 ~~~~~lCss~~~~c~is~~~p~~~~~~ 33 (150)
-+.++||.||++-|.-|+.+..+.-.+
T Consensus 10 iLalsla~s~gavCeesQeQ~~p~gg~ 36 (59)
T PF03823_consen 10 ILALSLARSFGAVCEESQEQVVPGGGH 36 (59)
T ss_pred HHHHHHHHHhhhhhhhhhhccCCCCCc
Confidence 345899999999999998866655443
No 80
>PRK05177 minC septum formation inhibitor; Reviewed
Probab=24.08 E-value=1.1e+02 Score=25.49 Aligned_cols=25 Identities=8% Similarity=0.089 Sum_probs=19.4
Q ss_pred CCEEEEEcCCCEEEecccCCCCCCCeEE
Q 031957 110 GSRQYIVFPGRFIYTQRLKGANVNDKVC 137 (150)
Q Consensus 110 GGKQYKVe~GdvI~VerLkgaEvGD~V~ 137 (150)
.|+|.....||+|.+ .++++|.+|.
T Consensus 142 SGQ~I~a~~gdliIl---G~Vn~GAEVi 166 (239)
T PRK05177 142 SGQSVVFPEGDVTVL---GSVASGAEVV 166 (239)
T ss_pred CCCEEEeCCCCEEEE---ccCCCCCEEE
Confidence 457766777999984 5678999988
No 81
>COG0298 HypC Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=23.50 E-value=1.1e+02 Score=22.84 Aligned_cols=28 Identities=25% Similarity=0.237 Sum_probs=19.1
Q ss_pred EEEEEeCCEEEEEcCCCEEEecccC-CCCCCCeEE
Q 031957 104 FAVVMIGSRQYIVFPGRFIYTQRLK-GANVNDKVC 137 (150)
Q Consensus 104 YAIVeiGGKQYKVe~GdvI~VerLk-gaEvGD~V~ 137 (150)
+|+|+.||-|-+|. ++.+. .+..||=|.
T Consensus 18 ~A~Vd~gGvkreV~------l~Lv~~~v~~GdyVL 46 (82)
T COG0298 18 LAIVDVGGVKREVN------LDLVGEEVKVGDYVL 46 (82)
T ss_pred eEEEEeccEeEEEE------eeeecCccccCCEEE
Confidence 99999999987763 33343 355666555
No 82
>TIGR03404 bicupin_oxalic bicupin, oxalate decarboxylase family. Members of this protein family are defined as bicupins as they have two copies of the cupin domain (pfam00190). Two different known activities for members of this family are oxalate decarboxylase (EC 4.1.1.2) and oxalate oxidase (EC 1.2.3.4), although the latter activity has more often been found in distantly related monocupin (germin) proteins.
Probab=23.48 E-value=1.3e+02 Score=26.57 Aligned_cols=32 Identities=22% Similarity=0.379 Sum_probs=22.1
Q ss_pred CCEEEEEcCCCEEEecc-----cCCCCCCCe-EEeeeccC
Q 031957 110 GSRQYIVFPGRFIYTQR-----LKGANVNDK-VCNFCAFS 143 (150)
Q Consensus 110 GGKQYKVe~GdvI~Ver-----LkgaEvGD~-V~~~~~~~ 143 (150)
+++.+.|++||+++|.+ +. +.|++ ++.+|.++
T Consensus 287 ~~~~~~l~~GD~~~iP~g~~H~i~--N~G~e~l~fL~if~ 324 (367)
T TIGR03404 287 NARTFDYQAGDVGYVPRNMGHYVE--NTGDETLVFLEVFK 324 (367)
T ss_pred cEEEEEECCCCEEEECCCCeEEEE--ECCCCCEEEEEEEC
Confidence 36789999999999986 42 46654 33555443
No 83
>PRK04804 minC septum formation inhibitor; Reviewed
Probab=23.07 E-value=1.2e+02 Score=24.78 Aligned_cols=25 Identities=12% Similarity=0.145 Sum_probs=19.2
Q ss_pred CCEEEEEcCCCEEEecccCCCCCCCeEE
Q 031957 110 GSRQYIVFPGRFIYTQRLKGANVNDKVC 137 (150)
Q Consensus 110 GGKQYKVe~GdvI~VerLkgaEvGD~V~ 137 (150)
.|+|.....||+|.+ .++++|.+|.
T Consensus 123 SGQ~I~a~~gdliIl---GdVn~GAEVi 147 (221)
T PRK04804 123 SGQQIYAKNGDLVIL---GAVSNGAEVI 147 (221)
T ss_pred CCCEEEecCCCEEEE---ccCCCCCEEE
Confidence 457777778999984 5678898887
No 84
>cd03699 lepA_II lepA_II: This subfamily represents the domain II of LepA, a GTP-binding protein localized in the cytoplasmic membrane. The N-terminal domain of LepA shares regions of homology to translation factors. In terms of interaction with the ribosome, EF-G, EF-Tu and IF2 have all been demonstrated to interact at overlapping sites on the ribosome. Chemical protection studies demonstrate that they all include the universally conserved alpha-sarcin loop as part of their binding site. These data indicate that LepA may bind to this location on the ribosome as well. LepA has never been observed in archaea, and eukaryl LepA is organellar. LepA is therefore a true bacterial GTPase, found only in the bacterial lineage.
Probab=22.72 E-value=97 Score=21.14 Aligned_cols=23 Identities=26% Similarity=0.349 Sum_probs=16.5
Q ss_pred EEcCCCEEEecc----cCCCCCCCeEE
Q 031957 115 IVFPGRFIYTQR----LKGANVNDKVC 137 (150)
Q Consensus 115 KVe~GdvI~Ver----LkgaEvGD~V~ 137 (150)
.+..||...+-. ++++..||.+.
T Consensus 59 ~~~aGdI~~v~~g~~~l~~~~~Gdtl~ 85 (86)
T cd03699 59 ELSAGQVGYIIAGIKTVKDARVGDTIT 85 (86)
T ss_pred eECCCCEEEEEccccccCccccccEee
Confidence 357899987753 55677888874
No 85
>cd04091 mtEFG1_II_like mtEFG1_C: C-terminus of mitochondrial Elongation factor G1 (mtEFG1)-like proteins found in eukaryotes. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than that in prokaryotes, with both cytoplasmic and mitochondrial elongation factors and multiple isoforms being expressed in certain species. Eukaryotic EF-2 operates in the cytosolic protein synthesis machinery of eukaryotes, EF-Gs in protein synthesis in bacteria. Eukaryotic mtEFG1 proteins show significant homology to bacterial EF-Gs. Mutants in yeast mtEFG1 have impaired mitochondrial protein synthesis, respiratory defects and a tendency to lose mitochondrial DNA. There are two forms of mtEFG present in mammals
Probab=22.19 E-value=1e+02 Score=20.68 Aligned_cols=21 Identities=10% Similarity=0.004 Sum_probs=16.5
Q ss_pred EEcCCCEEEecccCCCCCCCeE
Q 031957 115 IVFPGRFIYTQRLKGANVNDKV 136 (150)
Q Consensus 115 KVe~GdvI~VerLkgaEvGD~V 136 (150)
.+..||++.+-.++ +.+||.+
T Consensus 59 ~~~aGdI~~i~g~~-~~~Gdtl 79 (81)
T cd04091 59 EAGAGDICAIFGID-CASGDTF 79 (81)
T ss_pred EECCCCEEEEECCC-cccCCEe
Confidence 36788888888886 7888876
No 86
>PF02563 Poly_export: Polysaccharide biosynthesis/export protein; InterPro: IPR003715 The extracellular polysaccharide colanic acid (CA) is produced by species of the family Enterobacteriaceae. In Escherichia coli (strain K12) the CA cluster comprises 19 genes. The wzx gene encodes a protein with multiple transmembrane segments that may function in export of the CA repeat unit from the cytoplasm into the periplasm in a process analogous to O-unit export. The CA gene clusters may be involved in the export of polysaccharide from the cell [].; GO: 0015159 polysaccharide transmembrane transporter activity, 0015774 polysaccharide transport, 0016020 membrane; PDB: 2W8I_E 2W8H_E 2J58_D.
Probab=21.67 E-value=53 Score=22.52 Aligned_cols=17 Identities=18% Similarity=0.321 Sum_probs=8.0
Q ss_pred EEEEEcCCCEEEecccC
Q 031957 112 RQYIVFPGRFIYTQRLK 128 (150)
Q Consensus 112 KQYKVe~GdvI~VerLk 128 (150)
..|++.+||.|.|.-..
T Consensus 9 ~~y~l~pGD~l~i~v~~ 25 (82)
T PF02563_consen 9 PEYRLGPGDVLRISVFG 25 (82)
T ss_dssp ------TT-EEEEEETT
T ss_pred CCCEECCCCEEEEEEec
Confidence 57999999999997553
No 87
>cd08379 C2D_MCTP_PRT_plant C2 domain fourth repeat found in Multiple C2 domain and Transmembrane region Proteins (MCTP); plant subset. MCTPs are involved in Ca2+ signaling at the membrane. Plant-MCTPs are composed of a variable N-terminal sequence, four C2 domains, two transmembrane regions (TMRs), and a short C-terminal sequence. It is one of four protein classes that are anchored to membranes via a transmembrane region; the others being synaptotagmins, extended synaptotagmins, and ferlins. MCTPs are the only membrane-bound C2 domain proteins that contain two functional TMRs. MCTPs are unique in that they bind Ca2+ but not phospholipids. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphate
Probab=20.24 E-value=1.3e+02 Score=22.49 Aligned_cols=18 Identities=11% Similarity=0.189 Sum_probs=14.5
Q ss_pred CCCCceEEEEEeCCEEEE
Q 031957 98 PKREEIFAVVMIGSRQYI 115 (150)
Q Consensus 98 ~~r~~MYAIVeiGGKQYK 115 (150)
.-..+.|++|+.|++.+|
T Consensus 21 ~g~sDPYv~i~~g~~~~r 38 (126)
T cd08379 21 RGSTDAYCVAKYGPKWVR 38 (126)
T ss_pred CCCCCeeEEEEECCEEeE
Confidence 446679999999998775
Done!