Query 034556
Match_columns 91
No_of_seqs 25 out of 27
Neff 2.9
Searched_HMMs 46136
Date Fri Mar 29 04:05:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034556.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034556hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4827 Uncharacterized conser 99.8 1E-19 2.2E-24 143.0 1.0 77 13-89 58-139 (279)
2 PF08381 BRX: Transcription fa 85.0 0.7 1.5E-05 29.8 1.9 27 42-68 19-45 (59)
3 smart00368 LRR_RI Leucine rich 76.8 4.1 9E-05 21.5 2.8 26 49-74 2-27 (28)
4 PF13516 LRR_6: Leucine Rich r 75.2 2.3 5E-05 21.2 1.5 21 50-70 3-23 (24)
5 KOG4237 Extracellular matrix p 73.7 1.3 2.8E-05 38.5 0.5 36 45-80 270-305 (498)
6 COG1724 Predicted RNA binding 70.7 4 8.7E-05 27.0 2.2 18 66-83 9-26 (66)
7 PF13504 LRR_7: Leucine rich r 64.7 3.2 6.9E-05 20.1 0.6 14 50-63 2-15 (17)
8 PF10828 DUF2570: Protein of u 59.0 1.9 4.1E-05 29.3 -1.1 29 62-90 76-104 (110)
9 PF11239 DUF3040: Protein of u 58.9 8.4 0.00018 24.8 2.0 14 59-72 1-14 (82)
10 cd00116 LRR_RI Leucine-rich re 57.3 12 0.00026 26.9 2.8 39 49-87 278-318 (319)
11 cd01389 MATA_HMG-box MATA_HMG- 55.4 8.2 0.00018 23.9 1.5 19 58-76 40-58 (77)
12 PRK10878 hypothetical protein; 55.0 12 0.00026 24.5 2.3 19 59-77 17-35 (72)
13 smart00398 HMG high mobility g 55.0 8.4 0.00018 22.2 1.4 19 58-76 40-58 (70)
14 PF08183 SpoV: Stage V sporula 54.4 5.8 0.00012 22.3 0.6 8 78-85 3-10 (26)
15 COG3623 SgaU Putative L-xylulo 54.3 6 0.00013 32.4 0.9 36 52-90 42-77 (287)
16 PF09011 HMG_box_2: HMG-box do 53.1 7.5 0.00016 23.9 1.0 18 59-76 44-61 (73)
17 PF08800 VirE_N: VirE N-termin 52.5 11 0.00023 26.4 1.8 46 31-78 12-58 (136)
18 smart00369 LRR_TYP Leucine-ric 51.9 5.8 0.00013 19.9 0.3 21 50-70 3-23 (26)
19 smart00370 LRR Leucine-rich re 51.9 5.8 0.00013 19.9 0.3 21 50-70 3-23 (26)
20 PRK14741 spoVM stage V sporula 50.7 8.5 0.00018 21.6 0.9 9 77-85 2-10 (26)
21 cd01390 HMGB-UBF_HMG-box HMGB- 48.8 11 0.00025 21.7 1.3 18 59-76 40-57 (66)
22 PF00505 HMG_box: HMG (high mo 47.9 7.9 0.00017 22.7 0.5 18 58-75 39-56 (69)
23 PTZ00199 high mobility group p 46.3 13 0.00028 24.4 1.4 18 59-76 64-81 (94)
24 PF00249 Myb_DNA-binding: Myb- 42.3 27 0.00059 19.8 2.2 20 58-77 1-20 (48)
25 PF06543 Lac_bphage_repr: Lact 41.8 28 0.0006 22.0 2.3 23 53-75 23-45 (49)
26 cd01388 SOX-TCF_HMG-box SOX-TC 41.5 18 0.00038 22.1 1.4 20 57-76 39-58 (72)
27 PF00560 LRR_1: Leucine Rich R 40.8 14 0.0003 18.4 0.7 13 51-63 2-14 (22)
28 cd07018 S49_SppA_67K_type Sign 40.7 21 0.00045 26.3 1.9 20 55-74 147-166 (222)
29 COG4899 Uncharacterized protei 39.4 19 0.00042 27.5 1.6 26 58-85 21-46 (166)
30 cd00084 HMG-box High Mobility 37.9 22 0.00047 20.2 1.3 18 59-76 40-57 (66)
31 PRK14626 hypothetical protein; 37.8 20 0.00043 24.9 1.3 34 41-74 42-75 (110)
32 PF12650 DUF3784: Domain of un 34.1 30 0.00065 22.4 1.6 15 57-71 25-39 (97)
33 PF11796 DUF3323: Protein of u 33.9 55 0.0012 24.3 3.2 31 52-84 5-37 (215)
34 PF11625 DUF3253: Protein of u 33.8 23 0.00049 24.1 1.1 11 75-85 73-83 (83)
35 PF00061 Lipocalin: Lipocalin 33.7 36 0.00078 21.6 2.0 32 47-78 100-132 (144)
36 PF07813 LTXXQ: LTXXQ motif fa 33.3 34 0.00075 21.0 1.8 15 58-72 85-99 (100)
37 PRK14622 hypothetical protein; 33.1 25 0.00054 24.1 1.2 34 41-74 38-71 (103)
38 PF02318 FYVE_2: FYVE-type zin 32.8 21 0.00045 24.3 0.8 17 60-76 2-18 (118)
39 PF14317 YcxB: YcxB-like prote 32.1 39 0.00084 18.8 1.7 22 53-74 41-62 (62)
40 PF04467 DUF483: Protein of un 32.0 41 0.00088 24.8 2.2 30 58-89 65-95 (128)
41 COG3040 Blc Bacterial lipocali 31.5 47 0.001 25.5 2.6 28 52-79 134-162 (174)
42 PF04829 PT-VENN: Pre-toxin do 31.3 40 0.00086 21.0 1.8 16 59-74 3-18 (55)
43 PF03937 Sdh5: Flavinator of s 30.7 29 0.00062 22.1 1.1 19 59-77 30-48 (74)
44 PRK14627 hypothetical protein; 29.7 30 0.00066 23.5 1.2 34 41-74 38-71 (100)
45 PF13855 LRR_8: Leucine rich r 29.3 4.3 9.2E-05 23.5 -2.7 31 44-74 20-50 (61)
46 PF09103 BRCA-2_OB1: BRCA2, ol 29.2 29 0.00064 24.3 1.0 20 64-83 29-48 (118)
47 COG2938 Uncharacterized conser 28.5 53 0.0011 22.7 2.2 19 59-77 42-60 (94)
48 TIGR02116 toxin_Txe_YoeB toxin 27.9 35 0.00077 21.3 1.2 10 75-84 48-57 (80)
49 cd04493 BRCA2DBD_OB1 BRCA2DBD_ 27.8 36 0.00079 23.8 1.3 13 71-83 24-36 (100)
50 cd01338 MDH_choloroplast_like 27.2 91 0.002 24.7 3.6 50 20-74 262-311 (322)
51 smart00364 LRR_BAC Leucine-ric 27.1 30 0.00064 19.0 0.6 15 49-63 2-16 (26)
52 PF01343 Peptidase_S49: Peptid 27.0 46 0.00099 23.1 1.7 19 56-74 75-93 (154)
53 PRK13920 putative anti-sigmaE 26.7 56 0.0012 23.8 2.2 19 58-76 6-24 (206)
54 COG4921 Uncharacterized protei 26.6 36 0.00077 25.2 1.1 10 73-82 13-22 (131)
55 PF08278 DnaG_DnaB_bind: DNA p 26.6 54 0.0012 21.6 1.9 16 58-73 112-127 (127)
56 PF10213 MRP-S28: Mitochondria 26.6 57 0.0012 23.1 2.2 22 53-74 32-53 (127)
57 PF13801 Metal_resist: Heavy-m 25.8 59 0.0013 20.0 1.9 18 57-74 38-55 (125)
58 PF03161 LAGLIDADG_2: LAGLIDAD 25.8 1.4E+02 0.003 21.2 4.0 37 52-88 125-174 (178)
59 COG3170 FimV Tfp pilus assembl 25.5 21 0.00047 32.7 -0.2 34 51-86 77-110 (755)
60 PF14794 DUF4479: Domain of un 25.4 60 0.0013 21.1 1.9 20 59-78 46-65 (73)
61 PRK00587 hypothetical protein; 24.6 43 0.00093 23.1 1.2 34 41-74 37-70 (99)
62 PF09999 DUF2240: Uncharacteri 23.5 81 0.0017 23.1 2.5 45 34-78 7-51 (144)
63 TIGR00053 addiction module tox 23.2 50 0.0011 20.7 1.2 8 76-83 55-62 (89)
64 smart00717 SANT SANT SWI3, AD 23.2 97 0.0021 16.0 2.2 19 59-77 2-20 (49)
65 TIGR00705 SppA_67K signal pept 23.1 61 0.0013 27.9 2.1 20 55-74 195-214 (584)
66 PRK11713 16S ribosomal RNA met 22.9 80 0.0017 23.5 2.4 27 60-90 189-215 (234)
67 cd01336 MDH_cytoplasmic_cytoso 22.8 1.2E+02 0.0025 24.0 3.4 35 35-74 281-315 (325)
68 PF04809 HupH_C: HupH hydrogen 22.6 48 0.001 23.3 1.1 29 45-74 20-48 (120)
69 PF09143 AvrPphF-ORF-2: AvrPph 22.2 52 0.0011 25.4 1.3 22 46-71 4-25 (175)
70 PF02216 B: B domain; InterPr 22.1 73 0.0016 20.5 1.8 18 59-76 20-37 (54)
71 PRK14629 hypothetical protein; 21.9 54 0.0012 22.6 1.3 33 41-73 40-72 (99)
72 TIGR01573 cas2 CRISPR-associat 21.9 48 0.001 21.8 1.0 18 64-81 16-33 (95)
73 COG3549 HigB Plasmid maintenan 21.6 57 0.0012 22.9 1.3 18 68-85 53-71 (94)
74 PF11491 DUF3213: Protein of u 21.4 35 0.00077 23.8 0.3 28 54-83 3-31 (88)
75 cd05293 LDH_1 A subgroup of L- 21.4 1.3E+02 0.0028 23.7 3.5 49 21-74 256-304 (312)
76 PF14226 DIOX_N: non-haem diox 21.3 1.7E+02 0.0036 18.6 3.4 34 51-84 1-35 (116)
77 PF14584 DUF4446: Protein of u 21.1 73 0.0016 23.2 1.9 15 57-71 135-149 (151)
78 TIGR00084 ruvA Holliday juncti 20.9 84 0.0018 23.3 2.2 18 61-78 63-80 (191)
79 PF07051 OCIA: Ovarian carcino 20.5 66 0.0014 23.0 1.5 26 58-84 23-48 (111)
80 PRK14600 ruvA Holliday junctio 20.1 87 0.0019 23.4 2.1 17 61-77 64-80 (186)
No 1
>KOG4827 consensus Uncharacterized conserved protein [Function unknown]
Probab=99.76 E-value=1e-19 Score=142.97 Aligned_cols=77 Identities=27% Similarity=0.201 Sum_probs=71.4
Q ss_pred CCCCC-CCceeEEeecCC---CCCCC-CccccccccccccccccceeEeecccCCHHHHHHHHHHhhcCCeEEEEeeccc
Q 034556 13 NQPPK-LTAVQATHHHNT---LPLPT-NTPQNLLKISSHSVQTLTKLLFSRNAFKREDKEKFEKLRKDDDFYLICYLAGC 87 (91)
Q Consensus 13 ~~~~e-~~~v~f~LEHs~---ef~~a-g~FsaRlk~~~~g~q~LtkLrlsRn~lse~ek~kfkeL~~~DgfYrIRvPsnv 87 (91)
++|+. +.++||+|||+| +|.++ |+||+|+|+|+|||++++|||+++|.|+.+||++|+.+++.|+||+||+|+++
T Consensus 58 ~dpTdldkk~QftlEhaFGdkdF~~anGtfSaR~ks~shgGkn~~klrf~~~dF~aeekdaF~n~lkgddf~kiqL~s~~ 137 (279)
T KOG4827|consen 58 GDPTDLDKKAQFTLEHAFGDKDFEAANGTFSARAKSSSHGGKNFLKLRFDPCDFLAEEKDAFHNFLKGDDFEKIQLHSLT 137 (279)
T ss_pred CCcccccchhhhhHHhhccccccccccceeEEEeecccCCCcceeeeccChhhhhhhHHHHHHHHHhcccHhhhccccce
Confidence 34444 789999999995 89999 99999999999999999999999999999999999999999999999999997
Q ss_pred cC
Q 034556 88 HP 89 (91)
Q Consensus 88 l~ 89 (91)
..
T Consensus 138 i~ 139 (279)
T KOG4827|consen 138 IF 139 (279)
T ss_pred ec
Confidence 63
No 2
>PF08381 BRX: Transcription factor regulating root and shoot growth via Pin3; InterPro: IPR013591 This is a short domain, approximately 35 residues in length that is found near the C terminus in a number of plant proteins, being repeated in some members. It is found in Brevis radix-like proteins. These may act as a regulator of cell proliferation and elongation in the root []. It is also found in proteins annotated as involved in disease resistance and in the regulation of chromosome condensation, which also contain other domains with varied functions, such as TIR (IPR000157 from INTERPRO) and FYVE (IPR000306 from INTERPRO) respectively.
Probab=85.03 E-value=0.7 Score=29.84 Aligned_cols=27 Identities=22% Similarity=0.293 Sum_probs=23.1
Q ss_pred ccccccccccceeEeecccCCHHHHHH
Q 034556 42 KISSHSVQTLTKLLFSRNAFKREDKEK 68 (91)
Q Consensus 42 k~~~~g~q~LtkLrlsRn~lse~ek~k 68 (91)
...+.|+..|..+||||--|+|.+.++
T Consensus 19 ~~~p~G~~~LkRVRFSR~~F~e~qA~~ 45 (59)
T PF08381_consen 19 VSLPDGGNDLKRVRFSRERFSEWQAER 45 (59)
T ss_pred EECCCCCeeEEEEEEhhhhcCHHHHHH
Confidence 367788999999999999999877654
No 3
>smart00368 LRR_RI Leucine rich repeat, ribonuclease inhibitor type.
Probab=76.75 E-value=4.1 Score=21.51 Aligned_cols=26 Identities=23% Similarity=0.272 Sum_probs=22.3
Q ss_pred cccceeEeecccCCHHHHHHHHHHhh
Q 034556 49 QTLTKLLFSRNAFKREDKEKFEKLRK 74 (91)
Q Consensus 49 q~LtkLrlsRn~lse~ek~kfkeL~~ 74 (91)
..|..|.|+.|.|.++=-.++-+.++
T Consensus 2 ~~L~~LdL~~N~i~~~G~~~L~~~L~ 27 (28)
T smart00368 2 PSLRELDLSNNKLGDEGARALAEALK 27 (28)
T ss_pred CccCEEECCCCCCCHHHHHHHHHHhc
Confidence 46899999999999998888887764
No 4
>PF13516 LRR_6: Leucine Rich repeat; PDB: 3RGZ_A 3RJ0_A 3RIZ_A 3RGX_A 1DFJ_I 2BNH_A 3VQ1_A 3VQ2_A 2Z64_A 2OMX_A ....
Probab=75.22 E-value=2.3 Score=21.21 Aligned_cols=21 Identities=24% Similarity=0.295 Sum_probs=15.7
Q ss_pred ccceeEeecccCCHHHHHHHH
Q 034556 50 TLTKLLFSRNAFKREDKEKFE 70 (91)
Q Consensus 50 ~LtkLrlsRn~lse~ek~kfk 70 (91)
.|+.|.|+.|+++++.-..+.
T Consensus 3 ~L~~L~l~~n~i~~~g~~~l~ 23 (24)
T PF13516_consen 3 NLETLDLSNNQITDEGASALA 23 (24)
T ss_dssp T-SEEE-TSSBEHHHHHHHHH
T ss_pred CCCEEEccCCcCCHHHHHHhC
Confidence 578999999999998776653
No 5
>KOG4237 consensus Extracellular matrix protein slit, contains leucine-rich and EGF-like repeats [Extracellular structures; Signal transduction mechanisms]
Probab=73.72 E-value=1.3 Score=38.54 Aligned_cols=36 Identities=28% Similarity=0.402 Sum_probs=30.7
Q ss_pred cccccccceeEeecccCCHHHHHHHHHHhhcCCeEE
Q 034556 45 SHSVQTLTKLLFSRNAFKREDKEKFEKLRKDDDFYL 80 (91)
Q Consensus 45 ~~g~q~LtkLrlsRn~lse~ek~kfkeL~~~DgfYr 80 (91)
.++-..|.||.|++|++|+.+..+|++++..-.+|-
T Consensus 270 f~~L~~L~~lnlsnN~i~~i~~~aFe~~a~l~eL~L 305 (498)
T KOG4237|consen 270 FKKLPNLRKLNLSNNKITRIEDGAFEGAAELQELYL 305 (498)
T ss_pred HhhcccceEeccCCCccchhhhhhhcchhhhhhhhc
Confidence 345567899999999999999999999998877763
No 6
>COG1724 Predicted RNA binding protein (dsRBD-like fold), HicA family [General function prediction only]
Probab=70.71 E-value=4 Score=27.05 Aligned_cols=18 Identities=22% Similarity=0.265 Sum_probs=15.0
Q ss_pred HHHHHHHhhcCCeEEEEe
Q 034556 66 KEKFEKLRKDDDFYLICY 83 (91)
Q Consensus 66 k~kfkeL~~~DgfYrIRv 83 (91)
-..+.+++..||||.+|.
T Consensus 9 ~ke~ik~Le~~Gf~~vrq 26 (66)
T COG1724 9 AKEVIKALEKDGFQLVRQ 26 (66)
T ss_pred HHHHHHHHHhCCcEEEEe
Confidence 346788999999999985
No 7
>PF13504 LRR_7: Leucine rich repeat; PDB: 3OJA_B 3G06_A 1OOK_G 1QYY_G 1SQ0_B 1P9A_G 1GWB_A 1P8V_A 1M0Z_A 1U0N_D ....
Probab=64.73 E-value=3.2 Score=20.05 Aligned_cols=14 Identities=29% Similarity=0.335 Sum_probs=9.1
Q ss_pred ccceeEeecccCCH
Q 034556 50 TLTKLLFSRNAFKR 63 (91)
Q Consensus 50 ~LtkLrlsRn~lse 63 (91)
.|+.|+++.|+|++
T Consensus 2 ~L~~L~l~~n~L~~ 15 (17)
T PF13504_consen 2 NLRTLDLSNNRLTS 15 (17)
T ss_dssp T-SEEEETSS--SS
T ss_pred ccCEEECCCCCCCC
Confidence 47899999999874
No 8
>PF10828 DUF2570: Protein of unknown function (DUF2570); InterPro: IPR022538 This entry is represented by Bacteriophage IME08, pseT.3. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a family of proteins with unknown function.
Probab=59.01 E-value=1.9 Score=29.30 Aligned_cols=29 Identities=17% Similarity=0.116 Sum_probs=25.9
Q ss_pred CHHHHHHHHHHhhcCCeEEEEeeccccCC
Q 034556 62 KREDKEKFEKLRKDDDFYLICYLAGCHPA 90 (91)
Q Consensus 62 se~ek~kfkeL~~~DgfYrIRvPsnvl~~ 90 (91)
+++-++++++.++.|.=|+-.+|..|++-
T Consensus 76 ~e~~~e~ik~~lk~d~Ca~~~~P~~V~d~ 104 (110)
T PF10828_consen 76 SEERRESIKTALKDDPCANTAVPDAVIDS 104 (110)
T ss_pred HHHHHHHHHHHHccCccccCCCCHHHHHH
Confidence 56778999999999999999999998763
No 9
>PF11239 DUF3040: Protein of unknown function (DUF3040); InterPro: IPR021401 Some members in this family of proteins with unknown function are annotated as membrane proteins however this cannot be confirmed.
Probab=58.88 E-value=8.4 Score=24.81 Aligned_cols=14 Identities=7% Similarity=0.427 Sum_probs=12.2
Q ss_pred ccCCHHHHHHHHHH
Q 034556 59 NAFKREDKEKFEKL 72 (91)
Q Consensus 59 n~lse~ek~kfkeL 72 (91)
++|||+||..++|+
T Consensus 1 M~LSe~E~r~L~ei 14 (82)
T PF11239_consen 1 MPLSEHEQRRLEEI 14 (82)
T ss_pred CCCCHHHHHHHHHH
Confidence 47999999999886
No 10
>cd00116 LRR_RI Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1).
Probab=57.27 E-value=12 Score=26.88 Aligned_cols=39 Identities=13% Similarity=0.153 Sum_probs=30.8
Q ss_pred cccceeEeecccCCHHHHHHHHHHhhcC--CeEEEEeeccc
Q 034556 49 QTLTKLLFSRNAFKREDKEKFEKLRKDD--DFYLICYLAGC 87 (91)
Q Consensus 49 q~LtkLrlsRn~lse~ek~kfkeL~~~D--gfYrIRvPsnv 87 (91)
..|..|.++.|.++++...++.++++.- -.+.+.|..|.
T Consensus 278 ~~L~~l~l~~N~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 318 (319)
T cd00116 278 ESLLELDLRGNKFGEEGAQLLAESLLEPGNELESLWVKDDS 318 (319)
T ss_pred CCccEEECCCCCCcHHHHHHHHHHHhhcCCchhhcccCCCC
Confidence 4678889999999999888888888765 67777776654
No 11
>cd01389 MATA_HMG-box MATA_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include the fungal mating type gene products MC, MATA1 and Ste11.
Probab=55.43 E-value=8.2 Score=23.88 Aligned_cols=19 Identities=16% Similarity=0.254 Sum_probs=16.0
Q ss_pred cccCCHHHHHHHHHHhhcC
Q 034556 58 RNAFKREDKEKFEKLRKDD 76 (91)
Q Consensus 58 Rn~lse~ek~kfkeL~~~D 76 (91)
=+.||++||+.|.+.++.|
T Consensus 40 Wk~ls~eeK~~y~~~A~~~ 58 (77)
T cd01389 40 WRSESPEVKAYYKELAEEE 58 (77)
T ss_pred HhhCCHHHHHHHHHHHHHH
Confidence 3578999999999998765
No 12
>PRK10878 hypothetical protein; Provisional
Probab=55.04 E-value=12 Score=24.50 Aligned_cols=19 Identities=26% Similarity=0.496 Sum_probs=16.7
Q ss_pred ccCCHHHHHHHHHHhhcCC
Q 034556 59 NAFKREDKEKFEKLRKDDD 77 (91)
Q Consensus 59 n~lse~ek~kfkeL~~~Dg 77 (91)
.+||++|++.|+.|+..++
T Consensus 17 ~~l~~~e~~~Fe~LL~~~D 35 (72)
T PRK10878 17 DSLSDDEKRIFIRLLECDD 35 (72)
T ss_pred hhCCHHHHHHHHHHHcCCC
Confidence 4689999999999998765
No 13
>smart00398 HMG high mobility group.
Probab=55.01 E-value=8.4 Score=22.22 Aligned_cols=19 Identities=26% Similarity=0.440 Sum_probs=16.1
Q ss_pred cccCCHHHHHHHHHHhhcC
Q 034556 58 RNAFKREDKEKFEKLRKDD 76 (91)
Q Consensus 58 Rn~lse~ek~kfkeL~~~D 76 (91)
=+.||+++|..+.+.++.|
T Consensus 40 W~~l~~~ek~~y~~~a~~~ 58 (70)
T smart00398 40 WKLLSEEEKAPYEEKAKKD 58 (70)
T ss_pred HHcCCHHHHHHHHHHHHHH
Confidence 4679999999999988764
No 14
>PF08183 SpoV: Stage V sporulation protein family; InterPro: IPR012609 This family consists of the stage V sporulation (SpoV) proteins of Bacillus subtilis which includes SpoVM. SpoVM is an small, 26 residue-long protein that is produced in the mother cell chamber of the sporangium during the process of sporulation in B. subtilis. SpoVM forms an amphipathic alpha-helix and is recruited to the polar septum shortly after the sporangium undergoes asymmetric division. The function of SpoVM depends on proper subcellular localisation [].
Probab=54.37 E-value=5.8 Score=22.26 Aligned_cols=8 Identities=38% Similarity=0.501 Sum_probs=7.2
Q ss_pred eEEEEeec
Q 034556 78 FYLICYLA 85 (91)
Q Consensus 78 fYrIRvPs 85 (91)
||+|++|.
T Consensus 3 fYtIKLpk 10 (26)
T PF08183_consen 3 FYTIKLPK 10 (26)
T ss_pred ceeeechH
Confidence 89999995
No 15
>COG3623 SgaU Putative L-xylulose-5-phosphate 3-epimerase [Carbohydrate transport and metabolism]
Probab=54.30 E-value=6 Score=32.43 Aligned_cols=36 Identities=11% Similarity=0.217 Sum_probs=31.8
Q ss_pred ceeEeecccCCHHHHHHHHHHhhcCCeEEEEeeccccCC
Q 034556 52 TKLLFSRNAFKREDKEKFEKLRKDDDFYLICYLAGCHPA 90 (91)
Q Consensus 52 tkLrlsRn~lse~ek~kfkeL~~~DgfYrIRvPsnvl~~ 90 (91)
+-=||+|-.-|++|+.++-+...+-| ||+|+-||+|
T Consensus 42 sDeRLaRLDWs~~er~~l~~ai~etg---v~ipSmClSa 77 (287)
T COG3623 42 SDERLARLDWSKEERLALVNAIQETG---VRIPSMCLSA 77 (287)
T ss_pred hHHHHHhcCCCHHHHHHHHHHHHHhC---CCccchhhhh
Confidence 44488999999999999999999876 6999999987
No 16
>PF09011 HMG_box_2: HMG-box domain; InterPro: IPR015101 This domain is predominantly found in Maelstrom homologue proteins. It has no known function. ; GO: 0005634 nucleus; PDB: 2EQZ_A 1V64_A 2CTO_A 1H5P_A 3TQ6_A 3FGH_A 3TMM_A 1J3X_A 2YRQ_A 1AAB_A ....
Probab=53.12 E-value=7.5 Score=23.88 Aligned_cols=18 Identities=33% Similarity=0.641 Sum_probs=14.6
Q ss_pred ccCCHHHHHHHHHHhhcC
Q 034556 59 NAFKREDKEKFEKLRKDD 76 (91)
Q Consensus 59 n~lse~ek~kfkeL~~~D 76 (91)
..||++||+.+++.++.|
T Consensus 44 k~Ls~~EK~~Y~~~A~~~ 61 (73)
T PF09011_consen 44 KSLSEEEKEPYEERAKED 61 (73)
T ss_dssp HHS-HHHHHHHHHHHHHH
T ss_pred HhcCHHHHHHHHHHHHHH
Confidence 368999999999998865
No 17
>PF08800 VirE_N: VirE N-terminal domain; InterPro: IPR014907 This domain is associated with the N terminus of Virulence E proteins. The function of the domain is unknown.
Probab=52.49 E-value=11 Score=26.40 Aligned_cols=46 Identities=15% Similarity=0.222 Sum_probs=32.8
Q ss_pred CCCCCcccc-ccccccccccccceeEeecccCCHHHHHHHHHHhhcCCe
Q 034556 31 PLPTNTPQN-LLKISSHSVQTLTKLLFSRNAFKREDKEKFEKLRKDDDF 78 (91)
Q Consensus 31 f~~ag~Fsa-Rlk~~~~g~q~LtkLrlsRn~lse~ek~kfkeL~~~Dgf 78 (91)
|.++|+|+. |.......-.-| +-+-=|.|+.+|-+.+++.+..|-+
T Consensus 12 vt~~g~F~~~r~~~~l~~~sgl--v~lDiD~l~~ee~~~~r~~l~~~p~ 58 (136)
T PF08800_consen 12 VTPSGTFSGGRNADNLKAYSGL--VVLDIDHLDPEEAEELRQLLFEDPY 58 (136)
T ss_pred EEEEEEECCCcchhhhhhCCCc--EEEEeCCCCHHHHHHHHHHHhcCCc
Confidence 678999998 665444433333 4445567778999999999988864
No 18
>smart00369 LRR_TYP Leucine-rich repeats, typical (most populated) subfamily.
Probab=51.90 E-value=5.8 Score=19.95 Aligned_cols=21 Identities=24% Similarity=0.301 Sum_probs=17.4
Q ss_pred ccceeEeecccCCHHHHHHHH
Q 034556 50 TLTKLLFSRNAFKREDKEKFE 70 (91)
Q Consensus 50 ~LtkLrlsRn~lse~ek~kfk 70 (91)
.|..|.|+.|+|+.-....|.
T Consensus 3 ~L~~L~L~~N~l~~lp~~~f~ 23 (26)
T smart00369 3 NLRELDLSNNQLSSLPPGAFQ 23 (26)
T ss_pred CCCEEECCCCcCCcCCHHHcc
Confidence 468899999999988777775
No 19
>smart00370 LRR Leucine-rich repeats, outliers.
Probab=51.90 E-value=5.8 Score=19.95 Aligned_cols=21 Identities=24% Similarity=0.301 Sum_probs=17.4
Q ss_pred ccceeEeecccCCHHHHHHHH
Q 034556 50 TLTKLLFSRNAFKREDKEKFE 70 (91)
Q Consensus 50 ~LtkLrlsRn~lse~ek~kfk 70 (91)
.|..|.|+.|+|+.-....|.
T Consensus 3 ~L~~L~L~~N~l~~lp~~~f~ 23 (26)
T smart00370 3 NLRELDLSNNQLSSLPPGAFQ 23 (26)
T ss_pred CCCEEECCCCcCCcCCHHHcc
Confidence 468899999999988777775
No 20
>PRK14741 spoVM stage V sporulation protein M; Provisional
Probab=50.68 E-value=8.5 Score=21.56 Aligned_cols=9 Identities=33% Similarity=0.464 Sum_probs=7.7
Q ss_pred CeEEEEeec
Q 034556 77 DFYLICYLA 85 (91)
Q Consensus 77 gfYrIRvPs 85 (91)
-||+|.+|.
T Consensus 2 kfytiklpk 10 (26)
T PRK14741 2 KFYTIKLPK 10 (26)
T ss_pred ceEEEeccH
Confidence 399999996
No 21
>cd01390 HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and III members of the HMG-box superfamily of DNA-binding proteins. These proteins bind the minor groove of DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions.
Probab=48.81 E-value=11 Score=21.71 Aligned_cols=18 Identities=28% Similarity=0.571 Sum_probs=15.4
Q ss_pred ccCCHHHHHHHHHHhhcC
Q 034556 59 NAFKREDKEKFEKLRKDD 76 (91)
Q Consensus 59 n~lse~ek~kfkeL~~~D 76 (91)
+.||++||..|.+.++.|
T Consensus 40 ~~ls~~eK~~y~~~a~~~ 57 (66)
T cd01390 40 KELSEEEKKKYEEKAEKD 57 (66)
T ss_pred HhCCHHHHHHHHHHHHHH
Confidence 579999999999988765
No 22
>PF00505 HMG_box: HMG (high mobility group) box; InterPro: IPR000910 High mobility group (HMG or HMGB) proteins are a family of relatively low molecular weight non-histone components in chromatin. HMG1 (also called HMG-T in fish) and HMG2 are two highly related proteins that bind single-stranded DNA preferentially and unwind double-stranded DNA. Although they have no sequence specificity, they have a high affinity for bent or distorted DNA, and bend linear DNA. HMG1 and HMG2 contain two DNA-binding HMG-box domains (A and B) that show structural and functional differences, and have a long acidic C-terminal domain rich in aspartic and glutamic acid residues. The acidic tail modulates the affinity of the tandem HMG boxes in HMG1 and 2 for a variety of DNA targets. HMG1 and 2 appear to play important architectural roles in the assembly of nucleoprotein complexes in a variety of biological processes, for example V(D)J recombination, the initiation of transcription, and DNA repair []. The profile in this entry describing the HMG-domains is much more general than the signature. In addition to the HMG1 and HMG2 proteins, HMG-domains occur in single or multiple copies in the following protein classes; the SOX family of transcription factors; SRY sex determining region Y protein and related proteins []; LEF1 lymphoid enhancer binding factor 1 []; SSRP recombination signal recognition protein; MTF1 mitochondrial transcription factor 1; UBF1/2 nucleolar transcription factors; Abf2 yeast ARS-binding factor []; and Saccharomyces cerevisiae transcription factors Ixr1, Rox1, Nhp6a, Nhp6b and Spp41.; GO: 0003677 DNA binding; PDB: 1I11_A 1J3C_A 1J3D_A 1WZ6_A 1WGF_A 2D7L_A 1GT0_D 3U2B_C 2CRJ_A 2CS1_A ....
Probab=47.86 E-value=7.9 Score=22.69 Aligned_cols=18 Identities=11% Similarity=0.340 Sum_probs=15.0
Q ss_pred cccCCHHHHHHHHHHhhc
Q 034556 58 RNAFKREDKEKFEKLRKD 75 (91)
Q Consensus 58 Rn~lse~ek~kfkeL~~~ 75 (91)
=+.||++||+.|++.+..
T Consensus 39 W~~l~~~eK~~y~~~a~~ 56 (69)
T PF00505_consen 39 WKNLSEEEKAPYKEEAEE 56 (69)
T ss_dssp HHCSHHHHHHHHHHHHHH
T ss_pred HhcCCHHHHHHHHHHHHH
Confidence 357999999999998764
No 23
>PTZ00199 high mobility group protein; Provisional
Probab=46.26 E-value=13 Score=24.41 Aligned_cols=18 Identities=33% Similarity=0.610 Sum_probs=16.3
Q ss_pred ccCCHHHHHHHHHHhhcC
Q 034556 59 NAFKREDKEKFEKLRKDD 76 (91)
Q Consensus 59 n~lse~ek~kfkeL~~~D 76 (91)
+.||++||..|.+.++.|
T Consensus 64 k~ls~eeK~~y~~~A~~d 81 (94)
T PTZ00199 64 NKLSEEEKAPYEKKAQED 81 (94)
T ss_pred HcCCHHHHHHHHHHHHHH
Confidence 578999999999999877
No 24
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=42.25 E-value=27 Score=19.81 Aligned_cols=20 Identities=25% Similarity=0.356 Sum_probs=15.3
Q ss_pred cccCCHHHHHHHHHHhhcCC
Q 034556 58 RNAFKREDKEKFEKLRKDDD 77 (91)
Q Consensus 58 Rn~lse~ek~kfkeL~~~Dg 77 (91)
|.+.|++|-++|.++++.-|
T Consensus 1 r~~Wt~eE~~~l~~~v~~~g 20 (48)
T PF00249_consen 1 RGPWTEEEDEKLLEAVKKYG 20 (48)
T ss_dssp S-SS-HHHHHHHHHHHHHST
T ss_pred CCCCCHHHHHHHHHHHHHhC
Confidence 46789999999999988655
No 25
>PF06543 Lac_bphage_repr: Lactococcus bacteriophage repressor; InterPro: IPR009498 This entry represents the C terminus of various Lactococcus bacteriophage repressor proteins.
Probab=41.78 E-value=28 Score=22.03 Aligned_cols=23 Identities=17% Similarity=0.175 Sum_probs=19.6
Q ss_pred eeEeecccCCHHHHHHHHHHhhc
Q 034556 53 KLLFSRNAFKREDKEKFEKLRKD 75 (91)
Q Consensus 53 kLrlsRn~lse~ek~kfkeL~~~ 75 (91)
-++|-.-|||++.|++.+.+...
T Consensus 23 wvSf~GrPltdevK~a~k~i~~~ 45 (49)
T PF06543_consen 23 WVSFDGRPLTDEVKEAMKLIFGK 45 (49)
T ss_pred heeeCCeeCCHHHHHHHHHHHhh
Confidence 46888899999999999988753
No 26
>cd01388 SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and vertebrates, and transcription factor-like proteins, TCF-1, -3, -4, and LEF-1. They appear to bind the minor groove of the A/T C A A A G/C-motif.
Probab=41.47 E-value=18 Score=22.15 Aligned_cols=20 Identities=20% Similarity=0.240 Sum_probs=16.3
Q ss_pred ecccCCHHHHHHHHHHhhcC
Q 034556 57 SRNAFKREDKEKFEKLRKDD 76 (91)
Q Consensus 57 sRn~lse~ek~kfkeL~~~D 76 (91)
.=..||++||..|.+.++.|
T Consensus 39 ~Wk~ls~~eK~~y~~~a~~~ 58 (72)
T cd01388 39 RWKALSNEEKQPYYEEAKKL 58 (72)
T ss_pred HHHcCCHHHHHHHHHHHHHH
Confidence 34678999999999988765
No 27
>PF00560 LRR_1: Leucine Rich Repeat; InterPro: IPR001611 Leucine-rich repeats (LRR) consist of 2-45 motifs of 20-30 amino acids in length that generally folds into an arc or horseshoe shape []. LRRs occur in proteins ranging from viruses to eukaryotes, and appear to provide a structural framework for the formation of protein-protein interactions [, ].Proteins containing LRRs include tyrosine kinase receptors, cell-adhesion molecules, virulence factors, and extracellular matrix-binding glycoproteins, and are involved in a variety of biological processes, including signal transduction, cell adhesion, DNA repair, recombination, transcription, RNA processing, disease resistance, apoptosis, and the immune response []. Sequence analyses of LRR proteins suggested the existence of several different subfamilies of LRRs. The significance of this classification is that repeats from different subfamilies never occur simultaneously and have most probably evolved independently. It is, however, now clear that all major classes of LRR have curved horseshoe structures with a parallel beta sheet on the concave side and mostly helical elements on the convex side. At least six families of LRR proteins, characterised by different lengths and consensus sequences of the repeats, have been identified. Eleven-residue segments of the LRRs (LxxLxLxxN/CxL), corresponding to the beta-strand and adjacent loop regions, are conserved in LRR proteins, whereas the remaining parts of the repeats (herein termed variable) may be very different. Despite the differences, each of the variable parts contains two half-turns at both ends and a "linear" segment (as the chain follows a linear path overall), usually formed by a helix, in the middle. The concave face and the adjacent loops are the most common protein interaction surfaces on LRR proteins. 3D structure of some LRR proteins-ligand complexes show that the concave surface of LRR domain is ideal for interaction with alpha-helix, thus supporting earlier conclusions that the elongated and curved LRR structure provides an outstanding framework for achieving diverse protein-protein interactions []. Molecular modeling suggests that the conserved pattern LxxLxL, which is shorter than the previously proposed LxxLxLxxN/CxL is sufficient to impart the characteristic horseshoe curvature to proteins with 20- to 30-residue repeats []. ; GO: 0005515 protein binding; PDB: 4ECO_B 2A0Z_A 3ULU_A 1ZIW_A 3ULV_A 1DCE_C 1LTX_A 3J0A_B 3A79_B 4FCG_A ....
Probab=40.84 E-value=14 Score=18.35 Aligned_cols=13 Identities=31% Similarity=0.268 Sum_probs=11.1
Q ss_pred cceeEeecccCCH
Q 034556 51 LTKLLFSRNAFKR 63 (91)
Q Consensus 51 LtkLrlsRn~lse 63 (91)
|..|.|+.|+|++
T Consensus 2 L~~Ldls~n~l~~ 14 (22)
T PF00560_consen 2 LEYLDLSGNNLTS 14 (22)
T ss_dssp ESEEEETSSEESE
T ss_pred ccEEECCCCcCEe
Confidence 6789999999984
No 28
>cd07018 S49_SppA_67K_type Signal peptide peptidase A (SppA) 67K type, a serine protease, has catalytic Ser-Lys dyad. Signal peptide peptidase A (SppA; Peptidase S49; Protease IV) 67K type: SppA is found in all three domains of life and is involved in the cleavage of signal peptides after their removal from the precursor proteins by signal peptidases. Members in this subfamily contain an amino-terminal domain in addition to the carboxyl-terminal protease domain that is conserved in all the S49 family members (sometimes referred to as 67K type), similar to E. coli and Arabidopsis thaliana SppA peptidases. Unlike the eukaryotic functional homologs that are proposed to be aspartic proteases, site-directed mutagenesis and sequence analysis have shown that members in this subfamily, mostly bacterial, are serine proteases. The predicted active site serine for members in this family occurs in a transmembrane domain. Mutagenesis studies also suggest that the catalytic center comprises a Ser-Lys
Probab=40.75 E-value=21 Score=26.31 Aligned_cols=20 Identities=25% Similarity=0.436 Sum_probs=17.2
Q ss_pred EeecccCCHHHHHHHHHHhh
Q 034556 55 LFSRNAFKREDKEKFEKLRK 74 (91)
Q Consensus 55 rlsRn~lse~ek~kfkeL~~ 74 (91)
.|+|+++|+++|+.+++++.
T Consensus 147 ~~~~~~~s~~~r~~~~~~l~ 166 (222)
T cd07018 147 PFTRDDMSPEAREQTQALLD 166 (222)
T ss_pred hhhcccCCHHHHHHHHHHHH
Confidence 36788999999999998875
No 29
>COG4899 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=39.43 E-value=19 Score=27.50 Aligned_cols=26 Identities=23% Similarity=0.257 Sum_probs=23.1
Q ss_pred cccCCHHHHHHHHHHhhcCCeEEEEeec
Q 034556 58 RNAFKREDKEKFEKLRKDDDFYLICYLA 85 (91)
Q Consensus 58 Rn~lse~ek~kfkeL~~~DgfYrIRvPs 85 (91)
-|+|+|+|+.+ .+.-+|+|--|+.|.
T Consensus 21 ~~aL~E~E~~A--Qv~~DdD~Cqi~~p~ 46 (166)
T COG4899 21 VFALPEAELDA--QVRYDDDMCQILNPK 46 (166)
T ss_pred hhcCCHHHhhh--hheecccceeecCCC
Confidence 58999999999 888999999999773
No 30
>cd00084 HMG-box High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4; and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III member
Probab=37.86 E-value=22 Score=20.20 Aligned_cols=18 Identities=28% Similarity=0.591 Sum_probs=15.1
Q ss_pred ccCCHHHHHHHHHHhhcC
Q 034556 59 NAFKREDKEKFEKLRKDD 76 (91)
Q Consensus 59 n~lse~ek~kfkeL~~~D 76 (91)
+.||+++|+.|.+.+..+
T Consensus 40 ~~l~~~~k~~y~~~a~~~ 57 (66)
T cd00084 40 KSLSEEEKKKYEEKAEKD 57 (66)
T ss_pred HhCCHHHHHHHHHHHHHH
Confidence 578999999999988754
No 31
>PRK14626 hypothetical protein; Provisional
Probab=37.81 E-value=20 Score=24.93 Aligned_cols=34 Identities=12% Similarity=0.293 Sum_probs=29.5
Q ss_pred cccccccccccceeEeecccCCHHHHHHHHHHhh
Q 034556 41 LKISSHSVQTLTKLLFSRNAFKREDKEKFEKLRK 74 (91)
Q Consensus 41 lk~~~~g~q~LtkLrlsRn~lse~ek~kfkeL~~ 74 (91)
.+....|.+++.++.++..-|+++|++.+++|+.
T Consensus 42 VkV~~nG~~ev~~i~Id~~ll~~ed~e~LeDLI~ 75 (110)
T PRK14626 42 VKVVSNGLGEIKDVEIDKSLLNEDEYEVLKDLLI 75 (110)
T ss_pred EEEEEECCccEEEEEECHHHcCcccHHHHHHHHH
Confidence 3456778899999999999999999999999863
No 32
>PF12650 DUF3784: Domain of unknown function (DUF3784); InterPro: IPR017259 This group represents an uncharacterised conserved protein.
Probab=34.07 E-value=30 Score=22.43 Aligned_cols=15 Identities=40% Similarity=0.771 Sum_probs=11.7
Q ss_pred ecccCCHHHHHHHHH
Q 034556 57 SRNAFKREDKEKFEK 71 (91)
Q Consensus 57 sRn~lse~ek~kfke 71 (91)
--|..|+|||++.++
T Consensus 25 Gyntms~eEk~~~D~ 39 (97)
T PF12650_consen 25 GYNTMSKEEKEKYDK 39 (97)
T ss_pred hcccCCHHHHHHhhH
Confidence 347789999999843
No 33
>PF11796 DUF3323: Protein of unknown function N-terminus (DUF3323); InterPro: IPR024466 This domain is found to the N terminus of bacterial conserved hypothetical proteins which are encoded within a conserved gene four-gene neighbourhood found sporadically in a phylogenetically broad range of bacteria including: Nocardia farcinica, Symbiobacterium thermophilum, and Streptomyces avermitilis (Actinobacteria), Geobacillus kaustophilus (Firmicutes), Azoarcus sp. EbN1 and Ralstonia solanacearum (Beta-proteobacteria).
Probab=33.93 E-value=55 Score=24.34 Aligned_cols=31 Identities=16% Similarity=0.105 Sum_probs=24.0
Q ss_pred ceeEeecccCCHHHHHHHHHHhhcCCe--EEEEee
Q 034556 52 TKLLFSRNAFKREDKEKFEKLRKDDDF--YLICYL 84 (91)
Q Consensus 52 tkLrlsRn~lse~ek~kfkeL~~~Dgf--YrIRvP 84 (91)
++++|+ .+|++||+++..++-.|-. .+|+||
T Consensus 5 G~v~L~--~~t~~Er~al~~llGr~~~~~~~~~v~ 37 (215)
T PF11796_consen 5 GTVRLT--NLTEEEREALAGLLGRDFSGGKSIRVS 37 (215)
T ss_pred eEEEeC--CCCHHHHHHHHHHhCCCCCCCCCeeee
Confidence 456665 7999999999999987755 566665
No 34
>PF11625 DUF3253: Protein of unknown function (DUF3253); InterPro: IPR021660 This bacterial family of proteins has no known function. ; PDB: 2NS0_A.
Probab=33.83 E-value=23 Score=24.09 Aligned_cols=11 Identities=9% Similarity=-0.375 Sum_probs=4.8
Q ss_pred cCCeEEEEeec
Q 034556 75 DDDFYLICYLA 85 (91)
Q Consensus 75 ~DgfYrIRvPs 85 (91)
.-|.||||+|+
T Consensus 73 ~rGpiRirlp~ 83 (83)
T PF11625_consen 73 FRGPIRIRLPR 83 (83)
T ss_dssp --S--EEEE--
T ss_pred CcCCeEeeccC
Confidence 35999999985
No 35
>PF00061 Lipocalin: Lipocalin / cytosolic fatty-acid binding protein family fatty acid-binding protein signature lipocalin signature; InterPro: IPR000566 Proteins which transport small hydrophobic molecules such as steroids, bilins, retinoids, and lipids share limited regions of sequence homology and a common tertiary structure architecture [, , , , ]. This is an eight stranded antiparallel beta-barrel with a repeated + 1 topology enclosing a internal ligand binding site [, ]. The name 'lipocalin' has been proposed [] for this protein family, but cytosolic fatty-acid binding proteins are also included. The sequences of most members of the family, the core or kernal lipocalins, are characterised by three short conserved stretches of residues, while others, the outlier lipocalin group, share only one or two of these [, ]. Proteins known to belong to this family include alpha-1-microglobulin (protein HC); alpha-1-acid glycoprotein (orosomucoid) []; aphrodisin; apolipoprotein D; beta-lactoglobulin; complement component C8 gamma chain []; crustacyanin []; epididymal-retinoic acid binding protein (E-RABP) []; insectacyanin; odorant-binding protein (OBP); human pregnancy-associated endometrial alpha-2 globulin; probasin (PB), a rat prostatic protein; prostaglandin D synthase (5.3.99.2 from EC) []; purpurin; Von Ebner's gland protein (VEGP) []; and lizard epididymal secretory protein IV (LESP IV) [].; GO: 0005488 binding; PDB: 1I05_A 1MUP_A 2LB6_A 1I04_A 1I06_A 1DC9_A 1URE_A 1AEL_A 1T8V_A 1ICM_A ....
Probab=33.72 E-value=36 Score=21.63 Aligned_cols=32 Identities=31% Similarity=0.421 Sum_probs=23.6
Q ss_pred cccccceeEeecc-cCCHHHHHHHHHHhhcCCe
Q 034556 47 SVQTLTKLLFSRN-AFKREDKEKFEKLRKDDDF 78 (91)
Q Consensus 47 g~q~LtkLrlsRn-~lse~ek~kfkeL~~~Dgf 78 (91)
|..+..---++|. .++++-.++|+++++.=|+
T Consensus 100 g~~~~~~~l~~R~~~l~~~~~~~f~~~~~~~gi 132 (144)
T PF00061_consen 100 GKHTIVAWLLSRTPELSPEALEKFKKFAKSLGI 132 (144)
T ss_dssp TEEEEEEEEEESSSEEEHHHHHHHHHHHHHTTE
T ss_pred CceEEEEEEEcCCCcCCHHHHHHHHHHHHhCCC
Confidence 3344333345999 9999999999999987654
No 36
>PF07813 LTXXQ: LTXXQ motif family protein; InterPro: IPR012899 This five residue motif is found in a number of bacterial proteins bearing similarity to the protein CpxP (P32158 from SWISSPROT). This is a periplasmic protein that aids in combating extracytoplasmic protein-mediated toxicity, and may also be involved in the response to alkaline pH []. Another member of this family, Spy (P77754 from SWISSPROT) is also a periplasmic protein that may be involved in the response to stress []. The homology between CpxP and Spy may indicate that these two proteins are functionally related []. The motif is found repeated twice in many members of this entry. ; GO: 0042597 periplasmic space; PDB: 3ITF_B 3QZC_B 3OEO_D 3O39_A.
Probab=33.35 E-value=34 Score=21.03 Aligned_cols=15 Identities=40% Similarity=0.643 Sum_probs=11.8
Q ss_pred cccCCHHHHHHHHHH
Q 034556 58 RNAFKREDKEKFEKL 72 (91)
Q Consensus 58 Rn~lse~ek~kfkeL 72 (91)
.+-||+|.|++|+++
T Consensus 85 ~~vLt~eQk~~~~~l 99 (100)
T PF07813_consen 85 YAVLTPEQKEKFDQL 99 (100)
T ss_dssp HTTS-HHHHHHHHHH
T ss_pred HhcCCHHHHHHHHHh
Confidence 467999999999876
No 37
>PRK14622 hypothetical protein; Provisional
Probab=33.13 E-value=25 Score=24.14 Aligned_cols=34 Identities=24% Similarity=0.326 Sum_probs=29.3
Q ss_pred cccccccccccceeEeecccCCHHHHHHHHHHhh
Q 034556 41 LKISSHSVQTLTKLLFSRNAFKREDKEKFEKLRK 74 (91)
Q Consensus 41 lk~~~~g~q~LtkLrlsRn~lse~ek~kfkeL~~ 74 (91)
.+....|.+++.++++...-|.++|++.+++|+-
T Consensus 38 VkV~~nG~~~v~~i~Idp~~l~~ed~e~LeDLI~ 71 (103)
T PRK14622 38 VKVAMNGKCEVTRLTVDPKAVDPNDKAMLEDLVT 71 (103)
T ss_pred EEEEEEcCceEEEEEECHHHcCcccHHHHHHHHH
Confidence 3456678899999999999999999999999863
No 38
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=32.81 E-value=21 Score=24.30 Aligned_cols=17 Identities=18% Similarity=0.343 Sum_probs=14.0
Q ss_pred cCCHHHHHHHHHHhhcC
Q 034556 60 AFKREDKEKFEKLRKDD 76 (91)
Q Consensus 60 ~lse~ek~kfkeL~~~D 76 (91)
.||++|++...+|++-|
T Consensus 2 ~Lt~eE~~~I~~Vl~R~ 18 (118)
T PF02318_consen 2 HLTEEEREIILQVLQRD 18 (118)
T ss_dssp TS-CHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHhH
Confidence 58999999999998765
No 39
>PF14317 YcxB: YcxB-like protein
Probab=32.07 E-value=39 Score=18.80 Aligned_cols=22 Identities=32% Similarity=0.676 Sum_probs=17.3
Q ss_pred eeEeecccCCHHHHHHHHHHhh
Q 034556 53 KLLFSRNAFKREDKEKFEKLRK 74 (91)
Q Consensus 53 kLrlsRn~lse~ek~kfkeL~~ 74 (91)
-+-+-...|+++|.++|.++++
T Consensus 41 ~~~iPk~~f~~~e~~~f~~~lk 62 (62)
T PF14317_consen 41 AFIIPKRAFSEEEKEEFREFLK 62 (62)
T ss_pred EEEEEHHHCCHhHHHHHHHHhC
Confidence 3455667899999999999874
No 40
>PF04467 DUF483: Protein of unknown function (DUF483); InterPro: IPR007556 This is a family of uncharacterised prokaryotic proteins.
Probab=31.96 E-value=41 Score=24.82 Aligned_cols=30 Identities=17% Similarity=0.249 Sum_probs=19.1
Q ss_pred cccCCHHHH-HHHHHHhhcCCeEEEEeeccccC
Q 034556 58 RNAFKREDK-EKFEKLRKDDDFYLICYLAGCHP 89 (91)
Q Consensus 58 Rn~lse~ek-~kfkeL~~~DgfYrIRvPsnvl~ 89 (91)
+..|.+.++ .+|.+. .-|-|.|.+|+|+.|
T Consensus 65 ~~~Lke~ee~~~~~~~--~kg~~aI~~psnFiP 95 (128)
T PF04467_consen 65 SEHLKECEEMKVFVFN--EKGIYAIILPSNFIP 95 (128)
T ss_pred HHHHhhHHHccchhhh--cccceEEEeecCccc
Confidence 344444443 333333 457899999999987
No 41
>COG3040 Blc Bacterial lipocalin [Cell envelope biogenesis, outer membrane]
Probab=31.50 E-value=47 Score=25.53 Aligned_cols=28 Identities=21% Similarity=0.324 Sum_probs=24.2
Q ss_pred ceeEeeccc-CCHHHHHHHHHHhhcCCeE
Q 034556 52 TKLLFSRNA-FKREDKEKFEKLRKDDDFY 79 (91)
Q Consensus 52 tkLrlsRn~-lse~ek~kfkeL~~~DgfY 79 (91)
----|||++ +|++.++++-+.++.=||=
T Consensus 134 ylWlLsRtP~~s~~~~~~ml~~ak~~Gfd 162 (174)
T COG3040 134 YLWLLSRTPTLSQETLKRMLEIAKRRGFD 162 (174)
T ss_pred eEEEEecCCCCCHHHHHHHHHHHHHcCCC
Confidence 344689999 9999999999999998873
No 42
>PF04829 PT-VENN: Pre-toxin domain with VENN motif; InterPro: IPR006914 This group of proteins, mainly from Neisseria meningitidis, may have haemagglutinin or haemolysin activity. A number of them have a second conserved domain, IPR006915 from INTERPRO, which is found in possible Pseudomonas aeruginosa haemagglutinins []. Filamentous haemagglutinin (FHA) is a major virulence attachment factor produced by certain bacterial species that functions as both a primary adhesin and an immunomodulator. Haemolysin is pore-forming toxin.
Probab=31.31 E-value=40 Score=21.02 Aligned_cols=16 Identities=25% Similarity=0.480 Sum_probs=13.2
Q ss_pred ccCCHHHHHHHHHHhh
Q 034556 59 NAFKREDKEKFEKLRK 74 (91)
Q Consensus 59 n~lse~ek~kfkeL~~ 74 (91)
+.|||+||++...+.+
T Consensus 3 ~~Lte~eK~~v~~ls~ 18 (55)
T PF04829_consen 3 SELTEEEKQKVSALSQ 18 (55)
T ss_pred HhcCHHHHHHHHHHHH
Confidence 6899999999887654
No 43
>PF03937 Sdh5: Flavinator of succinate dehydrogenase; InterPro: IPR005631 This entry represents a group of uncharacterised small proteins found in both eukaryotes and prokaryotes, including NMA1147 from Neisseria meningitidis [] and YgfY from Escherichia coli []. YgfY may be involved in transcriptional regulation. The structure of these proteins consists of a complex bundle of five alpha-helices, which is composed of an up-down 3-helix bundle plus an orthogonal 2-helix bundle. ; PDB: 2LM4_A 1PUZ_A 2JR5_A 1X6I_A 1X6J_A.
Probab=30.67 E-value=29 Score=22.12 Aligned_cols=19 Identities=26% Similarity=0.550 Sum_probs=15.0
Q ss_pred ccCCHHHHHHHHHHhhcCC
Q 034556 59 NAFKREDKEKFEKLRKDDD 77 (91)
Q Consensus 59 n~lse~ek~kfkeL~~~Dg 77 (91)
+.+|++|.+.|+.|++.++
T Consensus 30 ~~l~~~el~~fe~lL~~~D 48 (74)
T PF03937_consen 30 DSLSEEELDAFERLLDLED 48 (74)
T ss_dssp HHS-HHHHHHHHHHHTS-H
T ss_pred hhCCHHHHHHHHHHHcCCC
Confidence 5799999999999998764
No 44
>PRK14627 hypothetical protein; Provisional
Probab=29.71 E-value=30 Score=23.53 Aligned_cols=34 Identities=12% Similarity=0.236 Sum_probs=29.1
Q ss_pred cccccccccccceeEeecccCCHHHHHHHHHHhh
Q 034556 41 LKISSHSVQTLTKLLFSRNAFKREDKEKFEKLRK 74 (91)
Q Consensus 41 lk~~~~g~q~LtkLrlsRn~lse~ek~kfkeL~~ 74 (91)
.+....|.+++.++.+...-|.++|++-+++|+-
T Consensus 38 VkV~~~G~~~v~~i~Idp~ll~~ed~e~LeDLI~ 71 (100)
T PRK14627 38 ITVKMNGHREVQSITISPEVVDPDDVEMLQDLLL 71 (100)
T ss_pred EEEEEEcCccEEEEEECHHHcCcccHHHHHHHHH
Confidence 3455668899999999999999999999999863
No 45
>PF13855 LRR_8: Leucine rich repeat; PDB: 2O6S_A 3A79_B 3RFS_A 3G39_A 3VQ2_A 3VQ1_B 2Z64_A 2Z66_C 3FXI_A 2Z63_A ....
Probab=29.34 E-value=4.3 Score=23.55 Aligned_cols=31 Identities=23% Similarity=0.284 Sum_probs=21.9
Q ss_pred ccccccccceeEeecccCCHHHHHHHHHHhh
Q 034556 44 SSHSVQTLTKLLFSRNAFKREDKEKFEKLRK 74 (91)
Q Consensus 44 ~~~g~q~LtkLrlsRn~lse~ek~kfkeL~~ 74 (91)
+..+-..|..|.++.|.++.-+.+.|+.+-+
T Consensus 20 ~f~~l~~L~~L~l~~N~l~~i~~~~f~~l~~ 50 (61)
T PF13855_consen 20 SFSNLPNLETLDLSNNNLTSIPPDAFSNLPN 50 (61)
T ss_dssp TTTTGTTESEEEETSSSESEEETTTTTTSTT
T ss_pred HHcCCCCCCEeEccCCccCccCHHHHcCCCC
Confidence 3344567888888888888777777666544
No 46
>PF09103 BRCA-2_OB1: BRCA2, oligonucleotide/oligosaccharide-binding, domain 1; InterPro: IPR015187 This domain assumes an OB fold, which consists of a highly curved five-stranded beta-sheet that closes on itself to form a beta-barrel. OB1 has a shallow groove formed by one face of the curved sheet and is demarcated by two loops, one between beta 1 and beta 2 and another between beta 4 and beta 5, which allows for weak single strand DNA binding. The domain also binds the 70-amino acid DSS1 (deleted in split-hand/split foot syndrome) protein, which was originally identified as one of three genes that map to a 1.5-Mb locus deleted in an inherited developmental malformation syndrome []. ; GO: 0000724 double-strand break repair via homologous recombination; PDB: 1IYJ_D 1MIU_A.
Probab=29.18 E-value=29 Score=24.27 Aligned_cols=20 Identities=25% Similarity=0.283 Sum_probs=8.0
Q ss_pred HHHHHHHHHhhcCCeEEEEe
Q 034556 64 EDKEKFEKLRKDDDFYLICY 83 (91)
Q Consensus 64 ~ek~kfkeL~~~DgfYrIRv 83 (91)
.+...-..|.=-||+|.|+.
T Consensus 29 ~~~~~~~~lelTDGWY~Ika 48 (118)
T PF09103_consen 29 NDSPESAILELTDGWYSIKA 48 (118)
T ss_dssp --------EEEE-SS-EEEE
T ss_pred CCCCccCEEEEecCCEEEEE
Confidence 33344455666799999984
No 47
>COG2938 Uncharacterized conserved protein [Function unknown]
Probab=28.53 E-value=53 Score=22.71 Aligned_cols=19 Identities=26% Similarity=0.592 Sum_probs=16.6
Q ss_pred ccCCHHHHHHHHHHhhcCC
Q 034556 59 NAFKREDKEKFEKLRKDDD 77 (91)
Q Consensus 59 n~lse~ek~kfkeL~~~Dg 77 (91)
..||++|++.|..|++.++
T Consensus 42 ~~lsd~el~~f~~LLe~~D 60 (94)
T COG2938 42 DSLSDEELDEFERLLECED 60 (94)
T ss_pred hhCCHHHHHHHHHHHcCCc
Confidence 4789999999999998765
No 48
>TIGR02116 toxin_Txe_YoeB toxin-antitoxin system, toxin component, Txe/YoeB family. The Axe-Txe pair in Enterococcus faecium and the homologous YefM-YoeB pair in Escherichia coli have been shown to act as an antitoxin-toxin pair. This model describes the toxin component. Nearly every example found is next to an identifiable antitoxin, as indicated by matches to TIGR01552 and/or pfam02604.
Probab=27.88 E-value=35 Score=21.32 Aligned_cols=10 Identities=0% Similarity=-0.094 Sum_probs=8.0
Q ss_pred cCCeEEEEee
Q 034556 75 DDDFYLICYL 84 (91)
Q Consensus 75 ~DgfYrIRvP 84 (91)
-+|||++||-
T Consensus 48 ~~g~~r~rig 57 (80)
T TIGR02116 48 LSGYWSRRIT 57 (80)
T ss_pred CCCcEEEEcC
Confidence 3689999984
No 49
>cd04493 BRCA2DBD_OB1 BRCA2DBD_OB1: A subfamily of OB folds corresponding to the first OB fold (OB1) of the 800-amino acid C-terminal ssDNA binding domain (DBD) of BRCA2 (breast cancer susceptibility gene 2) protein, called BRCA2DBD. BRCA2 participates in homologous recombination-mediated repair of double-strand DNA breaks. It stimulates the displacement of Replication protein A (RPA), the most abundant eukaryotic ssDNA binding protein. It also facilitates filament formation. Mutations that map throughout the BRCA2 protein are associated with breast cancer susceptibility. BRCA2 is a large nuclear protein and its most conserved region is the C-terminal BRCA2DBD. BRCA2DBD binds ssDNA in vitro, and is composed of five structural domains, three of which are OB folds (OB1, OB2, and OB3). BRCA2DBD OB2 and OB3 are arranged in tandem, and their mode of binding can be considered qualitatively similar to two OB folds of RPA1, DBD-A and DBD-B (the major DBDs of RPA). BRCA2DBD OB1 binds DNA weakly.
Probab=27.84 E-value=36 Score=23.75 Aligned_cols=13 Identities=23% Similarity=0.327 Sum_probs=9.9
Q ss_pred HHhhcCCeEEEEe
Q 034556 71 KLRKDDDFYLICY 83 (91)
Q Consensus 71 eL~~~DgfYrIRv 83 (91)
.+---||+|.|+.
T Consensus 24 ~lEltDGWYsi~a 36 (100)
T cd04493 24 IIELTDGWYSIRA 36 (100)
T ss_pred EEEEecCeEEEEE
Confidence 4445699999985
No 50
>cd01338 MDH_choloroplast_like Chloroplast-like malate dehydrogenases. MDH is one of the key enzymes in the citric acid cycle, facilitating both the conversion of malate to oxaloacetate and replenishing levels of oxalacetate by reductive carboxylation of pyruvate. Members of this subfamily are bacterial MDHs, and plant MDHs localized to the choloroplasts. MDHs are part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of protein families including the NAD(P)-binding domains of alcohol dehydrogenases, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate dehydrogenases, formate/glycerate dehydrogenases, siroheme synthases, 6-phosphogluconate dehydrogenases, aminoacid dehydrogenases, repressor rex, and NAD-binding potassium channel domains, among others.
Probab=27.16 E-value=91 Score=24.71 Aligned_cols=50 Identities=4% Similarity=-0.112 Sum_probs=31.0
Q ss_pred ceeEEeecCCCCCCCCccccccccccccccccceeEeecccCCHHHHHHHHHHhh
Q 034556 20 AVQATHHHNTLPLPTNTPQNLLKISSHSVQTLTKLLFSRNAFKREDKEKFEKLRK 74 (91)
Q Consensus 20 ~v~f~LEHs~ef~~ag~FsaRlk~~~~g~q~LtkLrlsRn~lse~ek~kfkeL~~ 74 (91)
.+++.++--.+....-.|+--...-.+|...+.. -+|+++|+++|++-++
T Consensus 262 ~~sv~~~g~yg~~~~v~~s~P~~ig~~Gv~~i~~-----l~L~~~E~~~l~~s~~ 311 (322)
T cd01338 262 SMAVPSDGSYGIPEGLIFSFPVRSKGGGYEIVEG-----LEIDDFAREKIDATLA 311 (322)
T ss_pred EEEEEccCccCCCCCeEEEEEEEEeCCEEEEEeC-----CCCCHHHHHHHHHHHH
Confidence 4555555434432334466666666666655333 3899999999998654
No 51
>smart00364 LRR_BAC Leucine-rich repeats, bacterial type.
Probab=27.14 E-value=30 Score=19.03 Aligned_cols=15 Identities=27% Similarity=0.350 Sum_probs=12.1
Q ss_pred cccceeEeecccCCH
Q 034556 49 QTLTKLLFSRNAFKR 63 (91)
Q Consensus 49 q~LtkLrlsRn~lse 63 (91)
+.|+.|..+.|+|++
T Consensus 2 ~~L~~L~vs~N~Lt~ 16 (26)
T smart00364 2 PSLKELNVSNNQLTS 16 (26)
T ss_pred cccceeecCCCcccc
Confidence 357889999999874
No 52
>PF01343 Peptidase_S49: Peptidase family S49 peptidase classification.; InterPro: IPR002142 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) [, ]. This group of serine peptidases belong to MEROPS peptidase family S49 (protease IV family, clan S-). The predicted active site serine for members of this family occurs in a transmembrane domain. The domain defines sequences in viruses, archaea, bacteria and plants. These sequences are variously annotated in the different taxonomic groups, examples are: Viruses: capsid protein Archaea: proteinase IV homolog Bacteria: proteinase IV, sohB, SppA, pfaP, putative protease Plants: SppA, protease IV This group also contains proteins classified as non-peptidase homologues that either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity of peptidases. Related proteins, non-peptidase homologs and unclassified S49 members are also to be found in IPR002810 from INTERPRO.; GO: 0008233 peptidase activity, 0006508 proteolysis; PDB: 3RST_B 3BEZ_D 3BF0_A.
Probab=27.03 E-value=46 Score=23.11 Aligned_cols=19 Identities=26% Similarity=0.655 Sum_probs=15.3
Q ss_pred eecccCCHHHHHHHHHHhh
Q 034556 56 FSRNAFKREDKEKFEKLRK 74 (91)
Q Consensus 56 lsRn~lse~ek~kfkeL~~ 74 (91)
++++++|+++|+.+++++.
T Consensus 75 ~~~~~~s~~~r~~~~~~l~ 93 (154)
T PF01343_consen 75 FPRDPMSEEERENLQELLD 93 (154)
T ss_dssp CTTSS--HHHHHHHHHHHH
T ss_pred CcCCCCCHHHHHHHHHHHH
Confidence 7899999999999998874
No 53
>PRK13920 putative anti-sigmaE protein; Provisional
Probab=26.74 E-value=56 Score=23.80 Aligned_cols=19 Identities=16% Similarity=0.204 Sum_probs=16.6
Q ss_pred cccCCHHHHHHHHHHhhcC
Q 034556 58 RNAFKREDKEKFEKLRKDD 76 (91)
Q Consensus 58 Rn~lse~ek~kfkeL~~~D 76 (91)
-+.+|++|+..|++.++.|
T Consensus 6 lG~Ls~eE~~~ve~~L~~d 24 (206)
T PRK13920 6 LGALSPEERARVEAALEAY 24 (206)
T ss_pred cCCCCHHHHHHHHHHHHHC
Confidence 3678999999999999877
No 54
>COG4921 Uncharacterized protein conserved in archaea [Function unknown]
Probab=26.62 E-value=36 Score=25.24 Aligned_cols=10 Identities=20% Similarity=0.541 Sum_probs=8.0
Q ss_pred hhcCCeEEEE
Q 034556 73 RKDDDFYLIC 82 (91)
Q Consensus 73 ~~~DgfYrIR 82 (91)
..+||||||.
T Consensus 13 ~e~Dg~yrV~ 22 (131)
T COG4921 13 AEEDGHYRVT 22 (131)
T ss_pred ccccceEEEE
Confidence 3579999985
No 55
>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=26.61 E-value=54 Score=21.62 Aligned_cols=16 Identities=25% Similarity=0.557 Sum_probs=10.5
Q ss_pred cccCCHHHHHHHHHHh
Q 034556 58 RNAFKREDKEKFEKLR 73 (91)
Q Consensus 58 Rn~lse~ek~kfkeL~ 73 (91)
+.+||++||+.+..|+
T Consensus 112 ~~~Lt~eEk~el~~Ll 127 (127)
T PF08278_consen 112 RGGLTDEEKQELRRLL 127 (127)
T ss_dssp TT---HHHHHHHHHHH
T ss_pred cCCcCHHHHHHHHHhC
Confidence 3779999999988874
No 56
>PF10213 MRP-S28: Mitochondrial ribosomal subunit protein ; InterPro: IPR019349 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 [, ]. This entry represents a conserved region of approx. 125 residues of one of the proteins that makes up the small subunit of the mitochondrial ribosome. In Saccharomyces cerevisiae (Baker's yeast) it is mitochondrial ribosomal protein S24 whereas in humans it is S35.
Probab=26.56 E-value=57 Score=23.13 Aligned_cols=22 Identities=14% Similarity=0.240 Sum_probs=17.4
Q ss_pred eeEeecccCCHHHHHHHHHHhh
Q 034556 53 KLLFSRNAFKREDKEKFEKLRK 74 (91)
Q Consensus 53 kLrlsRn~lse~ek~kfkeL~~ 74 (91)
.+.++.-.||+.++.||+.|+.
T Consensus 32 ~v~l~dL~L~~~a~~Kl~~LaG 53 (127)
T PF10213_consen 32 QVKLSDLGLSEKARHKLKLLAG 53 (127)
T ss_pred EEEHHhcCCCHHHHHHHHHHhh
Confidence 3556666999999999997763
No 57
>PF13801 Metal_resist: Heavy-metal resistance; PDB: 3EPV_C 2Y3D_A 2Y3H_D 2Y3G_B 2Y3B_A 2Y39_A 3LAY_H.
Probab=25.85 E-value=59 Score=20.03 Aligned_cols=18 Identities=17% Similarity=0.200 Sum_probs=14.1
Q ss_pred ecccCCHHHHHHHHHHhh
Q 034556 57 SRNAFKREDKEKFEKLRK 74 (91)
Q Consensus 57 sRn~lse~ek~kfkeL~~ 74 (91)
....||++++++++++..
T Consensus 38 ~~l~Lt~eQ~~~l~~~~~ 55 (125)
T PF13801_consen 38 DMLNLTPEQQAKLRALMD 55 (125)
T ss_dssp HHS-TTHHHHHHHHHHHH
T ss_pred hhcCCCHHHHHHHHHHHH
Confidence 346899999999999875
No 58
>PF03161 LAGLIDADG_2: LAGLIDADG DNA endonuclease family; InterPro: IPR004860 This is a family of site-specific DNA endonucleases encoded by DNA mobile elements. Similar to the homing endonuclease LAGLIDADG/HNH domain (IPR001982 from INTERPRO), the members of this family are also LAGLIDADG endonucleases. ; GO: 0004519 endonuclease activity; PDB: 3OOR_A 3OOL_A 3C0W_A 1R7M_A 3C0X_A.
Probab=25.79 E-value=1.4e+02 Score=21.20 Aligned_cols=37 Identities=22% Similarity=0.374 Sum_probs=25.9
Q ss_pred ceeEeecccCCHHHHHHHHHHhhc-------------CCeEEEEeecccc
Q 034556 52 TKLLFSRNAFKREDKEKFEKLRKD-------------DDFYLICYLAGCH 88 (91)
Q Consensus 52 tkLrlsRn~lse~ek~kfkeL~~~-------------DgfYrIRvPsnvl 88 (91)
..+.|+=+.||.+|...+.+++.. .+-|+|.+|+.-.
T Consensus 125 ~g~~l~T~sFt~~Ev~~L~~~L~~kf~l~~~i~~~~~~~~y~i~i~~~s~ 174 (178)
T PF03161_consen 125 RGIRLCTNSFTKEEVERLQNILKTKFGLKCSIHKHGKKNQYRIYIPAKSM 174 (178)
T ss_dssp --EEE--TTS-HHHHHHHHHHHHHHH---EEEEEET--TEEEEEE-GGGH
T ss_pred CcEEEEECCCCHHHHHHHHHHHHHHhCeEEEEEEcCCCceEEEEEeHHHH
Confidence 679999999999999999998864 3689999987643
No 59
>COG3170 FimV Tfp pilus assembly protein FimV [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=25.48 E-value=21 Score=32.69 Aligned_cols=34 Identities=15% Similarity=0.226 Sum_probs=29.1
Q ss_pred cceeEeecccCCHHHHHHHHHHhhcCCeEEEEeecc
Q 034556 51 LTKLLFSRNAFKREDKEKFEKLRKDDDFYLICYLAG 86 (91)
Q Consensus 51 LtkLrlsRn~lse~ek~kfkeL~~~DgfYrIRvPsn 86 (91)
.-+--|+||++.-+.| |..|.+-+|-|.|||-++
T Consensus 77 faragl~r~~~l~~lr--fs~v~q~~g~~vIRVsS~ 110 (755)
T COG3170 77 FARAGLERNPFLSDLR--FSPVHQPRGKAVIRVSSA 110 (755)
T ss_pred HHHhccccccceeeee--eeeeecCCCceEEEeecC
Confidence 3455678999999988 999999999999999775
No 60
>PF14794 DUF4479: Domain of unknown function (DUF4479); PDB: 3BU2_C.
Probab=25.37 E-value=60 Score=21.11 Aligned_cols=20 Identities=15% Similarity=0.232 Sum_probs=14.6
Q ss_pred ccCCHHHHHHHHHHhhcCCe
Q 034556 59 NAFKREDKEKFEKLRKDDDF 78 (91)
Q Consensus 59 n~lse~ek~kfkeL~~~Dgf 78 (91)
-.||++.-+++.++++.-||
T Consensus 46 V~Lt~eqv~~LN~~l~~~Gf 65 (73)
T PF14794_consen 46 VFLTEEQVAKLNQALQKAGF 65 (73)
T ss_dssp ----HHHHHHHHHHHHHTT-
T ss_pred EEcCHHHHHHHHHHHHHcCC
Confidence 36899999999999999998
No 61
>PRK00587 hypothetical protein; Provisional
Probab=24.60 E-value=43 Score=23.06 Aligned_cols=34 Identities=18% Similarity=0.337 Sum_probs=29.6
Q ss_pred cccccccccccceeEeecccCCHHHHHHHHHHhh
Q 034556 41 LKISSHSVQTLTKLLFSRNAFKREDKEKFEKLRK 74 (91)
Q Consensus 41 lk~~~~g~q~LtkLrlsRn~lse~ek~kfkeL~~ 74 (91)
.+....|.+++.++.+...-|.++|++-+++|+.
T Consensus 37 VkV~~nG~~~i~~i~Idp~lld~eD~E~LeDLI~ 70 (99)
T PRK00587 37 ILIKIKGNLNIEKIEINKELIDPEDKETLQDMLR 70 (99)
T ss_pred EEEEEEcCccEEEEEECHHHcCCccHHHHHHHHH
Confidence 4566778899999999999999999999999863
No 62
>PF09999 DUF2240: Uncharacterized protein conserved in archaea (DUF2240); InterPro: IPR018716 This family of various hypothetical archaeal proteins has no known function.
Probab=23.50 E-value=81 Score=23.15 Aligned_cols=45 Identities=9% Similarity=0.062 Sum_probs=35.0
Q ss_pred CCccccccccccccccccceeEeecccCCHHHHHHHHHHhhcCCe
Q 034556 34 TNTPQNLLKISSHSVQTLTKLLFSRNAFKREDKEKFEKLRKDDDF 78 (91)
Q Consensus 34 ag~FsaRlk~~~~g~q~LtkLrlsRn~lse~ek~kfkeL~~~Dgf 78 (91)
++-|..+++....-+-=.-.|+|-+.=+|.++..++-+.+..-|+
T Consensus 7 AapFk~kg~~~L~~sefv~~Ls~D~~WmspdqAk~li~~A~~eGL 51 (144)
T PF09999_consen 7 AAPFKQKGKDRLSKSEFVFALSFDRKWMSPDQAKRLIDEAIEEGL 51 (144)
T ss_pred hHHHHHcCccccChhheEeeEeeecCCCCHHHHHHHHHHHHHCCC
Confidence 455777777666655555789999999999999999998866554
No 63
>TIGR00053 addiction module toxin component, YafQ family. This model represents a cluster of eubacterial proteins and a cluster of archaeal proteins, all of which are uncharacterized, from 85 to 102 residues in length, and similar in sequence. These include YafQ, a ribosome-associated endoribonuclease that serves as part of a toxin-antitoxin system, for which DinJ is the antidote component.
Probab=23.21 E-value=50 Score=20.69 Aligned_cols=8 Identities=13% Similarity=0.023 Sum_probs=6.9
Q ss_pred CCeEEEEe
Q 034556 76 DDFYLICY 83 (91)
Q Consensus 76 DgfYrIRv 83 (91)
.|||||||
T Consensus 55 ~g~~r~rv 62 (89)
T TIGR00053 55 KGFRRCHI 62 (89)
T ss_pred CCCEEEee
Confidence 47999999
No 64
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=23.20 E-value=97 Score=15.96 Aligned_cols=19 Identities=21% Similarity=0.288 Sum_probs=14.8
Q ss_pred ccCCHHHHHHHHHHhhcCC
Q 034556 59 NAFKREDKEKFEKLRKDDD 77 (91)
Q Consensus 59 n~lse~ek~kfkeL~~~Dg 77 (91)
.+.|++|.+.|.++++.=|
T Consensus 2 ~~Wt~~E~~~l~~~~~~~g 20 (49)
T smart00717 2 GEWTEEEDELLIELVKKYG 20 (49)
T ss_pred CCCCHHHHHHHHHHHHHHC
Confidence 5689999999998876533
No 65
>TIGR00705 SppA_67K signal peptide peptidase SppA, 67K type. E. coli SohB, which is most closely homologous to the C-terminal duplication of SppA, is predicted to perform a similar function of small peptide degradation, but in the periplasm. Many prokaryotes have a single SppA/SohB homolog that may perform the function of either or both.
Probab=23.10 E-value=61 Score=27.89 Aligned_cols=20 Identities=20% Similarity=0.428 Sum_probs=17.5
Q ss_pred EeecccCCHHHHHHHHHHhh
Q 034556 55 LFSRNAFKREDKEKFEKLRK 74 (91)
Q Consensus 55 rlsRn~lse~ek~kfkeL~~ 74 (91)
-|+|+++|+++|+.++.++.
T Consensus 195 pf~r~~mS~e~re~~~~~l~ 214 (584)
T TIGR00705 195 PFSRKDMSPEARRNYQRWLG 214 (584)
T ss_pred cccCCCCCHHHHHHHHHHHH
Confidence 36889999999999999875
No 66
>PRK11713 16S ribosomal RNA methyltransferase RsmE; Provisional
Probab=22.92 E-value=80 Score=23.51 Aligned_cols=27 Identities=15% Similarity=0.156 Sum_probs=22.1
Q ss_pred cCCHHHHHHHHHHhhcCCeEEEEeeccccCC
Q 034556 60 AFKREDKEKFEKLRKDDDFYLICYLAGCHPA 90 (91)
Q Consensus 60 ~lse~ek~kfkeL~~~DgfYrIRvPsnvl~~ 90 (91)
-||++|.+.|++. ||+.|.+-.++|-+
T Consensus 189 Gfs~~Ei~~l~~~----g~~~vsLG~~ILR~ 215 (234)
T PRK11713 189 GFSPEEIELLREA----GFTPVSLGPRILRT 215 (234)
T ss_pred CCCHHHHHHHHHC----CCEEeccCCCchhh
Confidence 4899999988874 89999998887753
No 67
>cd01336 MDH_cytoplasmic_cytosolic Cytoplasmic and cytosolic Malate dehydrogenases. MDH is one of the key enzymes in the citric acid cycle, facilitating both the conversion of malate to oxaloacetate and replenishing levels of oxalacetate by reductive carboxylation of pyruvate. Members of this subfamily are eukaryotic MDHs localized to the cytoplasm and cytosol. MDHs are part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of protein families including the NAD(P)-binding domains of alcohol dehydrogenases, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate dehydrogenases, formate/glycerate dehydrogenases, siroheme synthases, 6-phosphogluconate dehydrogenases, aminoacid dehydrogenases, repressor rex, and NAD-binding potassium channel domains, among others.
Probab=22.82 E-value=1.2e+02 Score=24.02 Aligned_cols=35 Identities=11% Similarity=0.040 Sum_probs=23.9
Q ss_pred CccccccccccccccccceeEeecccCCHHHHHHHHHHhh
Q 034556 35 NTPQNLLKISSHSVQTLTKLLFSRNAFKREDKEKFEKLRK 74 (91)
Q Consensus 35 g~FsaRlk~~~~g~q~LtkLrlsRn~lse~ek~kfkeL~~ 74 (91)
-.|+--..+-..|...+-.| +|+++|+++|++-++
T Consensus 281 v~~s~P~~ig~~Gv~~i~~~-----~L~~~E~~~l~~s~~ 315 (325)
T cd01336 281 LIFSFPVTCKNGKWKIVQGL-----SIDDFSREKIDATAK 315 (325)
T ss_pred eEEEEEEEEeCCEEEEecCC-----CCCHHHHHHHHHHHH
Confidence 34565555655666554333 899999999998654
No 68
>PF04809 HupH_C: HupH hydrogenase expression protein, C-terminal conserved region; InterPro: IPR006894 This entry represents the C-terminal conserved domain found in bacterial hydrogenase expression proteins (HupH), which are necessary for hydrogenase synthesis. The precise function of HupH is unknown [].; PDB: 3SB1_A.
Probab=22.63 E-value=48 Score=23.27 Aligned_cols=29 Identities=3% Similarity=0.001 Sum_probs=19.0
Q ss_pred cccccccceeEeecccCCHHHHHHHHHHhh
Q 034556 45 SHSVQTLTKLLFSRNAFKREDKEKFEKLRK 74 (91)
Q Consensus 45 ~~g~q~LtkLrlsRn~lse~ek~kfkeL~~ 74 (91)
..|++. ..+.|+.-|||++|+..+.+++-
T Consensus 20 ~~~~~~-~~I~L~~lPLs~~D~~~L~~~LG 48 (120)
T PF04809_consen 20 RPGGPP-HVINLTLLPLSPADRALLDETLG 48 (120)
T ss_dssp HHH----EEEEGGGS---HHHHHHHHHHH-
T ss_pred cCCCCC-eEEEecCCCCCHHHHHHHHHHcC
Confidence 344455 78999999999999999999874
No 69
>PF09143 AvrPphF-ORF-2: AvrPphF-ORF-2; InterPro: IPR015226 Many Gram-negative pathogenic bacteria directly translocate effector proteins into eukaryotic host cells via a type III secretion system. Type III effector proteins are determinants of virulence on susceptible plant hosts; they are also the proteins that trigger specific disease resistance in resistant plant hosts. Evolution of type III effectors is dominated by competing forces: the likely requirement for conservation of virulence function, the avoidance of host defenses, and possible adaptation to new hosts. Members of this family of plant pathogenic proteins adopt an elongated structure somewhat reminiscent of a mushroom that can be divided into 'stalk' and 'head' subdomains. The stalk subdomain is composed of the N-terminal helix (alpha1) and beta strands beta3-beta4. An antiparallel beta sheet (beta5, beta7-beta8) forms the base of the head subdomain that interacts with the stalk. A pair of twisted antiparallel beta sheets (beta1 and beta6; beta2 and beta9/9') supported by alpha2 form the dome of the head. The head subdomain possesses weak structural similarity with the catalytic portion of a number of ADP-ribosylt ransferase toxins []. ; PDB: 1S21_A.
Probab=22.24 E-value=52 Score=25.39 Aligned_cols=22 Identities=27% Similarity=0.351 Sum_probs=13.1
Q ss_pred ccccccceeEeecccCCHHHHHHHHH
Q 034556 46 HSVQTLTKLLFSRNAFKREDKEKFEK 71 (91)
Q Consensus 46 ~g~q~LtkLrlsRn~lse~ek~kfke 71 (91)
-|+++||++ +||+.++|++|-+
T Consensus 4 vgg~~~tsv----~qL~~~~r~~fL~ 25 (175)
T PF09143_consen 4 VGGQTLTSV----YQLSPEERKAFLN 25 (175)
T ss_dssp TT-----BG----GGS-HHHHHHHHH
T ss_pred ccCccccch----hhCCHHHHHHHHH
Confidence 477887765 7999999999965
No 70
>PF02216 B: B domain; InterPro: IPR003132 This entry represents the immunoglobulin-binding domain found in the Staphylococcus aureus virulence factor protein A (SpA). Protein A contains five highly homologous Ig-binding domains in tandem (designated domains E, D, A, B and C), which share a common structure consisting of three helices in a closed left-handed twist. Protein A can exist in both secreted and membrane-bound forms, and has two distinct Ig-binding activities: each domain can bind Fc-gamma (the constant region of IgG involved in effector functions) and Fab (the Ig fragment responsible for antigen recognition) [].; GO: 0019865 immunoglobulin binding, 0009405 pathogenesis; PDB: 1EDL_A 1EDI_A 1EDJ_A 1EDK_A 2B88_A 2B87_A 2B89_A 1FC2_C 1DEE_H 1ZXG_A ....
Probab=22.11 E-value=73 Score=20.46 Aligned_cols=18 Identities=22% Similarity=0.381 Sum_probs=13.5
Q ss_pred ccCCHHHHHHHHHHhhcC
Q 034556 59 NAFKREDKEKFEKLRKDD 76 (91)
Q Consensus 59 n~lse~ek~kfkeL~~~D 76 (91)
..||||+|+.|-+-+++|
T Consensus 20 ~nLteeQrn~yI~~lKdd 37 (54)
T PF02216_consen 20 PNLTEEQRNGYIQSLKDD 37 (54)
T ss_dssp TTS-HHHHHHHHHHHHH-
T ss_pred CCcCHHHHHhHHHHHhhC
Confidence 468999999998888877
No 71
>PRK14629 hypothetical protein; Provisional
Probab=21.92 E-value=54 Score=22.62 Aligned_cols=33 Identities=15% Similarity=0.246 Sum_probs=28.9
Q ss_pred cccccccccccceeEeecccCCHHHHHHHHHHh
Q 034556 41 LKISSHSVQTLTKLLFSRNAFKREDKEKFEKLR 73 (91)
Q Consensus 41 lk~~~~g~q~LtkLrlsRn~lse~ek~kfkeL~ 73 (91)
.+.+..|.+++.++.+.-.-+.++|++-+++|+
T Consensus 40 VkV~~nG~~~v~~i~Idp~lld~eD~e~LeDLI 72 (99)
T PRK14629 40 VVVEMNGEFNVKKVSIKEEFFDDLDNEALEHMI 72 (99)
T ss_pred EEEEEEcCccEEEEEECHHHcCcccHHHHHHHH
Confidence 345667889999999999999999999999986
No 72
>TIGR01573 cas2 CRISPR-associated endoribonuclease Cas2. This model describes most members of the family of Cas2, one of the first four protein families found to mark prokaryotic genomes that contain multiple CRISPR elements. It is an endoribonuclease, capable of cleaving single-stranded RNA. CRISPR is an acronym for Clustered Regularly Interspaced Short Palindromic Repeats. The cas genes are found near the repeats. A distinct branch of the Cas2 family shows a very low level of sequence identity and is modeled by TIGR01873 instead.
Probab=21.89 E-value=48 Score=21.76 Aligned_cols=18 Identities=17% Similarity=0.276 Sum_probs=14.9
Q ss_pred HHHHHHHHHhhcCCeEEE
Q 034556 64 EDKEKFEKLRKDDDFYLI 81 (91)
Q Consensus 64 ~ek~kfkeL~~~DgfYrI 81 (91)
..+.|+.+++...||.||
T Consensus 16 k~r~kv~k~L~~~G~~rv 33 (95)
T TIGR01573 16 KRRRKLRKLLEKYGLQRV 33 (95)
T ss_pred HHHHHHHHHHHHcchhhe
Confidence 478889999999998776
No 73
>COG3549 HigB Plasmid maintenance system killer protein [General function prediction only]
Probab=21.60 E-value=57 Score=22.93 Aligned_cols=18 Identities=33% Similarity=0.366 Sum_probs=11.9
Q ss_pred HHHHHh-hcCCeEEEEeec
Q 034556 68 KFEKLR-KDDDFYLICYLA 85 (91)
Q Consensus 68 kfkeL~-~~DgfYrIRvPs 85 (91)
-|++|- ..+|+|.|||--
T Consensus 53 ~~E~L~gd~~g~ySIrvN~ 71 (94)
T COG3549 53 HFEKLGGDLKGLYSIRVNQ 71 (94)
T ss_pred hHHHcCCCccCcEEEEECC
Confidence 344442 457999999843
No 74
>PF11491 DUF3213: Protein of unknown function (DUF3213) ; InterPro: IPR021583 The backbone structure of this family of proteins has been determined however the function remains unknown. The protein has an alpha and beta structure with a ferredoxin-like fold []. ; PDB: 2F40_A.
Probab=21.38 E-value=35 Score=23.79 Aligned_cols=28 Identities=25% Similarity=0.372 Sum_probs=14.1
Q ss_pred eEeecccCCHHHHH-HHHHHhhcCCeEEEEe
Q 034556 54 LLFSRNAFKREDKE-KFEKLRKDDDFYLICY 83 (91)
Q Consensus 54 LrlsRn~lse~ek~-kfkeL~~~DgfYrIRv 83 (91)
|+| +.+|.||.. +==+|..+|++|||=+
T Consensus 3 lkf--g~It~eeA~~~QYeLsk~~~vyRvFi 31 (88)
T PF11491_consen 3 LKF--GNITPEEAMVKQYELSKNEAVYRVFI 31 (88)
T ss_dssp EE----S-TTTTTHHHHHTTTTTTTB-----
T ss_pred ccc--CCCCHHHHHHHHHHhhcccceeeeee
Confidence 455 666766644 4448999999999843
No 75
>cd05293 LDH_1 A subgroup of L-lactate dehydrogenases. L-lactate dehydrogenases (LDH) are tetrameric enzymes catalyzing the last step of glycolysis in which pyruvate is converted to L-lactate. This subgroup is composed of eukaryotic LDHs. Vertebrate LDHs are non-allosteric. This is in contrast to some bacterial LDHs that are activated by an allosteric effector such as fructose-1,6-bisphosphate. LDHs are part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of protein families including the NAD(P)-binding domains of alcohol dehydrogenases, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate dehydrogenases, formate/glycerate dehydrogenases, siroheme synthases, 6-phosphogluconate dehydrogenases, aminoacid dehydrogenases, repressor rex, and NAD-binding potassium channel domains, among others.
Probab=21.37 E-value=1.3e+02 Score=23.65 Aligned_cols=49 Identities=12% Similarity=0.026 Sum_probs=29.0
Q ss_pred eeEEeecCCCCCCCCccccccccccccccccceeEeecccCCHHHHHHHHHHhh
Q 034556 21 VQATHHHNTLPLPTNTPQNLLKISSHSVQTLTKLLFSRNAFKREDKEKFEKLRK 74 (91)
Q Consensus 21 v~f~LEHs~ef~~ag~FsaRlk~~~~g~q~LtkLrlsRn~lse~ek~kfkeL~~ 74 (91)
+++.++--.+..+...|+-=...-..|...+..| +|+++|+++|++-++
T Consensus 256 vsv~~~g~yg~~~d~~~svP~~ig~~Gi~~i~~l-----~L~~~E~~~l~~s~~ 304 (312)
T cd05293 256 VSTLVKGLHGIEDEVFLSLPCILGENGITHVIKQ-----PLTEEEQEKLQKSAD 304 (312)
T ss_pred EEEEeCCccCCCCCeEEEEeEEEeCCceEEEecC-----CCCHHHHHHHHHHHH
Confidence 3444443223323344555555556666654333 799999999998764
No 76
>PF14226 DIOX_N: non-haem dioxygenase in morphine synthesis N-terminal; PDB: 3OOX_A 1BK0_A 1IPS_B 1QIQ_A 1OC1_A 2Y86_A 2Y60_A 1W03_A 2VE1_A 1QJF_A ....
Probab=21.26 E-value=1.7e+02 Score=18.56 Aligned_cols=34 Identities=12% Similarity=0.195 Sum_probs=20.0
Q ss_pred cceeEeeccc-CCHHHHHHHHHHhhcCCeEEEEee
Q 034556 51 LTKLLFSRNA-FKREDKEKFEKLRKDDDFYLICYL 84 (91)
Q Consensus 51 LtkLrlsRn~-lse~ek~kfkeL~~~DgfYrIRvP 84 (91)
|+.+.|+.+. =.++..+++.+-+...||+.|.-.
T Consensus 1 iPvIDls~~~~~~~~~~~~l~~A~~~~GFf~l~nh 35 (116)
T PF14226_consen 1 IPVIDLSPDPADREEVAEQLRDACEEWGFFYLVNH 35 (116)
T ss_dssp --EEEHGGCHHHHHHHHHHHHHHHHHTSEEEEESS
T ss_pred CCeEECCCCCccHHHHHHHHHHHHHhCCEEEEecc
Confidence 3456666511 012344677778889999988654
No 77
>PF14584 DUF4446: Protein of unknown function (DUF4446)
Probab=21.11 E-value=73 Score=23.22 Aligned_cols=15 Identities=40% Similarity=0.554 Sum_probs=12.6
Q ss_pred ecccCCHHHHHHHHH
Q 034556 57 SRNAFKREDKEKFEK 71 (91)
Q Consensus 57 sRn~lse~ek~kfke 71 (91)
|.-+||+||++++++
T Consensus 135 S~~~LS~EE~eal~~ 149 (151)
T PF14584_consen 135 SSYPLSEEEKEALEK 149 (151)
T ss_pred ccccCCHHHHHHHHH
Confidence 456899999999876
No 78
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=20.93 E-value=84 Score=23.34 Aligned_cols=18 Identities=28% Similarity=0.353 Sum_probs=16.0
Q ss_pred CCHHHHHHHHHHhhcCCe
Q 034556 61 FKREDKEKFEKLRKDDDF 78 (91)
Q Consensus 61 lse~ek~kfkeL~~~Dgf 78 (91)
+|.+||+-|++|..+.|.
T Consensus 63 ~~~~Er~lF~~L~~V~GI 80 (191)
T TIGR00084 63 NTLEERELFKELIKVNGV 80 (191)
T ss_pred CCHHHHHHHHHHhCCCCC
Confidence 589999999999998874
No 79
>PF07051 OCIA: Ovarian carcinoma immunoreactive antigen (OCIA); InterPro: IPR009764 This family consists of several ovarian carcinoma immunoreactive antigen (OCIA) and related eukaryotic sequences. The function of this family is unknown [,].
Probab=20.54 E-value=66 Score=22.99 Aligned_cols=26 Identities=8% Similarity=0.230 Sum_probs=18.9
Q ss_pred cccCCHHHHHHHHHHhhcCCeEEEEee
Q 034556 58 RNAFKREDKEKFEKLRKDDDFYLICYL 84 (91)
Q Consensus 58 Rn~lse~ek~kfkeL~~~DgfYrIRvP 84 (91)
..++|+||+..|+|--.+-=+|| -||
T Consensus 23 ~~~~T~EE~kvlrEC~~ESFwyR-slP 48 (111)
T PF07051_consen 23 PYQLTEEERKVLRECNEESFWYR-SLP 48 (111)
T ss_pred CccCCHHHHHHHHHHHHhhhHhc-cCc
Confidence 35799999999999876654443 444
No 80
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=20.14 E-value=87 Score=23.37 Aligned_cols=17 Identities=24% Similarity=0.376 Sum_probs=15.6
Q ss_pred CCHHHHHHHHHHhhcCC
Q 034556 61 FKREDKEKFEKLRKDDD 77 (91)
Q Consensus 61 lse~ek~kfkeL~~~Dg 77 (91)
.|++||+-|+.|..+.|
T Consensus 64 ~~~~Er~lF~~LisV~G 80 (186)
T PRK14600 64 LNREEQDCLRMLVKVSG 80 (186)
T ss_pred CCHHHHHHHHHHhCcCC
Confidence 48999999999999887
Done!