Query 032021
Match_columns 148
No_of_seqs 19 out of 21
Neff 2.1
Searched_HMMs 46136
Date Fri Mar 29 08:31:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032021.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032021hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF07544 Med9: RNA polymerase 92.6 0.24 5.2E-06 34.7 4.2 59 85-147 4-64 (83)
2 PF07197 DUF1409: Protein of u 89.4 0.33 7.2E-06 33.0 2.4 40 106-145 8-50 (51)
3 TIGR02481 hemeryth_dom hemeryt 75.1 12 0.00025 26.3 5.5 46 81-126 16-65 (126)
4 PF10264 Stork_head: Winged he 71.7 2.8 6E-05 30.5 1.8 56 81-136 5-68 (80)
5 cd00446 GrpE GrpE is the adeni 65.5 24 0.00051 26.1 5.6 42 84-125 40-81 (137)
6 PRK00808 hypothetical protein; 61.4 22 0.00047 26.6 4.9 45 82-126 21-68 (150)
7 PF00804 Syntaxin: Syntaxin; 58.0 16 0.00034 23.9 3.2 27 104-130 46-72 (103)
8 KOG3598 Thyroid hormone recept 57.1 6.1 0.00013 42.1 1.6 12 104-115 2190-2201(2220)
9 PRK12333 nucleoside triphospha 56.1 19 0.00041 30.0 4.1 35 74-114 23-57 (204)
10 PF05008 V-SNARE: Vesicle tran 55.9 54 0.0012 21.6 5.6 48 86-134 5-52 (79)
11 PRK10697 DNA-binding transcrip 55.8 22 0.00047 27.3 4.1 43 102-144 76-118 (118)
12 PF08965 DUF1870: Domain of un 55.1 24 0.00051 27.4 4.2 35 97-132 37-71 (118)
13 PF02607 B12-binding_2: B12 bi 53.7 47 0.001 21.4 4.9 27 87-114 3-29 (79)
14 TIGR01220 Pmev_kin_Gr_pos phos 50.7 26 0.00056 29.7 4.1 42 86-135 255-300 (358)
15 PF04316 FlgM: Anti-sigma-28 f 49.5 23 0.00049 23.0 2.9 25 88-112 29-53 (57)
16 cd00522 Hemerythrin Hemerythri 49.3 53 0.0011 23.3 5.0 43 82-127 19-61 (113)
17 PF01025 GrpE: GrpE; InterPro 47.6 37 0.00081 25.1 4.2 41 85-125 67-107 (165)
18 PRK14151 heat shock protein Gr 46.8 46 0.001 26.6 4.8 53 84-139 75-127 (176)
19 PRK14141 heat shock protein Gr 46.6 42 0.00092 27.7 4.7 56 84-139 86-143 (209)
20 TIGR02978 phageshock_pspC phag 43.7 43 0.00093 25.5 4.0 41 104-144 81-121 (121)
21 PF10458 Val_tRNA-synt_C: Valy 43.4 37 0.00079 22.6 3.2 43 105-147 2-51 (66)
22 PF13964 Kelch_6: Kelch motif 41.9 16 0.00035 21.9 1.2 13 7-19 37-49 (50)
23 PRK14149 heat shock protein Gr 41.2 70 0.0015 26.2 5.2 29 84-112 91-119 (191)
24 PF09720 Unstab_antitox: Putat 41.2 79 0.0017 20.0 4.4 33 86-119 8-40 (54)
25 PF07304 SRA1: Steroid recepto 41.0 21 0.00046 27.7 2.1 39 86-125 91-130 (157)
26 PRK14140 heat shock protein Gr 38.9 96 0.0021 25.3 5.6 48 84-135 92-139 (191)
27 PRK14159 heat shock protein Gr 38.6 85 0.0018 25.3 5.2 29 84-112 78-106 (176)
28 PF04912 Dynamitin: Dynamitin 38.2 34 0.00073 29.4 3.0 61 87-147 316-383 (388)
29 PRK14162 heat shock protein Gr 36.8 76 0.0016 26.0 4.7 56 78-139 90-145 (194)
30 PRK14157 heat shock protein Gr 36.4 51 0.0011 27.9 3.7 19 84-102 132-150 (227)
31 PF02268 TFIIA_gamma_N: Transc 36.4 70 0.0015 21.4 3.7 30 87-119 14-43 (49)
32 PRK14161 heat shock protein Gr 35.4 1E+02 0.0022 24.8 5.1 50 84-135 74-123 (178)
33 PF09824 ArsR: ArsR transcript 35.3 26 0.00057 28.6 1.8 51 86-144 107-157 (160)
34 PRK14155 heat shock protein Gr 35.1 92 0.002 25.7 5.0 52 84-136 68-119 (208)
35 PF07011 DUF1313: Protein of u 34.9 46 0.001 24.9 2.9 44 88-131 28-73 (87)
36 PRK14164 heat shock protein Gr 34.9 70 0.0015 26.7 4.3 23 77-101 120-142 (218)
37 PF07904 Eaf7: Chromatin modif 34.0 46 0.00099 23.9 2.7 37 81-117 20-58 (91)
38 PRK14142 heat shock protein Gr 33.9 59 0.0013 27.5 3.8 25 77-103 83-107 (223)
39 cd07354 HN_L-delphilin-R1_like 33.8 45 0.00097 24.6 2.7 45 88-132 22-68 (80)
40 PF13418 Kelch_4: Galactose ox 33.6 18 0.00039 21.4 0.5 12 7-18 38-49 (49)
41 COG0576 GrpE Molecular chapero 33.6 1.1E+02 0.0024 24.5 5.1 26 77-104 86-111 (193)
42 PRK14148 heat shock protein Gr 33.5 1.1E+02 0.0024 25.0 5.2 33 78-112 91-123 (195)
43 PF04108 APG17: Autophagy prot 32.9 60 0.0013 28.5 3.7 22 107-128 210-231 (412)
44 PF01858 RB_A: Retinoblastoma- 32.5 55 0.0012 26.1 3.2 38 82-128 146-184 (194)
45 TIGR03824 FlgM_jcvi flagellar 32.5 65 0.0014 22.7 3.2 26 87-112 66-91 (95)
46 PRK14153 heat shock protein Gr 31.8 1.2E+02 0.0026 24.8 5.1 57 77-139 83-139 (194)
47 cd03415 CbiX_CbiC Archaeal sir 31.6 36 0.00077 25.5 1.9 22 96-117 6-27 (125)
48 PRK14139 heat shock protein Gr 31.5 1.1E+02 0.0023 24.9 4.8 52 77-136 82-133 (185)
49 PF06013 WXG100: Proteins of 1 31.4 1.2E+02 0.0027 18.5 4.1 47 85-132 30-76 (86)
50 PRK14150 heat shock protein Gr 31.1 1.2E+02 0.0027 24.4 5.0 58 77-139 88-145 (193)
51 PF08020 DUF1706: Protein of u 30.3 65 0.0014 25.5 3.3 33 103-135 5-37 (166)
52 cd03414 CbiX_SirB_C Sirohydroc 29.5 48 0.001 22.9 2.1 23 96-118 6-28 (117)
53 smart00388 HisKA His Kinase A 29.0 1.1E+02 0.0024 17.0 5.6 35 94-128 25-59 (66)
54 PRK14143 heat shock protein Gr 28.0 1.5E+02 0.0031 25.0 5.1 58 77-140 117-175 (238)
55 PRK06663 flagellar hook-associ 27.8 1.5E+02 0.0032 25.9 5.3 59 84-146 310-368 (419)
56 PF06295 DUF1043: Protein of u 27.5 69 0.0015 23.9 2.9 19 110-128 46-64 (128)
57 PF08580 KAR9: Yeast cortical 27.3 53 0.0011 31.3 2.6 46 84-132 68-113 (683)
58 PF06266 HrpF: HrpF protein; 27.2 91 0.002 22.7 3.3 26 104-129 3-28 (74)
59 COG3443 Predicted periplasmic 26.9 17 0.00036 30.6 -0.6 10 78-87 149-158 (193)
60 PF14361 RsbRD_N: RsbT co-anta 26.5 85 0.0018 22.0 3.0 39 85-132 41-79 (105)
61 TIGR00058 Hemerythrin hemeryth 26.5 1.5E+02 0.0032 21.3 4.3 41 82-126 22-62 (115)
62 PRK14146 heat shock protein Gr 26.5 1.6E+02 0.0036 24.3 5.1 29 84-112 109-137 (215)
63 PF10158 LOH1CR12: Tumour supp 25.7 71 0.0015 24.6 2.7 24 109-132 89-112 (131)
64 PRK10325 heat shock protein Gr 25.4 1.5E+02 0.0034 23.9 4.7 52 84-139 94-146 (197)
65 PF12776 Myb_DNA-bind_3: Myb/S 25.3 1E+02 0.0022 20.4 3.1 15 87-101 9-23 (96)
66 PRK14156 heat shock protein Gr 25.0 1.2E+02 0.0027 24.4 4.1 23 78-102 78-100 (177)
67 PRK08027 flgL flagellar hook-a 24.9 1.6E+02 0.0034 24.8 4.7 63 84-146 199-266 (317)
68 PF00512 HisKA: His Kinase A ( 24.8 1.7E+02 0.0038 17.8 5.6 43 86-128 17-61 (68)
69 COG2747 FlgM Negative regulato 24.4 1.2E+02 0.0025 22.6 3.5 27 85-111 59-85 (93)
70 PF14966 DNA_repr_REX1B: DNA r 23.9 2.1E+02 0.0045 20.8 4.7 41 90-131 24-64 (97)
71 PRK01885 greB transcription el 23.8 90 0.0019 24.2 2.9 18 88-105 30-47 (157)
72 PF03127 GAT: GAT domain; Int 23.8 2.6E+02 0.0057 19.5 5.7 46 87-132 21-66 (100)
73 PF04212 MIT: MIT (microtubule 23.7 2.1E+02 0.0046 18.4 4.6 39 87-125 30-68 (69)
74 PF12806 Acyl-CoA_dh_C: Acetyl 23.7 61 0.0013 23.4 1.9 18 84-101 106-123 (130)
75 PLN02372 violaxanthin de-epoxi 23.6 64 0.0014 30.2 2.4 20 87-106 361-380 (455)
76 PRK14145 heat shock protein Gr 23.5 2E+02 0.0044 23.6 5.1 28 84-114 100-127 (196)
77 PF08649 DASH_Dad1: DASH compl 23.5 1.3E+02 0.0028 20.8 3.4 28 104-131 6-33 (58)
78 PF06580 His_kinase: Histidine 23.2 2.3E+02 0.0051 19.2 4.6 56 79-145 9-64 (82)
79 PRK07192 flgL flagellar hook-a 23.0 2.2E+02 0.0047 23.1 5.1 62 84-145 190-254 (305)
80 PRK14158 heat shock protein Gr 23.0 2.2E+02 0.0049 23.3 5.2 47 84-135 95-141 (194)
81 PF14461 Prok-E2_B: Prokaryoti 23.0 1.5E+02 0.0032 21.8 3.8 33 85-117 93-125 (133)
82 KOG3182 Predicted cation trans 22.9 95 0.0021 26.6 3.1 41 85-126 156-196 (212)
83 KOG3661 Uncharacterized conser 22.8 88 0.0019 31.6 3.3 47 98-144 577-626 (1019)
84 PF01903 CbiX: CbiX; InterPro 22.3 1.1E+02 0.0024 20.5 2.9 21 98-118 1-21 (105)
85 PF01920 Prefoldin_2: Prefoldi 22.3 1.2E+02 0.0026 20.4 3.0 44 103-146 58-101 (106)
86 PF01497 Peripla_BP_2: Peripla 22.2 2.6E+02 0.0057 20.5 5.0 39 85-126 98-136 (238)
87 PF07445 priB_priC: Primosomal 22.1 3.9E+02 0.0085 21.0 6.2 63 70-133 102-171 (173)
88 PF08388 GIIM: Group II intron 22.1 1.8E+02 0.0038 18.8 3.7 28 88-115 4-31 (80)
89 PF08780 NTase_sub_bind: Nucle 22.0 2.5E+02 0.0055 20.7 4.9 39 85-124 6-44 (124)
90 PRK07701 flgL flagellar hook-a 21.9 2.6E+02 0.0056 22.7 5.3 58 84-146 190-247 (298)
91 PRK14144 heat shock protein Gr 21.6 1.9E+02 0.0041 23.9 4.5 47 84-135 100-146 (199)
92 cd03416 CbiX_SirB_N Sirohydroc 21.6 78 0.0017 21.3 2.0 23 96-118 5-27 (101)
93 cd00632 Prefoldin_beta Prefold 21.6 1.2E+02 0.0026 21.4 3.0 44 104-147 60-103 (105)
94 PTZ00332 paraflagellar rod pro 21.5 90 0.002 30.1 3.0 24 104-127 42-65 (589)
95 PRK09772 transcriptional antit 21.4 2.5E+02 0.0054 22.8 5.1 50 75-130 201-251 (278)
96 PF09577 Spore_YpjB: Sporulati 21.0 81 0.0017 26.5 2.3 30 102-131 6-36 (232)
97 KOG0992 Uncharacterized conser 20.9 1.6E+02 0.0034 28.7 4.4 60 87-146 215-277 (613)
98 PF03444 HrcA_DNA-bdg: Winged 20.8 49 0.0011 24.0 0.9 18 130-147 33-50 (78)
99 PRK13276 cell wall biosynthesi 20.7 2.2E+02 0.0048 23.8 4.8 45 85-129 93-146 (224)
100 TIGR02550 flagell_flgL flagell 20.7 1.1E+02 0.0024 24.5 2.9 40 107-146 217-256 (306)
101 PF14357 DUF4404: Domain of un 20.5 3.2E+02 0.007 19.3 5.3 48 85-132 27-82 (85)
102 COG1937 Uncharacterized protei 20.2 1.2E+02 0.0026 22.2 2.9 27 87-113 60-86 (89)
103 PRK11677 hypothetical protein; 20.2 1.5E+02 0.0032 23.1 3.5 6 78-83 51-56 (134)
No 1
>PF07544 Med9: RNA polymerase II transcription mediator complex subunit 9; InterPro: IPR011425 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. This entry represents subunit Med9 of the Mediator complex. Subunit Med9 is part of the middle module of the Mediator complex []; this associates with the core polymerase subunits to form the RNA polymerase II holoenzyme. Med9 alternatively known as the chromosome segregation protein, CSE2 (P33308 from SWISSPROT) is required, along with CSE1 (P33307 from SWISSPROT) for accurate mitotic chromosome segregation in Saccharomyces cerevisiae (Baker's yeast) [].; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=92.56 E-value=0.24 Score=34.75 Aligned_cols=59 Identities=19% Similarity=0.305 Sum_probs=44.0
Q ss_pred HHHHHHHHHHHHhc-CCCC-cchHHHHHHHHHhHHHHHHHHHHhhhhcccccceehhhhhhhhhc
Q 032021 85 LLHLMENLADAIEN-GTRD-QQSDALVNELNNHFEKCQQLLSSISESLDTKAMTVEGQRRKLEER 147 (148)
Q Consensus 85 L~~lve~Ladaie~-GtRD-Q~sDaLv~EL~s~FekcQQLLnSis~sl~tk~~TVegQk~kLEE~ 147 (148)
++|.+-++-..+++ |..| ...+.-+.+|.-+|.+|..++.++.+ -..||+-|..++++.
T Consensus 4 ~lP~i~~~l~~~~~d~~~~~kd~~~~~~~lk~Klq~ar~~i~~lpg----i~~s~eeq~~~i~~L 64 (83)
T PF07544_consen 4 FLPLIFDILHQISKDPPLSSKDLDTATGSLKHKLQKARAAIRELPG----IDRSVEEQEEEIEEL 64 (83)
T ss_pred ccchHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHHHHHHHhCCC----ccCCHHHHHHHHHHH
Confidence 56777777777776 6665 34567788899999999999999776 355677777776654
No 2
>PF07197 DUF1409: Protein of unknown function (DUF1409); InterPro: IPR010811 This represents a short conserved region (approximately 50 residues long), sometimes repeated, within a number of hypothetical Oryza sativa proteins of unknown function.
Probab=89.44 E-value=0.33 Score=32.97 Aligned_cols=40 Identities=30% Similarity=0.358 Sum_probs=35.2
Q ss_pred HHHHHH---HHHhHHHHHHHHHHhhhhcccccceehhhhhhhh
Q 032021 106 DALVNE---LNNHFEKCQQLLSSISESLDTKAMTVEGQRRKLE 145 (148)
Q Consensus 106 DaLv~E---L~s~FekcQQLLnSis~sl~tk~~TVegQk~kLE 145 (148)
|.||.. +.++|++|+-.|-.=...+.+-++.||-||-|||
T Consensus 8 d~lv~~cg~IrarleE~qa~i~~e~~~l~~~~~~lEq~~~KL~ 50 (51)
T PF07197_consen 8 DLLVVDCGSIRARLEEIQAQIPDELAKLATPAVYLEQHQFKLE 50 (51)
T ss_pred HHHHhccchHHHHHHHHHHHhhHHHHHhcChHHHHHHHHHHhc
Confidence 566665 4799999999999988999999999999999997
No 3
>TIGR02481 hemeryth_dom hemerythrin-like metal-binding domain. This model describes both members of the hemerythrin (TIGR00058) family of marine invertebrates and a broader collection of bacterial and archaeal homologs. Many of the latter group are multidomain proteins with signal-transducing domains such as the GGDEF diguanylate cyclase domain (TIGR00254, pfam00990) and methyl-accepting chemotaxis protein signaling domain (pfam00015). Most hemerythrins are oxygen-carriers with a bound non-heme iron, but at least one example is a cadmium-binding protein, apparently with a role in sequestering toxic metals rather than in binding oxygen. Patterns of conserved residues suggest that all prokaryotic instances of this domain bind iron or another heavy metal, but the exact function is unknown. Not surprisingly, the prokaryote with the most instances of this domain is Magnetococcus sp. MC-1, a magnetotactic bacterium.
Probab=75.13 E-value=12 Score=26.31 Aligned_cols=46 Identities=26% Similarity=0.486 Sum_probs=34.1
Q ss_pred hhhhHHHHHHHHHHHHhcCCCCcch----HHHHHHHHHhHHHHHHHHHHh
Q 032021 81 SNFHLLHLMENLADAIENGTRDQQS----DALVNELNNHFEKCQQLLSSI 126 (148)
Q Consensus 81 ShFhL~~lve~Ladaie~GtRDQ~s----DaLv~EL~s~FekcQQLLnSi 126 (148)
-|--|+-+|.+|.+|+++|..+... +.|+.-+..||..=+.++..+
T Consensus 16 qH~~l~~~in~l~~a~~~~~~~~~~~~~l~~L~~y~~~HF~~EE~~M~~~ 65 (126)
T TIGR02481 16 QHKELFELINELYDALSAGNGKDELKEILDELIDYTENHFADEEELMEEY 65 (126)
T ss_pred HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 4667899999999999988765443 344555588998877777664
No 4
>PF10264 Stork_head: Winged helix Storkhead-box1 domain; InterPro: IPR019391 In humans the Storkhead-box protein controls polyploidization of extravillus trophoblast and is implicated in pre-eclampsia []. This entry represents the conserved N-terminal winged-helix domain, which is likely to bind DNA.
Probab=71.68 E-value=2.8 Score=30.50 Aligned_cols=56 Identities=20% Similarity=0.305 Sum_probs=39.8
Q ss_pred hhhhHHHHHHHHHHHHhcCCCCcch---HHHHHHHHHhHHHH----HHHH-HHhhhhcccccce
Q 032021 81 SNFHLLHLMENLADAIENGTRDQQS---DALVNELNNHFEKC----QQLL-SSISESLDTKAMT 136 (148)
Q Consensus 81 ShFhL~~lve~Ladaie~GtRDQ~s---DaLv~EL~s~Fekc----QQLL-nSis~sl~tk~~T 136 (148)
+..++.||-|.|-+||..=++++.+ |+|++.|..+|-.- +.+| +.++.=|..++++
T Consensus 5 ~Q~qfiPL~EvlC~~I~dln~~~~~at~E~l~~~L~~~yp~i~~Ps~e~l~~~L~~Li~erkIY 68 (80)
T PF10264_consen 5 SQSQFIPLPEVLCWVISDLNAAGQPATQETLREHLRKHYPGIAIPSQEVLYNTLGTLIKERKIY 68 (80)
T ss_pred ccccceeHHHHHHHHHHHHhccCCcchHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHcCcee
Confidence 5677999999999999988888754 88999999998642 2222 3344444445443
No 5
>cd00446 GrpE GrpE is the adenine nucleotide exchange factor of DnaK (Hsp70)-type ATPases. The GrpE dimer binds to the ATPase domain of Hsp70 catalyzing the dissociation of ADP, which enables rebinding of ATP, one step in the Hsp70 reaction cycle in protein folding. In eukaryotes, only the mitochondrial Hsp70, not the cytosolic form, is GrpE dependent.
Probab=65.48 E-value=24 Score=26.06 Aligned_cols=42 Identities=21% Similarity=0.433 Sum_probs=29.7
Q ss_pred hHHHHHHHHHHHHhcCCCCcchHHHHHHHHHhHHHHHHHHHH
Q 032021 84 HLLHLMENLADAIENGTRDQQSDALVNELNNHFEKCQQLLSS 125 (148)
Q Consensus 84 hL~~lve~Ladaie~GtRDQ~sDaLv~EL~s~FekcQQLLnS 125 (148)
-|+|++++|..|++.+..+...++++.-+..=+.+...+|..
T Consensus 40 ~ll~v~D~le~a~~~~~~~~~~~~~~~g~~~i~~~l~~~L~~ 81 (137)
T cd00446 40 DLLPVLDNLERALEAAKKEEELKNLVEGVEMTLKQLLDVLEK 81 (137)
T ss_pred HHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHHHHHHHHH
Confidence 499999999999999887745455666555555555455543
No 6
>PRK00808 hypothetical protein; Provisional
Probab=61.44 E-value=22 Score=26.55 Aligned_cols=45 Identities=20% Similarity=0.287 Sum_probs=32.4
Q ss_pred hhhHHHHHHHHHHHHhcCCCCc---chHHHHHHHHHhHHHHHHHHHHh
Q 032021 82 NFHLLHLMENLADAIENGTRDQ---QSDALVNELNNHFEKCQQLLSSI 126 (148)
Q Consensus 82 hFhL~~lve~Ladaie~GtRDQ---~sDaLv~EL~s~FekcQQLLnSi 126 (148)
|-.|+-+|..|.+|++.|.++. -.+.|+.-...||..=+.++..+
T Consensus 21 H~~L~~lin~l~~a~~~~~~~~i~~~l~~L~~y~~~HF~~EE~lM~~~ 68 (150)
T PRK00808 21 HKRIVDYINHLHDAQDSPDRLAVAEVIDELIDYTLSHFAFEESLMEEA 68 (150)
T ss_pred HHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 5578999999999999886431 23344445588998878877664
No 7
>PF00804 Syntaxin: Syntaxin; InterPro: IPR006011 Syntaxins A and B are nervous system-specific proteins implicated in the docking of synaptic vesicles with the presynaptic plasma membrane. Syntaxins are a family of receptors for intracellular transport vesicles. Each target membrane may be identified by a specific member of the syntaxin family []. Members of the syntaxin family [, ] have a size ranging from 30 Kd to 40 Kd; a C-terminal extremity which is highly hydrophobic and anchors the protein on the cytoplasmic surface of cellular membranes; a central, well conserved region, which seems to be in a coiled-coil conformation. ; GO: 0016020 membrane; PDB: 1S94_B 1EZ3_A 3C98_B 1BR0_A 1FIO_A 2XHE_B.
Probab=57.96 E-value=16 Score=23.95 Aligned_cols=27 Identities=26% Similarity=0.447 Sum_probs=24.2
Q ss_pred chHHHHHHHHHhHHHHHHHHHHhhhhc
Q 032021 104 QSDALVNELNNHFEKCQQLLSSISESL 130 (148)
Q Consensus 104 ~sDaLv~EL~s~FekcQQLLnSis~sl 130 (148)
.-|+|+.+++..|.+|..-|..|+...
T Consensus 46 el~~l~~~i~~~~~~~~~~lk~l~~~~ 72 (103)
T PF00804_consen 46 ELDELTDEIKQLFQKIKKRLKQLSKDN 72 (103)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 457899999999999999999999884
No 8
>KOG3598 consensus Thyroid hormone receptor-associated protein complex, subunit TRAP230 [Transcription]
Probab=57.14 E-value=6.1 Score=42.08 Aligned_cols=12 Identities=42% Similarity=0.540 Sum_probs=6.6
Q ss_pred chHHHHHHHHHh
Q 032021 104 QSDALVNELNNH 115 (148)
Q Consensus 104 ~sDaLv~EL~s~ 115 (148)
.-.|||+-|--+
T Consensus 2190 qtaalVRQlQ~q 2201 (2220)
T KOG3598|consen 2190 QTAALVRQLQMQ 2201 (2220)
T ss_pred HHHHHHHHHHHH
Confidence 345666665444
No 9
>PRK12333 nucleoside triphosphate pyrophosphohydrolase; Reviewed
Probab=56.15 E-value=19 Score=29.98 Aligned_cols=35 Identities=34% Similarity=0.498 Sum_probs=26.4
Q ss_pred HHHHhhhhhhhHHHHHHHHHHHHhcCCCCcchHHHHHHHHH
Q 032021 74 QHHQSLASNFHLLHLMENLADAIENGTRDQQSDALVNELNN 114 (148)
Q Consensus 74 ~~hqsLAShFhL~~lve~Ladaie~GtRDQ~sDaLv~EL~s 114 (148)
+-|.||..+ |+-=+-.+.|||++|++ ++|.+||..
T Consensus 23 QT~~SL~~y--llEE~yEv~dAI~~~d~----~~l~EELGD 57 (204)
T PRK12333 23 QTHESLRPY--LLEEAAEAVDALSEGDP----QELAEELGD 57 (204)
T ss_pred cCHHHHHHH--HHHHHHHHHHHHHcCCH----HHHHHHHHH
Confidence 358899888 66666678899998865 678888764
No 10
>PF05008 V-SNARE: Vesicle transport v-SNARE protein N-terminus; InterPro: IPR007705 V-SNARE proteins are required for protein traffic between eukaryotic organelles. The v-SNAREs on transport vesicles interact with t-SNAREs on target membranes in order to facilitate this []. This domain is the N-terminal half of the V-Snare proteins. ; GO: 0006886 intracellular protein transport, 0016020 membrane; PDB: 2V8S_V 1VCS_A 3ONL_C 3ONJ_A 2QYW_A.
Probab=55.88 E-value=54 Score=21.61 Aligned_cols=48 Identities=15% Similarity=0.315 Sum_probs=32.8
Q ss_pred HHHHHHHHHHHhcCCCCcchHHHHHHHHHhHHHHHHHHHHhhhhccccc
Q 032021 86 LHLMENLADAIENGTRDQQSDALVNELNNHFEKCQQLLSSISESLDTKA 134 (148)
Q Consensus 86 ~~lve~Ladaie~GtRDQ~sDaLv~EL~s~FekcQQLLnSis~sl~tk~ 134 (148)
+--|.+.-+.|..-+.| .-.++|.++...++.|..+|..+.--+.+-+
T Consensus 5 ~~~i~~~l~~~~~~~~~-~r~~~i~~~e~~l~ea~~~l~qMe~E~~~~p 52 (79)
T PF05008_consen 5 TAEIKSKLERIKNLSGE-QRKSLIREIERDLDEAEELLKQMELEVRSLP 52 (79)
T ss_dssp HHHHHHHHHHGGGS-CH-HHHHHHHHHHHHHHHHHHHHHHHHHHHCTS-
T ss_pred HHHHHHHHHHhhccChH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Confidence 33445555555544444 4489999999999999999999766554443
No 11
>PRK10697 DNA-binding transcriptional activator PspC; Provisional
Probab=55.76 E-value=22 Score=27.26 Aligned_cols=43 Identities=19% Similarity=0.362 Sum_probs=38.5
Q ss_pred CcchHHHHHHHHHhHHHHHHHHHHhhhhcccccceehhhhhhh
Q 032021 102 DQQSDALVNELNNHFEKCQQLLSSISESLDTKAMTVEGQRRKL 144 (148)
Q Consensus 102 DQ~sDaLv~EL~s~FekcQQLLnSis~sl~tk~~TVegQk~kL 144 (148)
.+...+++++|.++|+++++=|..++.-+-|++-.|+-.-++|
T Consensus 76 ~~s~~~~l~~~~~~~~~~e~Rlr~mE~yVTS~~f~l~ref~~L 118 (118)
T PRK10697 76 QPSSSELLDEVDRELAAGEQRLREMERYVTSDTFTLRSRFRQL 118 (118)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCHHHHHhcC
Confidence 3467889999999999999999999999999999998877765
No 12
>PF08965 DUF1870: Domain of unknown function (DUF1870); InterPro: IPR015060 This family consist of hypothetical bacterial proteins. ; PDB: 1S4K_A.
Probab=55.12 E-value=24 Score=27.38 Aligned_cols=35 Identities=23% Similarity=0.389 Sum_probs=29.5
Q ss_pred hcCCCCcchHHHHHHHHHhHHHHHHHHHHhhhhccc
Q 032021 97 ENGTRDQQSDALVNELNNHFEKCQQLLSSISESLDT 132 (148)
Q Consensus 97 e~GtRDQ~sDaLv~EL~s~FekcQQLLnSis~sl~t 132 (148)
|+|.++=. |+.|++|..-+.+.+++++.|.+.|+.
T Consensus 37 E~G~~~IP-~~Vie~l~~m~~~R~~~i~ai~~~i~~ 71 (118)
T PF08965_consen 37 EKGERPIP-DDVIEELLEMKSQRKQRINAIIDKINN 71 (118)
T ss_dssp HTTSS----HHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_pred HcCCCCCC-HHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 68999888 999999999999999999999888873
No 13
>PF02607 B12-binding_2: B12 binding domain; InterPro: IPR003759 Cobalamin-dependent methionine synthase (2.1.1.13 from EC) is a large modular protein that catalyses methyl transfer from methyltetrahydrofolate (CH3-H4folate) to homocysteine. During the catalytic cycle, it supports three distinct methyl transfer reactions, each involving the cobalamin (vitamin B12) cofactor and a substrate bound to its own functional unit []. The cobalamin cofactor plays an essential role in this reaction, accepting the methyl group from CH3-H4folate to form methylcob(III)alamin, and in turn donating the methyl group to homocysteine to generate methionine and cob(I)alamin. Methionine synthase is a large enzyme composed of four structurally and functionally distinct modules: the first two modules bind homocysteine and CH3-H4folate, the third module binds the cobalamin cofactor and the C-terminal module binds S-adenosylmethionine. The cobalamin-binding module is composed of two structurally distinct domains: a 4-helical bundle cap domain (residues 651-740 in the Escherichia coli enzyme) and an alpha/beta B12-binding domain (residues 741-896) (IPR006158 from INTERPRO). The 4-helical bundle forms a cap over the alpha/beta domain, which acts to shield the methyl ligand of cobalamin from solvent []. Furthermore, in the conversion to the active conformation of this enzyme, the 4-helical cap rotates to allow the cobalamin cofactor to bind the activation domain (IPR004223 from INTERPRO). The alpha/beta domain is a common cobalamin-binding motif, whereas the 4-helical bundle domain with its methyl cap is a distinctive feature of methionine synthases. This entry represents the 4-helical bundle cap domain. This domain is also present in other shorter proteins that bind to B12, and is always found N terminus to the alpha/beta B12-binding domain.; GO: 0008705 methionine synthase activity, 0031419 cobalamin binding, 0046872 metal ion binding, 0009086 methionine biosynthetic process; PDB: 3EZX_A 3BUL_A 1K7Y_A 1BMT_A 3IV9_A 1K98_A 3IVA_A 2I2X_P.
Probab=53.73 E-value=47 Score=21.41 Aligned_cols=27 Identities=33% Similarity=0.526 Sum_probs=20.4
Q ss_pred HHHHHHHHHHhcCCCCcchHHHHHHHHH
Q 032021 87 HLMENLADAIENGTRDQQSDALVNELNN 114 (148)
Q Consensus 87 ~lve~Ladaie~GtRDQ~sDaLv~EL~s 114 (148)
+++++|.+|+-+|++|.- .++++++-+
T Consensus 3 ~~~~~l~~al~~~d~~~~-~~~~~~~l~ 29 (79)
T PF02607_consen 3 ELIERLLDALLAGDEEEA-EALLEEALA 29 (79)
T ss_dssp HHHHHHHHHHHTT-CCHH-HHHHHHHHH
T ss_pred HHHHHHHHHHHhCCHHHH-HHHHHHHHH
Confidence 688999999999999876 556665543
No 14
>TIGR01220 Pmev_kin_Gr_pos phosphomevalonate kinase, ERG8-type, Gram-positive branch. This enzyme is part of the mevalonate pathway, one of two alternative pathways for the biosynthesis of IPP. In an example of nonorthologous gene displacement, two different types of phosphomevalonate kinase are found - the animal type and this ERG8 type. This model represents the low GC Gram-positive organism forms of the ERG8 type of phosphomevalonate kinase.
Probab=50.68 E-value=26 Score=29.75 Aligned_cols=42 Identities=19% Similarity=0.415 Sum_probs=32.8
Q ss_pred HHHHHHHHHHHhcCCCCcchHHHHHHHHHhHHHHHHHHHHhhh----hcccccc
Q 032021 86 LHLMENLADAIENGTRDQQSDALVNELNNHFEKCQQLLSSISE----SLDTKAM 135 (148)
Q Consensus 86 ~~lve~Ladaie~GtRDQ~sDaLv~EL~s~FekcQQLLnSis~----sl~tk~~ 135 (148)
=.+++.+.+|++.|+ +++|...+.+.+.||.+|+. .|++..+
T Consensus 255 ~~i~~~~~~al~~~d--------~~~lg~~~~~~~~lL~~l~~~~~~~vs~~~l 300 (358)
T TIGR01220 255 TDCVESAITAFETGD--------ITSLQKEIRRNRQELARLDDEVGVGIETEKL 300 (358)
T ss_pred HHHHHHHHHHHHhCC--------HHHHHHHHHHHHHHHHHhhcccCCCcCCHHH
Confidence 366778888888875 66788889999999999877 5556554
No 15
>PF04316 FlgM: Anti-sigma-28 factor, FlgM; InterPro: IPR007412 FlgM binds and inhibits the activity of the transcription factor sigma 28. Inhibition of sigma 28 prevents the expression of genes from flagellar transcriptional class 3, which include genes for the filament and chemotaxis. Correctly assembled basal body-hook structures export FlgM, relieving inhibition of sigma 28 and allowing expression of class 3 genes. NMR studies show that free FlgM is mostly unfolded, which may facilitate its export. The C-terminal half of FlgM adopts a tertiary structure when it binds to sigma 28. All mutations in FlgM that prevent sigma 28 inhibition affect the C-terminal domain and is the region thought to constitute the binding domain. A minimal binding domain has been identified between Glu 64 and Arg 88 in Salmonella typhimurium (P26477 from SWISSPROT).The N-terminal portion remains unstructured and may be necessary for recognition by the export machinery [].; GO: 0045892 negative regulation of transcription, DNA-dependent, 0019861 flagellum; PDB: 1RP3_B 1SC5_B.
Probab=49.47 E-value=23 Score=22.98 Aligned_cols=25 Identities=16% Similarity=0.377 Sum_probs=16.9
Q ss_pred HHHHHHHHHhcCCCCcchHHHHHHH
Q 032021 88 LMENLADAIENGTRDQQSDALVNEL 112 (148)
Q Consensus 88 lve~Ladaie~GtRDQ~sDaLv~EL 112 (148)
-|+.|..+|++|+-.-+++.+-+-|
T Consensus 29 kV~~ik~~I~~G~Y~vd~~~iA~~m 53 (57)
T PF04316_consen 29 KVAEIKAAIASGTYKVDAEKIAEKM 53 (57)
T ss_dssp HHHHHHHHHHTT-----HHHHHHHH
T ss_pred HHHHHHHHHHcCCCCCCHHHHHHHH
Confidence 5899999999999999988876655
No 16
>cd00522 Hemerythrin Hemerythrin (Hr) is a non-heme diiron oxygen transport protein found in four marine invertebrate phyla including priapulida, brachiopoda, sipunculida, and annelida, as well as in protozoa. Myohemerythrin (Mhr), a hemerythrin homolog, is found in the muscle tissue of sipunculids as well as in polycheate and oligocheate annelids. In addition to oxygen transport, Mhr proteins are involved in cadmium fixation and host anti-bacterial defense. Hr and Mhr proteins have the same "four alpha helix bundle" motif and active site structure. Hr forms oligomers, the octameric form being most prevalent, while Mhr is monomeric.
Probab=49.27 E-value=53 Score=23.30 Aligned_cols=43 Identities=19% Similarity=0.307 Sum_probs=33.1
Q ss_pred hhhHHHHHHHHHHHHhcCCCCcchHHHHHHHHHhHHHHHHHHHHhh
Q 032021 82 NFHLLHLMENLADAIENGTRDQQSDALVNELNNHFEKCQQLLSSIS 127 (148)
Q Consensus 82 hFhL~~lve~Ladaie~GtRDQ~sDaLv~EL~s~FekcQQLLnSis 127 (148)
|=.|+-++.+|.+|++. ..-.+.|..-...||..=+.++..+.
T Consensus 19 H~~L~~l~n~l~~a~~~---~~~l~~L~~y~~~HF~~EE~~M~~~~ 61 (113)
T cd00522 19 HKTLFNGINDLSEANNR---ADNLKELVDYTVKHFKDEEALMEAAG 61 (113)
T ss_pred HHHHHHHHHHHHHHHhH---HHHHHHHHHHHHHHHHHHHHHHHHcC
Confidence 55789999999999986 44566777777999988777776643
No 17
>PF01025 GrpE: GrpE; InterPro: IPR000740 Molecular chaperones are a diverse family of proteins that function to protect proteins in the intracellular milieu from irreversible aggregation during synthesis and in times of cellular stress. The bacterial molecular chaperone DnaK is an enzyme that couples cycles of ATP binding, hydrolysis, and ADP release by an N-terminal ATP-hydrolysing domain to cycles of sequestration and release of unfolded proteins by a C-terminal substrate binding domain. In prokaryotes the grpE protein. Dimeric GrpE is the co-chaperone for DnaK, and acts as a nucleotide exchange factor, stimulating the rate of ADP release 5000-fold []. DnaK is itself a weak ATPase; ATP hydrolysis by DnaK is stimulated by its interaction with another co-chaperone, DnaJ. Thus the co-chaperones DnaJ and GrpE are capable of tightly regulating the nucleotide-bound and substrate-bound state of DnaK in ways that are necessary for the normal housekeeping functions and stress-related functions of the DnaK molecular chaperone cycle. The X-ray crystal structure of GrpE in complex with the ATPase domain of DnaK revealed that GrpE is an asymmetric homodimer, bent in a manner that favours extensive contacts with only one DnaKATPase monomer []. GrpE does not actively compete for the atomic positions occupied by the nucleotide. GrpE and ADP mutually reduce one another's affinity for DnaK 200-fold, and ATP instantly dissociates GrpE from DnaK.; GO: 0000774 adenyl-nucleotide exchange factor activity, 0042803 protein homodimerization activity, 0051087 chaperone binding, 0006457 protein folding; PDB: 3A6M_A 4ANI_A 1DKG_B.
Probab=47.62 E-value=37 Score=25.06 Aligned_cols=41 Identities=22% Similarity=0.485 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHHhcCCCCcchHHHHHHHHHhHHHHHHHHHH
Q 032021 85 LLHLMENLADAIENGTRDQQSDALVNELNNHFEKCQQLLSS 125 (148)
Q Consensus 85 L~~lve~Ladaie~GtRDQ~sDaLv~EL~s~FekcQQLLnS 125 (148)
|++++++|..|+++...+...+.|+.-+..-..+...+|..
T Consensus 67 ll~v~D~l~~a~~~~~~~~~~~~~~~g~~~~~~~l~~~L~~ 107 (165)
T PF01025_consen 67 LLPVLDNLERALEAAKSNEEEESLLEGLEMILKQLEDILEK 107 (165)
T ss_dssp HHHHHHHHHHHHCC-SHHCTCHHHHHHHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHHhhhccchHHHHHHHHHHHHHHHHHHHHH
Confidence 89999999999998865555567777777777766677765
No 18
>PRK14151 heat shock protein GrpE; Provisional
Probab=46.81 E-value=46 Score=26.57 Aligned_cols=53 Identities=15% Similarity=0.317 Sum_probs=30.6
Q ss_pred hHHHHHHHHHHHHhcCCCCcchHHHHHHHHHhHHHHHHHHHHhhhhcccccceehh
Q 032021 84 HLLHLMENLADAIENGTRDQQSDALVNELNNHFEKCQQLLSSISESLDTKAMTVEG 139 (148)
Q Consensus 84 hL~~lve~Ladaie~GtRDQ~sDaLv~EL~s~FekcQQLLnSis~sl~tk~~TVeg 139 (148)
-|||++++|..|++....+.. .+..+..-++--...|.++-...+=+.|...|
T Consensus 75 ~LLpv~DnlerAl~~~~~~~~---~~~~~~~Gv~mi~k~l~~~L~k~Gv~~i~~~G 127 (176)
T PRK14151 75 DLLPVVDSLERGLELSSADDE---AIKPMREGVELTLKMFQDTLKRYQLEAVDPHG 127 (176)
T ss_pred HHhhHHhHHHHHHhcccccch---hHHHHHHHHHHHHHHHHHHHHHCCCEEeCCCC
Confidence 399999999999998765432 22333333443333444455555555554444
No 19
>PRK14141 heat shock protein GrpE; Provisional
Probab=46.61 E-value=42 Score=27.75 Aligned_cols=56 Identities=21% Similarity=0.282 Sum_probs=35.4
Q ss_pred hHHHHHHHHHHHHhcCCCC--cchHHHHHHHHHhHHHHHHHHHHhhhhcccccceehh
Q 032021 84 HLLHLMENLADAIENGTRD--QQSDALVNELNNHFEKCQQLLSSISESLDTKAMTVEG 139 (148)
Q Consensus 84 hL~~lve~Ladaie~GtRD--Q~sDaLv~EL~s~FekcQQLLnSis~sl~tk~~TVeg 139 (148)
-|||++++|..|++...-+ .+.|..+..|..-|+-....|.++-...+=+.|-..|
T Consensus 86 dLLpViDnLerAl~~~~~~~~~~~~~~~~~l~eGv~mi~k~l~~vLek~GV~~I~~~G 143 (209)
T PRK14141 86 DMLSVSDNLRRALDAIPAEARAAADAGLKALIEGVEMTERAMLNALERHGVKKLDPEG 143 (209)
T ss_pred HHhhhHhHHHHHHhccccccccccchhHHHHHHHHHHHHHHHHHHHHHCCCEEECCCC
Confidence 4999999999999976443 2334445556556665555555665565555554334
No 20
>TIGR02978 phageshock_pspC phage shock protein C. All members of this protein family are the phage shock protein PspC. These proteins contain a PspC domain, as do other members of the larger family of proteins described by Pfam model pfam04024. The phage shock regulon is restricted to the Proteobacteria and somewhat sparsely distributed there. It is expressed, under positive control of a sigma-54-dependent transcription factor, PspF, which binds and is modulated by PspA. Stresses that induce the psp regulon include phage secretin overexpression, ethanol, heat shock, and protein export defects.
Probab=43.70 E-value=43 Score=25.49 Aligned_cols=41 Identities=12% Similarity=0.296 Sum_probs=37.0
Q ss_pred chHHHHHHHHHhHHHHHHHHHHhhhhcccccceehhhhhhh
Q 032021 104 QSDALVNELNNHFEKCQQLLSSISESLDTKAMTVEGQRRKL 144 (148)
Q Consensus 104 ~sDaLv~EL~s~FekcQQLLnSis~sl~tk~~TVegQk~kL 144 (148)
...+++++|.++|++.+.=|..++.-+-|++-+|+-.-++|
T Consensus 81 ~~~~~l~~~~~~~~~~e~Rl~~mE~yVTS~~f~l~ref~~L 121 (121)
T TIGR02978 81 SPRQALREVKREFRDLERRLRNMERYVTSDTFRLRREFRNL 121 (121)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccHHHHHhcC
Confidence 46789999999999999999999999999999998877665
No 21
>PF10458 Val_tRNA-synt_C: Valyl tRNA synthetase tRNA binding arm; InterPro: IPR019499 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This entry represents the C-terminal domain of Valyl-tRNA synthetase, which consists of two helices in a long alpha-hairpin. Valyl-tRNA synthetase (6.1.1.9 from EC) is an alpha monomer that belongs to class Ia.; GO: 0000166 nucleotide binding, 0004832 valine-tRNA ligase activity, 0005524 ATP binding, 0006438 valyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 1IVS_B 1GAX_B.
Probab=43.43 E-value=37 Score=22.56 Aligned_cols=43 Identities=28% Similarity=0.458 Sum_probs=35.9
Q ss_pred hHHHHHHHHHhHHHHHHHHHHhhhhcccccc-------eehhhhhhhhhc
Q 032021 105 SDALVNELNNHFEKCQQLLSSISESLDTKAM-------TVEGQRRKLEER 147 (148)
Q Consensus 105 sDaLv~EL~s~FekcQQLLnSis~sl~tk~~-------TVegQk~kLEE~ 147 (148)
.|+.+..|....+|++.-+..+.+-|++... -|+.-|.||+++
T Consensus 2 ~~~E~~rL~Kel~kl~~~i~~~~~kL~n~~F~~kAP~eVve~er~kl~~~ 51 (66)
T PF10458_consen 2 VEAEIERLEKELEKLEKEIERLEKKLSNENFVEKAPEEVVEKEREKLEEL 51 (66)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHHHHS-CCHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHcCccccccCCHHHHHHHHHHHHHH
Confidence 4778889999999999999999999887654 578888888775
No 22
>PF13964 Kelch_6: Kelch motif
Probab=41.86 E-value=16 Score=21.87 Aligned_cols=13 Identities=23% Similarity=0.994 Sum_probs=10.7
Q ss_pred CCcceeccCCCCC
Q 032021 7 SGSWNMMPSIPSH 19 (148)
Q Consensus 7 gGSwtMiPs~~s~ 19 (148)
-++|+.||++|.+
T Consensus 37 t~~W~~~~~mp~p 49 (50)
T PF13964_consen 37 TNTWEQLPPMPTP 49 (50)
T ss_pred CCcEEECCCCCCC
Confidence 3789999999854
No 23
>PRK14149 heat shock protein GrpE; Provisional
Probab=41.24 E-value=70 Score=26.19 Aligned_cols=29 Identities=24% Similarity=0.418 Sum_probs=21.8
Q ss_pred hHHHHHHHHHHHHhcCCCCcchHHHHHHH
Q 032021 84 HLLHLMENLADAIENGTRDQQSDALVNEL 112 (148)
Q Consensus 84 hL~~lve~Ladaie~GtRDQ~sDaLv~EL 112 (148)
-|||++++|..|+.....|....+|+.-+
T Consensus 91 ~LLpVlDnLerAl~~~~~~~~~~~l~~Gv 119 (191)
T PRK14149 91 DLLPVIDALLGALKSAAEVDKESALTKGL 119 (191)
T ss_pred HHhhHHhHHHHHHhccccccchHHHHHHH
Confidence 39999999999999887665545555444
No 24
>PF09720 Unstab_antitox: Putative addiction module component; InterPro: IPR013406 This entry defines several short bacterial proteins, typically about 75 amino acids long, which are always found as part of a pair (at least) of small genes. The other protein in the pair always belongs to a family of plasmid stabilisation proteins (IPR007712 from INTERPRO). It is likely that this protein and its partner comprise some form of addiction module - a pair of genes consisting of a stable toxin and an unstable antitoxin which mediate programmed cell death [] - although these gene pairs are usually found on the bacterial main chromosome.
Probab=41.19 E-value=79 Score=19.96 Aligned_cols=33 Identities=18% Similarity=0.270 Sum_probs=26.1
Q ss_pred HHHHHHHHHHHhcCCCCcchHHHHHHHHHhHHHH
Q 032021 86 LHLMENLADAIENGTRDQQSDALVNELNNHFEKC 119 (148)
Q Consensus 86 ~~lve~Ladaie~GtRDQ~sDaLv~EL~s~Fekc 119 (148)
+-||+.|-+.++.. .+.-.++-+.|+..|++..
T Consensus 8 ~~L~e~L~~sl~~~-~~~~~~~w~~el~rR~~~~ 40 (54)
T PF09720_consen 8 AELAEELWDSLDDP-DSEVEAWWKEELERRLAEY 40 (54)
T ss_pred HHHHHHHHHHhccc-cccCcHHHHHHHHHHHHHH
Confidence 35788999988887 5567778889999998854
No 25
>PF07304 SRA1: Steroid receptor RNA activator (SRA1); InterPro: IPR009917 This entry consists of several hypothetical mammalian steroid receptor RNA activator proteins. The SRA-RNAs encode stable proteins that are widely expressed and upregulated in breast cancer cell lines. SRA-RNA is a steroid receptor co-activator which acts as a functional RNA. This domain is also found at the C terminus of Sec31, a component of the coat protein complex II (COPII, which promotes the formation of transport vesicles from the endoplasmic reticulum (ER). COPII has two main functions, the physical deformation of the endoplasmic reticulum membrane into vesicles and the selection of cargo molecules. ; PDB: 2YRU_A.
Probab=41.02 E-value=21 Score=27.66 Aligned_cols=39 Identities=21% Similarity=0.469 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHhcCCCCcchHHHHHHH-HHhHHHHHHHHHH
Q 032021 86 LHLMENLADAIENGTRDQQSDALVNEL-NNHFEKCQQLLSS 125 (148)
Q Consensus 86 ~~lve~Ladaie~GtRDQ~sDaLv~EL-~s~FekcQQLLnS 125 (148)
..-+..|+.|+++|..|.. +++-++| ++|+++|-+-+--
T Consensus 91 ~~~L~~L~~aL~~~d~~~A-~~Ih~~L~t~h~~E~~~WmvG 130 (157)
T PF07304_consen 91 VDKLHQLAQALQARDYDAA-DEIHVDLMTDHVDECGNWMVG 130 (157)
T ss_dssp HHHHHHHHHHHHHT-HHHH-HHHHHHHHHSSHHHHTTTHHH
T ss_pred HHHHHHHHHHHHcCCHHHH-HHHHHHHHhccHHHhhhHHHH
Confidence 3445678889999998887 6666666 9999999765543
No 26
>PRK14140 heat shock protein GrpE; Provisional
Probab=38.93 E-value=96 Score=25.31 Aligned_cols=48 Identities=19% Similarity=0.305 Sum_probs=27.8
Q ss_pred hHHHHHHHHHHHHhcCCCCcchHHHHHHHHHhHHHHHHHHHHhhhhcccccc
Q 032021 84 HLLHLMENLADAIENGTRDQQSDALVNELNNHFEKCQQLLSSISESLDTKAM 135 (148)
Q Consensus 84 hL~~lve~Ladaie~GtRDQ~sDaLv~EL~s~FekcQQLLnSis~sl~tk~~ 135 (148)
-|||++++|..|++...-+...++++.- |+-....|.++-...+=+.+
T Consensus 92 ~LLpvlDnLerAl~~~~~~~~~~~i~~G----v~mi~k~l~~~L~k~GV~~i 139 (191)
T PRK14140 92 DLLPALDNFERALQIEADDEQTKSLLKG----VEMVHRQLLEALKKEGVEVI 139 (191)
T ss_pred HHHHHHHHHHHHHhccCccchHHHHHHH----HHHHHHHHHHHHHHCCCEee
Confidence 4999999999999986654443444433 33333333444444443333
No 27
>PRK14159 heat shock protein GrpE; Provisional
Probab=38.57 E-value=85 Score=25.27 Aligned_cols=29 Identities=21% Similarity=0.327 Sum_probs=20.8
Q ss_pred hHHHHHHHHHHHHhcCCCCcchHHHHHHH
Q 032021 84 HLLHLMENLADAIENGTRDQQSDALVNEL 112 (148)
Q Consensus 84 hL~~lve~Ladaie~GtRDQ~sDaLv~EL 112 (148)
-|||++++|..|++....|....+|+.-+
T Consensus 78 ~LLpV~DnlerAl~~~~~~~~~~~l~~Gv 106 (176)
T PRK14159 78 DLLDVLDALEAAVNVECHDEISLKIKEGV 106 (176)
T ss_pred HHhhHHhHHHHHHhcccccchHHHHHHHH
Confidence 39999999999999866554444444444
No 28
>PF04912 Dynamitin: Dynamitin ; InterPro: IPR006996 Dynamitin is a subunit of the microtubule-dependent motor complex, it is also implicated in cell adhesion by binding to macrophage-enriched myristoylated alanine-rice C kinase substrate (MacMARCKS) []. It is also thought to modulate cytoplasmic dynein binding to an organelle, and plays a role in prometaphase chromosome alignment and spindle organisation during mitosis. Dynamitin is also involved in anchoring microtubules to centrosomes and may play a role in synapse formation during brain development []. ; GO: 0007017 microtubule-based process, 0005869 dynactin complex
Probab=38.18 E-value=34 Score=29.38 Aligned_cols=61 Identities=28% Similarity=0.431 Sum_probs=50.8
Q ss_pred HHHHHHH-------HHHhcCCCCcchHHHHHHHHHhHHHHHHHHHHhhhhcccccceehhhhhhhhhc
Q 032021 87 HLMENLA-------DAIENGTRDQQSDALVNELNNHFEKCQQLLSSISESLDTKAMTVEGQRRKLEER 147 (148)
Q Consensus 87 ~lve~La-------daie~GtRDQ~sDaLv~EL~s~FekcQQLLnSis~sl~tk~~TVegQk~kLEE~ 147 (148)
+||++|. +|.+.+.+=.+.|....+|.+..+++..+|+.+..++..-.-+|++-..+||++
T Consensus 316 ~lv~RL~tL~~lH~~a~~~~~~l~~le~~q~~l~~~l~~~~~~L~~ve~~~~~N~~~i~~n~~~le~R 383 (388)
T PF04912_consen 316 SLVERLKTLKSLHEEAAEFSQTLSELESQQSDLQSQLKKWEELLNKVEEKFKENMETIEKNVKKLEER 383 (388)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3556663 467777777778888999999999999999999999888888999999998874
No 29
>PRK14162 heat shock protein GrpE; Provisional
Probab=36.79 E-value=76 Score=25.97 Aligned_cols=56 Identities=21% Similarity=0.313 Sum_probs=32.9
Q ss_pred hhhhhhhHHHHHHHHHHHHhcCCCCcchHHHHHHHHHhHHHHHHHHHHhhhhcccccceehh
Q 032021 78 SLASNFHLLHLMENLADAIENGTRDQQSDALVNELNNHFEKCQQLLSSISESLDTKAMTVEG 139 (148)
Q Consensus 78 sLAShFhL~~lve~Ladaie~GtRDQ~sDaLv~EL~s~FekcQQLLnSis~sl~tk~~TVeg 139 (148)
+++.= |||+++||..|+..+.-|....+| ..-|+-....|.++-...+=+.|-..|
T Consensus 90 ~~~~~--LLpV~DnLerAl~~~~~~~~~~~l----~~Gvemi~k~l~~vL~~~GV~~I~~~G 145 (194)
T PRK14162 90 SLAKD--VLPAMDNLERALAVKADDEAAKQL----KKGVQMTLDHLVKALKDHGVTEIKADG 145 (194)
T ss_pred HHHHH--HhhHHhHHHHHHhccccchhHHHH----HHHHHHHHHHHHHHHHHCCCEEeCCCC
Confidence 44444 999999999999987644333333 344444444444555555555543334
No 30
>PRK14157 heat shock protein GrpE; Provisional
Probab=36.43 E-value=51 Score=27.87 Aligned_cols=19 Identities=21% Similarity=0.347 Sum_probs=15.5
Q ss_pred hHHHHHHHHHHHHhcCCCC
Q 032021 84 HLLHLMENLADAIENGTRD 102 (148)
Q Consensus 84 hL~~lve~Ladaie~GtRD 102 (148)
-|||++++|..|++...-+
T Consensus 132 dLLpvlDnLeRAl~~~~~~ 150 (227)
T PRK14157 132 ALLPALDDIDRIREHSEMD 150 (227)
T ss_pred HHhhhhhhHHHHHhccccc
Confidence 4999999999999876433
No 31
>PF02268 TFIIA_gamma_N: Transcription initiation factor IIA, gamma subunit, helical domain; InterPro: IPR015872 Transcription factor IIA (TFIIA) is one of several factors that form part of a transcription pre-initiation complex along with RNA polymerase II, the TATA-box-binding protein (TBP) and TBP-associated factors, on the TATA-box sequence upstream of the initiation start site. After initiation, some components of the pre-initiation complex (including TFIIA) remain attached and re-initiate a subsequent round of transcription. TFIIA binds to TBP to stabilise TBP binding to the TATA element. TFIIA also inhibits the cytokine HMGB1 (high mobility group 1 protein) binding to TBP [], and can dissociate HMGB1 already bound to TBP/TATA-box. Human and Drosophila TFIIA have three subunits: two large subunits, LN/alpha and LC/beta, derived from the same gene, and a small subunit, S/gamma. Yeast TFIIA has two subunits: a large TOA1 subunit that shows sequence similarity to the N-terminal of LN/alpha and the C-terminal of LC/beta, and a small subunit, TOA2 that is highly homologous with S/gamma. The conserved regions of the large and small subunits of TFIIA combine to form two domains: a four-helix bundle (helical domain) composed of two helices from each of the N-terminal regions of TOA1 and TOA2 in yeast; and a beta-barrel (beta-barrel domain) composed of beta-sheets from the C-terminal regions of TOA1 and TOA2 []. This entry represents the alpha-helical domain found at the N-terminal of the gamma subunit of transcription factor TFIIA.; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005672 transcription factor TFIIA complex; PDB: 1NVP_D 1RM1_B 1YTF_D 1NH2_D.
Probab=36.36 E-value=70 Score=21.38 Aligned_cols=30 Identities=23% Similarity=0.423 Sum_probs=24.2
Q ss_pred HHHHHHHHHHhcCCCCcchHHHHHHHHHhHHHH
Q 032021 87 HLMENLADAIENGTRDQQSDALVNELNNHFEKC 119 (148)
Q Consensus 87 ~lve~Ladaie~GtRDQ~sDaLv~EL~s~Fekc 119 (148)
-|.|.|-|.|..|.=. -.|...+-++|+||
T Consensus 14 aL~dtLDeli~~~~I~---p~La~kVL~~FDks 43 (49)
T PF02268_consen 14 ALTDTLDELIQEGKIT---PQLAMKVLEQFDKS 43 (49)
T ss_dssp HHHHHHHHHHHTTSS----HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHcCCCC---HHHHHHHHHHHHHH
Confidence 4788888889888654 66889999999987
No 32
>PRK14161 heat shock protein GrpE; Provisional
Probab=35.43 E-value=1e+02 Score=24.77 Aligned_cols=50 Identities=14% Similarity=0.236 Sum_probs=29.9
Q ss_pred hHHHHHHHHHHHHhcCCCCcchHHHHHHHHHhHHHHHHHHHHhhhhcccccc
Q 032021 84 HLLHLMENLADAIENGTRDQQSDALVNELNNHFEKCQQLLSSISESLDTKAM 135 (148)
Q Consensus 84 hL~~lve~Ladaie~GtRDQ~sDaLv~EL~s~FekcQQLLnSis~sl~tk~~ 135 (148)
-|||++++|..|++.+..|... -+..+..-|+-...-|.++-...+=+.+
T Consensus 74 ~LLpv~DnlerAl~~~~~~~~~--~~~~~~~Gv~mi~k~l~~vL~~~Gv~~I 123 (178)
T PRK14161 74 ELLNVSDNLSRALAHKPANSDV--EVTNIIAGVQMTKDELDKVFHKHHIEEI 123 (178)
T ss_pred HHhhHHhHHHHHHhcCccccch--hHHHHHHHHHHHHHHHHHHHHHCCCEEe
Confidence 4999999999999998766432 1233334444444444444444444444
No 33
>PF09824 ArsR: ArsR transcriptional regulator; InterPro: IPR014517 Members of this family of archaeal proteins are conserved transcriptional regulators belonging to the ArsR family.
Probab=35.30 E-value=26 Score=28.61 Aligned_cols=51 Identities=18% Similarity=0.413 Sum_probs=38.1
Q ss_pred HHHHHHHHHHHhcCCCCcchHHHHHHHHHhHHHHHHHHHHhhhhcccccceehhhhhhh
Q 032021 86 LHLMENLADAIENGTRDQQSDALVNELNNHFEKCQQLLSSISESLDTKAMTVEGQRRKL 144 (148)
Q Consensus 86 ~~lve~Ladaie~GtRDQ~sDaLv~EL~s~FekcQQLLnSis~sl~tk~~TVegQk~kL 144 (148)
=-++|.|-..|++|+ .-+..|+..|.+.+=.|..|++- +..+.|.||+-++
T Consensus 107 ~~~~e~i~~~v~~Gn------~Sl~~lsr~l~~sp~firglAKR--s~~L~VkGq~lel 157 (160)
T PF09824_consen 107 RDYVEKIEKEVEAGN------TSLSDLSRKLGISPVFIRGLAKR--SPKLDVKGQRLEL 157 (160)
T ss_pred HHHHHHHHHHHHcCC------CcHHHHHHHhCCCHHHHHHHHHh--ccCcceecceEEe
Confidence 345666677777764 34667778888888888888888 7788999998655
No 34
>PRK14155 heat shock protein GrpE; Provisional
Probab=35.11 E-value=92 Score=25.67 Aligned_cols=52 Identities=23% Similarity=0.223 Sum_probs=32.3
Q ss_pred hHHHHHHHHHHHHhcCCCCcchHHHHHHHHHhHHHHHHHHHHhhhhcccccce
Q 032021 84 HLLHLMENLADAIENGTRDQQSDALVNELNNHFEKCQQLLSSISESLDTKAMT 136 (148)
Q Consensus 84 hL~~lve~Ladaie~GtRDQ~sDaLv~EL~s~FekcQQLLnSis~sl~tk~~T 136 (148)
-|||++++|-.|++....+.. +.-+..+..-|+-....|.++-...+=+.|.
T Consensus 68 ~LLpV~DnLerAl~~~~~~~~-~~~~~~i~~Gvemi~k~~~~~L~k~GV~~I~ 119 (208)
T PRK14155 68 DLLGAADNLGRATAASPKDSA-DPAVKNFIIGVEMTEKELLGAFERNGLKKID 119 (208)
T ss_pred HHhhHHhhHHHHHhccccccc-chHHHHHHHHHHHHHHHHHHHHHHCCCceec
Confidence 499999999999998765422 2223444445555444555555555555553
No 35
>PF07011 DUF1313: Protein of unknown function (DUF1313); InterPro: IPR009741 This family consists of several hypothetical plant proteins of around 100 residues in length. The function of this family is unknown.
Probab=34.95 E-value=46 Score=24.94 Aligned_cols=44 Identities=27% Similarity=0.419 Sum_probs=31.6
Q ss_pred HHHHHHHHHhcCCCCcch--HHHHHHHHHhHHHHHHHHHHhhhhcc
Q 032021 88 LMENLADAIENGTRDQQS--DALVNELNNHFEKCQQLLSSISESLD 131 (148)
Q Consensus 88 lve~Ladaie~GtRDQ~s--DaLv~EL~s~FekcQQLLnSis~sl~ 131 (148)
||..+-.-=|...+|-=+ =+||+||+.+..|.--|-..+|.+.+
T Consensus 28 LI~eINqNHeSr~PdnL~RNV~LIrELN~NI~rVv~lY~dLs~sFs 73 (87)
T PF07011_consen 28 LINEINQNHESRIPDNLSRNVGLIRELNGNISRVVDLYSDLSSSFS 73 (87)
T ss_pred HHHHHhhcccccCCchhhHhHHHHHHHHhhHHHHHHHHHHHhHHHH
Confidence 344444444556666432 47999999999999999888888765
No 36
>PRK14164 heat shock protein GrpE; Provisional
Probab=34.86 E-value=70 Score=26.69 Aligned_cols=23 Identities=26% Similarity=0.468 Sum_probs=17.8
Q ss_pred HhhhhhhhHHHHHHHHHHHHhcCCC
Q 032021 77 QSLASNFHLLHLMENLADAIENGTR 101 (148)
Q Consensus 77 qsLAShFhL~~lve~Ladaie~GtR 101 (148)
..++.- |||++++|.-|++++.-
T Consensus 120 ~~~~~~--LLpVlDnLerAl~~~~~ 142 (218)
T PRK14164 120 AGVATD--LLPILDDLDLAEQHGDL 142 (218)
T ss_pred HHHHHH--HhhHHhHHHHHHhcccc
Confidence 344444 99999999999988754
No 37
>PF07904 Eaf7: Chromatin modification-related protein EAF7; InterPro: IPR012423 The Saccharomyces cerevisiae (Baker's yeast) member of this family P53911 from SWISSPROT is part of NuA4, the only essential histone acetyltransferase complex in S. cerevisiae involved in global histone acetylation []. ; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus, 0043189 H4/H2A histone acetyltransferase complex
Probab=33.97 E-value=46 Score=23.92 Aligned_cols=37 Identities=16% Similarity=0.377 Sum_probs=29.1
Q ss_pred hhhhHHHHHHHHHHH--HhcCCCCcchHHHHHHHHHhHH
Q 032021 81 SNFHLLHLMENLADA--IENGTRDQQSDALVNELNNHFE 117 (148)
Q Consensus 81 ShFhL~~lve~Lada--ie~GtRDQ~sDaLv~EL~s~Fe 117 (148)
-|||++-+++.|... +....+.=.+|.+.+.|.+-|+
T Consensus 20 KHF~M~~I~~~l~~~~~~~~~~~~~t~~~IW~kL~~~Yd 58 (91)
T PF07904_consen 20 KHFHMICIVERLNNPGFDPKLNKHFTIDDIWKKLRTLYD 58 (91)
T ss_pred hHHHHHHHHHHHhccccCCccCCcCCHHHHHHHHHHhcC
Confidence 499999999999887 3344566678888888877665
No 38
>PRK14142 heat shock protein GrpE; Provisional
Probab=33.91 E-value=59 Score=27.48 Aligned_cols=25 Identities=28% Similarity=0.485 Sum_probs=18.9
Q ss_pred HhhhhhhhHHHHHHHHHHHHhcCCCCc
Q 032021 77 QSLASNFHLLHLMENLADAIENGTRDQ 103 (148)
Q Consensus 77 qsLAShFhL~~lve~Ladaie~GtRDQ 103 (148)
.+++.= |||+++||.-|++....+.
T Consensus 83 e~~~kd--LLpVlDnLERAL~~~~~~~ 107 (223)
T PRK14142 83 ASVVSQ--LLGVLDDLERARKHGDLES 107 (223)
T ss_pred HHHHHH--HhchHhHHHHHHhcccccc
Confidence 345544 9999999999998875443
No 39
>cd07354 HN_L-delphilin-R1_like First harmonin_N_like domain (repeat 1) of L-delphilin, and related domains. This subgroup contains the first of two harmonin_N_like domains of an alternatively spliced longer variant of mouse delphilin (L-delphilin, isoform 1), and related domains. Delphilin is a scaffold protein which binds the glutamate receptor delta-2 (GRID2) subunit and the monocarboxylate transporter 2 at the cerebellar parallel fiber-Purkinje cell synapses. The N-terminus of L-delphilin contains this harmonin_N_like domain preceded by a postsynaptic density-95/discs-large/ZO-1 (PDZ) protein-binding domain, PDZ1. L-delphilin, in common with the shorter C-terminal isoforms (S-delphilin/delphilin alpha and delphilin beta) has a second harmonin_N_like domain (not belonging to this subgroup) and a second PDZ domain, PDZ2. This first harmonin_N_like domain is a putative protein-binding module based on its sequence similarity to the harmonin N-domain.
Probab=33.79 E-value=45 Score=24.60 Aligned_cols=45 Identities=24% Similarity=0.217 Sum_probs=35.9
Q ss_pred HHHHHHHHHhcCCCCcchHHHHHHH--HHhHHHHHHHHHHhhhhccc
Q 032021 88 LMENLADAIENGTRDQQSDALVNEL--NNHFEKCQQLLSSISESLDT 132 (148)
Q Consensus 88 lve~Ladaie~GtRDQ~sDaLv~EL--~s~FekcQQLLnSis~sl~t 132 (148)
.-|+|-+|+..=..|.+.|.|+..| .=.=+++..||.+|-=-|-.
T Consensus 22 ~Ke~l~~aLk~Ya~~k~vd~l~~aL~~~L~~e~~~~Lld~IR~fIP~ 68 (80)
T cd07354 22 KKEQVFAALKQYAADKNVDCLVWALCGLLQTEAHKKLLDEIRIFIPK 68 (80)
T ss_pred HHHHHHHHHHHHHHHcCHHHHHHHHHHHhCcHHHHHHHHHhHhcCCc
Confidence 4578889999999999999999998 33468899999988654443
No 40
>PF13418 Kelch_4: Galactose oxidase, central domain; PDB: 2UVK_B.
Probab=33.64 E-value=18 Score=21.40 Aligned_cols=12 Identities=42% Similarity=1.146 Sum_probs=6.6
Q ss_pred CCcceeccCCCC
Q 032021 7 SGSWNMMPSIPS 18 (148)
Q Consensus 7 gGSwtMiPs~~s 18 (148)
.++|+-||++|+
T Consensus 38 ~~~W~~~~~~P~ 49 (49)
T PF13418_consen 38 TNTWTRLPSMPS 49 (49)
T ss_dssp TTEEEE--SS--
T ss_pred CCEEEECCCCCC
Confidence 478999988875
No 41
>COG0576 GrpE Molecular chaperone GrpE (heat shock protein) [Posttranslational modification, protein turnover, chaperones]
Probab=33.57 E-value=1.1e+02 Score=24.53 Aligned_cols=26 Identities=31% Similarity=0.585 Sum_probs=20.0
Q ss_pred HhhhhhhhHHHHHHHHHHHHhcCCCCcc
Q 032021 77 QSLASNFHLLHLMENLADAIENGTRDQQ 104 (148)
Q Consensus 77 qsLAShFhL~~lve~Ladaie~GtRDQ~ 104 (148)
+.++.- |||+++||-.|++...-+..
T Consensus 86 e~~~~d--lLpviDnlerAl~~~~~~~d 111 (193)
T COG0576 86 EKFAKD--LLPVIDNLERALEAAEDDKD 111 (193)
T ss_pred HHHHHH--HHHHHHHHHHHHHhcccccc
Confidence 445544 99999999999998766633
No 42
>PRK14148 heat shock protein GrpE; Provisional
Probab=33.46 E-value=1.1e+02 Score=25.00 Aligned_cols=33 Identities=15% Similarity=0.371 Sum_probs=22.7
Q ss_pred hhhhhhhHHHHHHHHHHHHhcCCCCcchHHHHHHH
Q 032021 78 SLASNFHLLHLMENLADAIENGTRDQQSDALVNEL 112 (148)
Q Consensus 78 sLAShFhL~~lve~Ladaie~GtRDQ~sDaLv~EL 112 (148)
.++.- |||++++|..|++....+....+|+.-+
T Consensus 91 ~~~~~--LLpV~DnlerAl~~~~~~~~~~~l~~Gv 123 (195)
T PRK14148 91 KFAKE--LLPVIDSIEQALKHEVKLEEAIAMKEGI 123 (195)
T ss_pred HHHHH--HhhHHhHHHHHHhccccchhHHHHHHHH
Confidence 45544 9999999999999876544334444443
No 43
>PF04108 APG17: Autophagy protein Apg17 ; InterPro: IPR007240 Macroautophagy is a bulk degradation process induced by starvation in eukaryotic cells. In yeast, 15 Apg proteins coordinate the formation of autophagosomes. No molecule involved in autophagy has yet been identified in higher eukaryotes []. The pre-autophagosomal structure contains at least five Apg proteins: Apg1p, Apg2p, Apg5p, Aut7p/Apg8p and Apg16p. It is found in the vacuole []. The C-terminal glycine of Apg12p is conjugated to a lysine residue of Apg5p via an isopeptide bond. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. Auotphagy protein 16 (Apg16) has been shown to be bind to Apg5 and is required for the function of the Apg12p-Apg5p conjugate []. Autophagy protein 5 (Apg5) is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway []. Autophagy protein 17 (Apg17) is required for activating Apg1 protein kinases. This entry also contains Autophagy protein 11 which is involved in cytoplasm to vacuole transport (Cvt) and pexophagy. ; GO: 0006914 autophagy
Probab=32.85 E-value=60 Score=28.46 Aligned_cols=22 Identities=27% Similarity=0.644 Sum_probs=17.3
Q ss_pred HHHHHHHHhHHHHHHHHHHhhh
Q 032021 107 ALVNELNNHFEKCQQLLSSISE 128 (148)
Q Consensus 107 aLv~EL~s~FekcQQLLnSis~ 128 (148)
.|.+-|++||++|.-.+.-.+|
T Consensus 210 ~lL~sLt~HfDqC~~a~~~~eg 231 (412)
T PF04108_consen 210 SLLESLTNHFDQCVTAVRHTEG 231 (412)
T ss_pred HHHHHHHHHHHHHHHHHHHhcc
Confidence 4666779999999998885544
No 44
>PF01858 RB_A: Retinoblastoma-associated protein A domain; InterPro: IPR002720 Retinoblastoma-like and retinoblastoma-associated proteins may have a function in cell cycle regulation. They form a complex with adenovirus E1A and Simian virus 40 (SV40) large T antigen, and may bind and modulate the function of certain cellular proteins with which T and E1A compete for pocket binding. The proteins may act as tumor suppressors, and are potent inhibitors of E2F-mediated trans-activation. This domain has the cyclin fold []. The crystal structure of the Rb pocket bound to a nine-residue E7 peptide containing the LxCxE motif, shared by other Rb-binding viral and cellular proteins, shows that the LxCxE peptide binds a highly conserved groove on the B-box portion of the pocket; the A-box portion appears to be required for the stable folding of the B box (see IPR002719 from INTERPRO). Also highly conserved is the extensive A-B interface, suggesting that it may be an additional protein-binding site. The A and B boxes each contain the cyclin-fold structural motif, with the LxCxE-binding site on the B-box cyclin fold being similar to a Cdk2-binding site of cyclin A and to a TBP-binding site of TFIIB []. The A and B boxes are found at the C-terminal end of the protein; the A-box is on N-terminal side of the B-box.; GO: 0051726 regulation of cell cycle, 0005634 nucleus; PDB: 1O9K_A 3POM_A 1GH6_B 1N4M_A 4ELL_B 1AD6_A 1GUX_A 2R7G_C 4ELJ_A.
Probab=32.52 E-value=55 Score=26.11 Aligned_cols=38 Identities=26% Similarity=0.476 Sum_probs=26.7
Q ss_pred hhhHHHHHHHHHHHHhcCCCCcchHHHHHHHHHhHHHHH-HHHHHhhh
Q 032021 82 NFHLLHLMENLADAIENGTRDQQSDALVNELNNHFEKCQ-QLLSSISE 128 (148)
Q Consensus 82 hFhL~~lve~Ladaie~GtRDQ~sDaLv~EL~s~FekcQ-QLLnSis~ 128 (148)
-||++-+||....+ -|.|=+||..||..++ ++|.|++=
T Consensus 146 ~f~f~KvIE~~Vr~---------~~~Lpr~lvkHL~~IEE~iLeslaW 184 (194)
T PF01858_consen 146 PFDFYKVIESFVRH---------EDGLPRELVKHLNSIEEQILESLAW 184 (194)
T ss_dssp HHHHHTTHHHHHHH----------TT--HHHHHHHHHHHHHHHHTGGG
T ss_pred hhhHhhHHHHHHHc---------cccCCHHHHHHHHHHHHHHHHHHHh
Confidence 37888999988776 2447888989988875 67777653
No 45
>TIGR03824 FlgM_jcvi flagellar biosynthesis anti-sigma factor FlgM. FlgM interacts with and inhibits the alternative sigma factor sigma(28) FliA. The C-terminus of FlgM contains the sigma(28)-binding domain.
Probab=32.47 E-value=65 Score=22.67 Aligned_cols=26 Identities=19% Similarity=0.424 Sum_probs=22.3
Q ss_pred HHHHHHHHHHhcCCCCcchHHHHHHH
Q 032021 87 HLMENLADAIENGTRDQQSDALVNEL 112 (148)
Q Consensus 87 ~lve~Ladaie~GtRDQ~sDaLv~EL 112 (148)
.-|+.|..+|++|+-.-+++.+..-|
T Consensus 66 ~kV~~ik~aI~~G~Y~vd~~~iA~~m 91 (95)
T TIGR03824 66 EKVAEIKAAIANGSYKVDAEKIADKL 91 (95)
T ss_pred HHHHHHHHHHHcCCCCCCHHHHHHHH
Confidence 57899999999999998888877655
No 46
>PRK14153 heat shock protein GrpE; Provisional
Probab=31.81 E-value=1.2e+02 Score=24.82 Aligned_cols=57 Identities=21% Similarity=0.366 Sum_probs=32.5
Q ss_pred HhhhhhhhHHHHHHHHHHHHhcCCCCcchHHHHHHHHHhHHHHHHHHHHhhhhcccccceehh
Q 032021 77 QSLASNFHLLHLMENLADAIENGTRDQQSDALVNELNNHFEKCQQLLSSISESLDTKAMTVEG 139 (148)
Q Consensus 77 qsLAShFhL~~lve~Ladaie~GtRDQ~sDaLv~EL~s~FekcQQLLnSis~sl~tk~~TVeg 139 (148)
+.++.- |||++++|..|++...-+....+|+ .-|+-...-|.++-...+=+.|-..|
T Consensus 83 ~~~~~~--LLpv~DnLerAl~~~~~~~~~~~l~----~Gvemi~k~~~~vL~k~Gv~~I~~~G 139 (194)
T PRK14153 83 EQVLLD--LLEVTDNFERALESARTAEDMNSIV----EGIEMVSKQFFSILEKYGLERIECEG 139 (194)
T ss_pred HHHHHH--HhhHHhHHHHHHhcccccchHHHHH----HHHHHHHHHHHHHHHHCCCeeeCCCC
Confidence 345544 9999999999999876544333344 33443333344444444444443333
No 47
>cd03415 CbiX_CbiC Archaeal sirohydrochlorin cobalt chelatase (CbiX) single domain. Proteins in this subgroup contain a single CbiX domain N-terminal to a precorrin-8X methylmutase (CbiC) domain. CbiX is a cobaltochelatase, responsible for the chelation of Co2+ into sirohydrochlorin, while CbiC catalyzes the conversion of cobalt-precorrin 8 to cobyrinic acid by methyl rearrangement. Both CbiX and CbiC are involved in vitamin B12 biosynthesis.
Probab=31.61 E-value=36 Score=25.51 Aligned_cols=22 Identities=23% Similarity=0.333 Sum_probs=19.7
Q ss_pred HhcCCCCcchHHHHHHHHHhHH
Q 032021 96 IENGTRDQQSDALVNELNNHFE 117 (148)
Q Consensus 96 ie~GtRDQ~sDaLv~EL~s~Fe 117 (148)
|.+|+||....+.|++|...+.
T Consensus 6 vgHGSR~~~~~~~~~~la~~l~ 27 (125)
T cd03415 6 ITHGSRRNTFNEDMEEWAAYLE 27 (125)
T ss_pred EecCCCChHHHHHHHHHHHHHH
Confidence 5789999999999999988876
No 48
>PRK14139 heat shock protein GrpE; Provisional
Probab=31.50 E-value=1.1e+02 Score=24.91 Aligned_cols=52 Identities=23% Similarity=0.270 Sum_probs=29.3
Q ss_pred HhhhhhhhHHHHHHHHHHHHhcCCCCcchHHHHHHHHHhHHHHHHHHHHhhhhcccccce
Q 032021 77 QSLASNFHLLHLMENLADAIENGTRDQQSDALVNELNNHFEKCQQLLSSISESLDTKAMT 136 (148)
Q Consensus 77 qsLAShFhL~~lve~Ladaie~GtRDQ~sDaLv~EL~s~FekcQQLLnSis~sl~tk~~T 136 (148)
..++.- |||++++|..|+...+.| .+.++.- |+--...|.+|-...+=+.|-
T Consensus 82 ~~~~~~--LLpv~DnLerAl~~~~~~--~~~l~~G----v~mi~k~l~~vL~k~Gv~~I~ 133 (185)
T PRK14139 82 ESFAES--LLPVKDSLEAALADESGD--LEKLREG----VELTLKQLTSAFEKGRVVEIN 133 (185)
T ss_pred HHHHHH--HhhHHhHHHHHHhcccch--HHHHHHH----HHHHHHHHHHHHHHCCCceeC
Confidence 345554 999999999999876433 2334433 333333344444444444443
No 49
>PF06013 WXG100: Proteins of 100 residues with WXG; InterPro: IPR010310 ESAT-6 is a small protein appears to be of fundamental importance in virulence and protective immunity in Mycobacterium tuberculosis. Homologues have been detected in other Gram-positive bacterial species. It may represent a novel secretion system potentially driven by the PF01580 from PFAM domains in the YukA-like proteins []. Members of this protein family include secretion targets for type main variants of type VII secretion systems (T7SS), one found in the Actinobacteria, one found in the Firmicutes. This model was derived through iteration from PF06013 from PFAM. The best characterised member of this family is ESAT-6 from Mycobacterium tuberculosis. Members of this family usually are ~100 amino acids in length but occasionally have long C-terminal extension. ; PDB: 3FAV_A 1WA8_A 3Q4H_B 2KG7_A 2VRZ_B 2VS0_B 3OGI_A 3H6P_B 3GVM_B 3GWK_C ....
Probab=31.41 E-value=1.2e+02 Score=18.55 Aligned_cols=47 Identities=19% Similarity=0.311 Sum_probs=33.1
Q ss_pred HHHHHHHHHHHHhcCCCCcchHHHHHHHHHhHHHHHHHHHHhhhhccc
Q 032021 85 LLHLMENLADAIENGTRDQQSDALVNELNNHFEKCQQLLSSISESLDT 132 (148)
Q Consensus 85 L~~lve~Ladaie~GtRDQ~sDaLv~EL~s~FekcQQLLnSis~sl~t 132 (148)
|--.|+.|.+.-+ |.-=...++.++++...|+++...|..|+..|..
T Consensus 30 l~~~~~~l~~~W~-G~a~~af~~~~~~~~~~~~~~~~~L~~~~~~l~~ 76 (86)
T PF06013_consen 30 LESSIDSLQASWQ-GEAADAFQDKFEEWNQAFRQLNEALEELSQALRQ 76 (86)
T ss_dssp HHHHHHHHGGGBT-SSTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHhhhCC-chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344455533333 5555566888899999999999999998887654
No 50
>PRK14150 heat shock protein GrpE; Provisional
Probab=31.06 E-value=1.2e+02 Score=24.41 Aligned_cols=58 Identities=17% Similarity=0.306 Sum_probs=30.9
Q ss_pred HhhhhhhhHHHHHHHHHHHHhcCCCCcchHHHHHHHHHhHHHHHHHHHHhhhhcccccceehh
Q 032021 77 QSLASNFHLLHLMENLADAIENGTRDQQSDALVNELNNHFEKCQQLLSSISESLDTKAMTVEG 139 (148)
Q Consensus 77 qsLAShFhL~~lve~Ladaie~GtRDQ~sDaLv~EL~s~FekcQQLLnSis~sl~tk~~TVeg 139 (148)
.+++.- |||++++|..|++....+.. .+..+..-|+--...|.++-...+=+.|-.-|
T Consensus 88 ~~~~~~--lL~v~DnlerAl~~~~~~~~---~~~~~~~Gv~mi~~~l~~~L~~~Gv~~i~~~G 145 (193)
T PRK14150 88 EKFANE--LLPVIDNLERALQAADKENE---ALKALIEGVELTLKSLLDTVAKFGVEVVGPVG 145 (193)
T ss_pred HHHHHH--HHhHHhHHHHHHhcccccch---hHHHHHHHHHHHHHHHHHHHHHCCCeeeCCCC
Confidence 345555 99999999999987643211 22333333333333344444444444443333
No 51
>PF08020 DUF1706: Protein of unknown function (DUF1706) ; InterPro: IPR012550 This family contains many hypothetical proteins from bacteria and yeast.
Probab=30.30 E-value=65 Score=25.45 Aligned_cols=33 Identities=18% Similarity=0.332 Sum_probs=28.0
Q ss_pred cchHHHHHHHHHhHHHHHHHHHHhhhhcccccc
Q 032021 103 QQSDALVNELNNHFEKCQQLLSSISESLDTKAM 135 (148)
Q Consensus 103 Q~sDaLv~EL~s~FekcQQLLnSis~sl~tk~~ 135 (148)
.+-++|+++...+|+|-..++++|+.+......
T Consensus 5 ~tK~eLl~ai~~~~~kL~~~~~~ipee~~~~~~ 37 (166)
T PF08020_consen 5 TTKAELLEAIEKNYEKLISEIDSIPEEQKDTPF 37 (166)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHhCCHHHhcCcc
Confidence 456899999999999999999999998655444
No 52
>cd03414 CbiX_SirB_C Sirohydrochlorin cobalt chelatase (CbiX) and sirohydrochlorin iron chelatase (SirB), C-terminal domain. SirB catalyzes the ferro-chelation of sirohydrochlorin to siroheme, the prosthetic group of sulfite and nitrite reductases. CbiX is a cobaltochelatase, responsible for the chelation of Co2+ into sirohydrochlorin, an important step in the vitamin B12 biosynthetic pathway. CbiX often contains a C-terminal histidine-rich region that may be important for metal delivery and/or storage, and may also contain an iron-sulfur center. Both CbiX and SirB are found in a wide range of bacteria.
Probab=29.47 E-value=48 Score=22.89 Aligned_cols=23 Identities=22% Similarity=0.430 Sum_probs=18.0
Q ss_pred HhcCCCCcchHHHHHHHHHhHHH
Q 032021 96 IENGTRDQQSDALVNELNNHFEK 118 (148)
Q Consensus 96 ie~GtRDQ~sDaLv~EL~s~Fek 118 (148)
+.+|+||..+.+-+++|...+++
T Consensus 6 v~HGS~~~~~~~~~~~l~~~l~~ 28 (117)
T cd03414 6 VGRGSSDPDANADVAKIARLLEE 28 (117)
T ss_pred EcCCCCCHHHHHHHHHHHHHHHH
Confidence 56899998888888888777764
No 53
>smart00388 HisKA His Kinase A (phosphoacceptor) domain. Dimerisation and phosphoacceptor domain of histidine kinases.
Probab=29.00 E-value=1.1e+02 Score=17.01 Aligned_cols=35 Identities=9% Similarity=0.259 Sum_probs=22.6
Q ss_pred HHHhcCCCCcchHHHHHHHHHhHHHHHHHHHHhhh
Q 032021 94 DAIENGTRDQQSDALVNELNNHFEKCQQLLSSISE 128 (148)
Q Consensus 94 daie~GtRDQ~sDaLv~EL~s~FekcQQLLnSis~ 128 (148)
+.+..+..+.....++..+....++...+++.+..
T Consensus 25 ~~l~~~~~~~~~~~~~~~~~~~~~~~~~~v~~l~~ 59 (66)
T smart00388 25 ELLEDTELSEEQREYLETILRSAERLLRLINDLLD 59 (66)
T ss_pred HHHHhCCCChHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33444445544467777777778888888877653
No 54
>PRK14143 heat shock protein GrpE; Provisional
Probab=27.97 E-value=1.5e+02 Score=25.02 Aligned_cols=58 Identities=21% Similarity=0.296 Sum_probs=32.7
Q ss_pred HhhhhhhhHHHHHHHHHHHHhcCCCCc-chHHHHHHHHHhHHHHHHHHHHhhhhcccccceehhh
Q 032021 77 QSLASNFHLLHLMENLADAIENGTRDQ-QSDALVNELNNHFEKCQQLLSSISESLDTKAMTVEGQ 140 (148)
Q Consensus 77 qsLAShFhL~~lve~Ladaie~GtRDQ-~sDaLv~EL~s~FekcQQLLnSis~sl~tk~~TVegQ 140 (148)
..++.- |||+++||..|++....+. ..++|+.- |+--...|.++-...+=+.|-..|+
T Consensus 117 ~~~~~~--lLpV~DnLerAl~~~~~~~~~~~~l~~G----ve~i~k~l~~~L~k~GV~~i~~~G~ 175 (238)
T PRK14143 117 CNTLSE--ILPVVDNFERARQQLKPEGEEAQALHRS----YQGLYKQLVDVLKRLGVSPMRVVGQ 175 (238)
T ss_pred HHHHHH--HHHHHhHHHHHHhcccccchhHHHHHHH----HHHHHHHHHHHHHHCCCeeeCCCCC
Confidence 344544 9999999999998765532 22344432 2222223344445556666655454
No 55
>PRK06663 flagellar hook-associated protein FlgL; Validated
Probab=27.82 E-value=1.5e+02 Score=25.94 Aligned_cols=59 Identities=12% Similarity=0.197 Sum_probs=38.0
Q ss_pred hHHHHHHHHHHHHhcCCCCcchHHHHHHHHHhHHHHHHHHHHhhhhcccccceehhhhhhhhh
Q 032021 84 HLLHLMENLADAIENGTRDQQSDALVNELNNHFEKCQQLLSSISESLDTKAMTVEGQRRKLEE 146 (148)
Q Consensus 84 hL~~lve~Ladaie~GtRDQ~sDaLv~EL~s~FekcQQLLnSis~sl~tk~~TVegQk~kLEE 146 (148)
.++-.+..|.++++.|+++. ++.+....++++..=+...-+.|+++-..||..+..+++
T Consensus 310 ~if~~l~~l~~~l~~~~~~~----~~~~al~~ld~a~~~v~~~ra~iGar~n~le~~~~~~~~ 368 (419)
T PRK06663 310 SIFDSLIQLRDALLNNDQEL----IGGRALGEIDEALDNLLTTLADLGAKENRLDRSYARISK 368 (419)
T ss_pred cHHHHHHHHHHHHhCCChhh----HHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHH
Confidence 47788899999999996643 333333444444444445557777777777766665554
No 56
>PF06295 DUF1043: Protein of unknown function (DUF1043); InterPro: IPR009386 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=27.53 E-value=69 Score=23.93 Aligned_cols=19 Identities=32% Similarity=0.754 Sum_probs=10.3
Q ss_pred HHHHHhHHHHHHHHHHhhh
Q 032021 110 NELNNHFEKCQQLLSSISE 128 (148)
Q Consensus 110 ~EL~s~FekcQQLLnSis~ 128 (148)
.+|+.||++.-+||+.+..
T Consensus 46 ~~V~~HF~~ta~Ll~~l~~ 64 (128)
T PF06295_consen 46 QEVNDHFAQTAELLDNLTQ 64 (128)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 3455556665555555444
No 57
>PF08580 KAR9: Yeast cortical protein KAR9; InterPro: IPR013889 The KAR9 protein in Saccharomyces cerevisiae (Baker's yeast) is a cytoskeletal protein required for karyogamy, correct positioning of the mitotic spindle and for orientation of cytoplasmic microtubules []. KAR9 localises at the shmoo tip in mating cells and at the tip of the growing bud in anaphase [].
Probab=27.26 E-value=53 Score=31.34 Aligned_cols=46 Identities=24% Similarity=0.336 Sum_probs=29.1
Q ss_pred hHHHHHHHHHHHHhcCCCCcchHHHHHHHHHhHHHHHHHHHHhhhhccc
Q 032021 84 HLLHLMENLADAIENGTRDQQSDALVNELNNHFEKCQQLLSSISESLDT 132 (148)
Q Consensus 84 hL~~lve~Ladaie~GtRDQ~sDaLv~EL~s~FekcQQLLnSis~sl~t 132 (148)
||+.|||.-..|||.+.-+.. ....+..-||.|-|++..|-..|.+
T Consensus 68 ~~l~lIe~~v~~ie~~q~r~d---i~~~~~dl~e~vsqm~~~vK~~L~~ 113 (683)
T PF08580_consen 68 RFLDLIEVYVSAIEDLQLRED---IANSLFDLIEEVSQMELDVKKTLIS 113 (683)
T ss_pred HHHHHHHhhcccccccccccc---ccccHHHHHHHHHHHHHHHHHHHHH
Confidence 488889988888887662111 1113555677888877766555443
No 58
>PF06266 HrpF: HrpF protein; InterPro: IPR009371 The species Pseudomonas syringae encompasses plant pathogens with differing host specificities and corresponding pathovar designations. P. syringae requires the Hrp (type III protein secretion) system, encoded by a 25-kb cluster of hrp and hrc genes, in order to elicit the hypersensitive response (HR) in nonhosts or to be pathogenic in hosts. The exact function of HrpF is unknown but the protein is needed for pathogenicity [].
Probab=27.21 E-value=91 Score=22.68 Aligned_cols=26 Identities=27% Similarity=0.391 Sum_probs=20.8
Q ss_pred chHHHHHHHHHhHHHHHHHHHHhhhh
Q 032021 104 QSDALVNELNNHFEKCQQLLSSISES 129 (148)
Q Consensus 104 ~sDaLv~EL~s~FekcQQLLnSis~s 129 (148)
.+++|=+.|-+.|++++.=++++.-.
T Consensus 3 s~~~LqrrLD~~~~rA~~~~d~aal~ 28 (74)
T PF06266_consen 3 SFNALQRRLDSQFERAQTNLDDAALN 28 (74)
T ss_pred chHHHHHHHHHHHHHHHhhHHHHHHh
Confidence 36788899999999999888875544
No 59
>COG3443 Predicted periplasmic or secreted protein [General function prediction only]
Probab=26.86 E-value=17 Score=30.61 Aligned_cols=10 Identities=40% Similarity=0.667 Sum_probs=7.9
Q ss_pred hhhhhhhHHH
Q 032021 78 SLASNFHLLH 87 (148)
Q Consensus 78 sLAShFhL~~ 87 (148)
.-|+||||+.
T Consensus 149 ~Ka~HfHif~ 158 (193)
T COG3443 149 RKASHFHIFM 158 (193)
T ss_pred cccceeEEEe
Confidence 3589999985
No 60
>PF14361 RsbRD_N: RsbT co-antagonist protein rsbRD N-terminal domain
Probab=26.53 E-value=85 Score=22.03 Aligned_cols=39 Identities=23% Similarity=0.311 Sum_probs=26.2
Q ss_pred HHHHHHHHHHHHhcCCCCcchHHHHHHHHHhHHHHHHHHHHhhhhccc
Q 032021 85 LLHLMENLADAIENGTRDQQSDALVNELNNHFEKCQQLLSSISESLDT 132 (148)
Q Consensus 85 L~~lve~Ladaie~GtRDQ~sDaLv~EL~s~FekcQQLLnSis~sl~t 132 (148)
.=|+...|+++++.| -| .....|+++-..|..|+.+-+-
T Consensus 41 ~~~v~~~l~~~l~~~-~d--------~~~~~~~~l~~~L~~lsr~RA~ 79 (105)
T PF14361_consen 41 ANPVLDALAAALESG-LD--------LAAPEWEELREALEELSRIRAV 79 (105)
T ss_pred HHHHHHHHHHHHHHh-hh--------ccccchHHHHHHHHHHHHHHHh
Confidence 457788888888888 22 2244557788888888776443
No 61
>TIGR00058 Hemerythrin hemerythrin family non-heme iron proteins. This family includes oxygen carrier proteins of various oligomeric states from the vascular fluid (hemerythrin) and muscle (myohemerythrin) of some marine invertebrates. Each unit binds 2 non-heme Fe using 5 H, one E and one D. One member of this family,from the sandworm Nereis diversicolor, is an unusual (non-metallothionein) cadmium-binding protein. Homologous proteins, excluded from this narrowly defined family, are found in archaea and bacteria (see pfam01814).
Probab=26.52 E-value=1.5e+02 Score=21.35 Aligned_cols=41 Identities=15% Similarity=0.116 Sum_probs=29.4
Q ss_pred hhhHHHHHHHHHHHHhcCCCCcchHHHHHHHHHhHHHHHHHHHHh
Q 032021 82 NFHLLHLMENLADAIENGTRDQQSDALVNELNNHFEKCQQLLSSI 126 (148)
Q Consensus 82 hFhL~~lve~Ladaie~GtRDQ~sDaLv~EL~s~FekcQQLLnSi 126 (148)
|=-|+-+|.+|.++.. ....+.|++-...||..=+.++..+
T Consensus 22 H~~L~~lin~l~~~~~----~~~l~~L~~y~~~HF~~EE~lM~~~ 62 (115)
T TIGR00058 22 HKTLFNGIFALAADNS----ATALKELIDVTVLHFLDEEAMMIAA 62 (115)
T ss_pred HHHHHHHHHHHHhcch----HHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 4457788888877653 2346677777799998888887764
No 62
>PRK14146 heat shock protein GrpE; Provisional
Probab=26.45 E-value=1.6e+02 Score=24.29 Aligned_cols=29 Identities=14% Similarity=0.268 Sum_probs=19.9
Q ss_pred hHHHHHHHHHHHHhcCCCCcchHHHHHHH
Q 032021 84 HLLHLMENLADAIENGTRDQQSDALVNEL 112 (148)
Q Consensus 84 hL~~lve~Ladaie~GtRDQ~sDaLv~EL 112 (148)
-|||+++||..|+...+-+....+|+.-+
T Consensus 109 ~lLpv~DnlerAl~~~~~~~~~~~l~~Gv 137 (215)
T PRK14146 109 GFLNPIDNLERVGATQNQSEELKPFVEGV 137 (215)
T ss_pred HHhhHHhHHHHHHhcccccchhhHHHHHH
Confidence 49999999999998754444444455433
No 63
>PF10158 LOH1CR12: Tumour suppressor protein; InterPro: IPR018780 This entry represents a region of 130 amino acids that is the most conserved part of some hypothetical proteins involved in loss of heterozygosity, and thus, tumour suppression []. The exact function of these proteins is not known.
Probab=25.74 E-value=71 Score=24.56 Aligned_cols=24 Identities=42% Similarity=0.751 Sum_probs=20.1
Q ss_pred HHHHHHhHHHHHHHHHHhhhhccc
Q 032021 109 VNELNNHFEKCQQLLSSISESLDT 132 (148)
Q Consensus 109 v~EL~s~FekcQQLLnSis~sl~t 132 (148)
|+||.....+|+-+|+.+..+|.+
T Consensus 89 v~els~~L~~~~~lL~~~v~~ie~ 112 (131)
T PF10158_consen 89 VNELSQQLSRCQSLLNQTVPSIET 112 (131)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 788889999999999998877643
No 64
>PRK10325 heat shock protein GrpE; Provisional
Probab=25.43 E-value=1.5e+02 Score=23.92 Aligned_cols=52 Identities=15% Similarity=0.318 Sum_probs=29.1
Q ss_pred hHHHHHHHHHHHHhcCCC-CcchHHHHHHHHHhHHHHHHHHHHhhhhcccccceehh
Q 032021 84 HLLHLMENLADAIENGTR-DQQSDALVNELNNHFEKCQQLLSSISESLDTKAMTVEG 139 (148)
Q Consensus 84 hL~~lve~Ladaie~GtR-DQ~sDaLv~EL~s~FekcQQLLnSis~sl~tk~~TVeg 139 (148)
-|||++++|..|++...- +...++|+.-+ +-....|.++-...+=+.|..-|
T Consensus 94 ~lLpv~DnlerAl~~~~~~~~~~~~l~~Gv----~m~~~~l~~~L~~~Gv~~i~~~G 146 (197)
T PRK10325 94 ELLPVIDSLDRALEVADKANPDMSAMVEGI----ELTLKSMLDVVRKFGVEVIAETN 146 (197)
T ss_pred HHhhHHhHHHHHHhcccccchhHHHHHHHH----HHHHHHHHHHHHHCcCeeeCCCC
Confidence 399999999999988642 23334444444 33333344444454544443333
No 65
>PF12776 Myb_DNA-bind_3: Myb/SANT-like DNA-binding domain; InterPro: IPR024752 This domain, found in a range of uncharacterised proteins, may be related to Myb/SANT-like DNA binding domains.
Probab=25.33 E-value=1e+02 Score=20.38 Aligned_cols=15 Identities=33% Similarity=0.658 Sum_probs=13.0
Q ss_pred HHHHHHHHHHhcCCC
Q 032021 87 HLMENLADAIENGTR 101 (148)
Q Consensus 87 ~lve~Ladaie~GtR 101 (148)
-||+.|.+.+..|.|
T Consensus 9 ~ll~~~~e~~~~g~~ 23 (96)
T PF12776_consen 9 FLLDLLIEQINKGNR 23 (96)
T ss_pred HHHHHHHHHHHhCCC
Confidence 378889999999999
No 66
>PRK14156 heat shock protein GrpE; Provisional
Probab=25.05 E-value=1.2e+02 Score=24.39 Aligned_cols=23 Identities=26% Similarity=0.323 Sum_probs=17.6
Q ss_pred hhhhhhhHHHHHHHHHHHHhcCCCC
Q 032021 78 SLASNFHLLHLMENLADAIENGTRD 102 (148)
Q Consensus 78 sLAShFhL~~lve~Ladaie~GtRD 102 (148)
.++.= |||++++|..|++.+..+
T Consensus 78 ~~~~~--LLpVlDnLerAl~~~~~~ 100 (177)
T PRK14156 78 DLAKA--ILPSLDNLERALAVEGLT 100 (177)
T ss_pred HHHHH--HhhHHhHHHHHHhCcccc
Confidence 34444 999999999999886543
No 67
>PRK08027 flgL flagellar hook-associated protein FlgL; Reviewed
Probab=24.87 E-value=1.6e+02 Score=24.80 Aligned_cols=63 Identities=11% Similarity=0.198 Sum_probs=33.4
Q ss_pred hHHHHHHHHHHHHhcCCCCcch-----HHHHHHHHHhHHHHHHHHHHhhhhcccccceehhhhhhhhh
Q 032021 84 HLLHLMENLADAIENGTRDQQS-----DALVNELNNHFEKCQQLLSSISESLDTKAMTVEGQRRKLEE 146 (148)
Q Consensus 84 hL~~lve~Ladaie~GtRDQ~s-----DaLv~EL~s~FekcQQLLnSis~sl~tk~~TVegQk~kLEE 146 (148)
.++..+++|.++++.|+.|... .+-+.+....++.+..-+...-.+|+++-..||-.+..+++
T Consensus 199 ~if~~l~~l~~~l~~~~~~~~~~~~~~~~~l~~a~~~id~~~~~v~~~~a~vGar~n~le~~~~~~~~ 266 (317)
T PRK08027 199 NLFAMLDSAIAALKTPVAGSDADKETAAAALDKTNRGLKNSLNNVLTVRAELGTQLNELESLDSLGSD 266 (317)
T ss_pred hHHHHHHHHHHHhcCCCCCchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccch
Confidence 4677889999999988755211 11222222334433333333345666666666655544443
No 68
>PF00512 HisKA: His Kinase A (phospho-acceptor) domain; InterPro: IPR003661 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. Signal transducing histidine kinases are the key elements in two-component signal transduction systems, which control complex processes such as the initiation of development in microorganisms [, ]. Examples of histidine kinases are EnvZ, which plays a central role in osmoregulation [], and CheA, which plays a central role in the chemotaxis system []. Histidine kinases usually have an N-terminal ligand-binding domain and a C-terminal kinase domain, but other domains may also be present. The kinase domain is responsible for the autophosphorylation of the histidine with ATP, the phosphotransfer from the kinase to an aspartate of the response regulator, and (with bifunctional enzymes) the phosphotransfer from aspartyl phosphate back to ADP or to water []. The kinase core has a unique fold, distinct from that of the Ser/Thr/Tyr kinase superfamily. HKs can be roughly divided into two classes: orthodox and hybrid kinases [, ]. Most orthodox HKs, typified by the Escherichia coli EnvZ protein, function as periplasmic membrane receptors and have a signal peptide and transmembrane segment(s) that separate the protein into a periplasmic N-terminal sensing domain and a highly conserved cytoplasmic C-terminal kinase core. Members of this family, however, have an integral membrane sensor domain. Not all orthodox kinases are membrane bound, e.g., the nitrogen regulatory kinase NtrB (GlnL) is a soluble cytoplasmic HK []. Hybrid kinases contain multiple phosphodonor and phosphoacceptor sites and use multi-step phospho-relay schemes instead of promoting a single phosphoryl transfer. In addition to the sensor domain and kinase core, they contain a CheY-like receiver domain and a His-containing phosphotransfer (HPt) domain. This entry represents the dimerisation and phosphoacceptor domain found in histidine kinases. It has been found in bacterial sensor protein/histidine kinases. Signal transducing histidine kinases are the key elements in two-component signal transduction systems, which control complex processes such as the initiation of development in microorganisms []. Examples of histidine kinases are EnvZ, which plays a central role in osmoregulation [], and CheA, which plays a central role in the chemotaxis system []. Histidine kinases usually have an N-terminal ligand-binding domain and a C-terminal kinase domain, but other domains may also be present. The kinase domain is responsible for the autophosphorylation of the histidine with ATP, the phosphotransfer from the kinase to an aspartate of the response regulator, and the phosphotransfer from aspartyl phosphate back to ADP or to water []. The homodimeric domain includes the site of histidine autophosphorylation and phosphate transfer reactions. The structure of the homodimeric domain comprises a closed, four-helical bundle with a left-handed twist, formed by two identical alpha-hairpin subunits.; GO: 0000155 two-component sensor activity, 0007165 signal transduction, 0016020 membrane; PDB: 3DGE_A 2C2A_A 3A0R_A 4EW8_A 2LFS_B 2LFR_B 3JZ3_A 1JOY_B 3ZRW_C 3ZRV_A ....
Probab=24.80 E-value=1.7e+02 Score=17.81 Aligned_cols=43 Identities=9% Similarity=0.314 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHhc-CCCCcch-HHHHHHHHHhHHHHHHHHHHhhh
Q 032021 86 LHLMENLADAIEN-GTRDQQS-DALVNELNNHFEKCQQLLSSISE 128 (148)
Q Consensus 86 ~~lve~Ladaie~-GtRDQ~s-DaLv~EL~s~FekcQQLLnSis~ 128 (148)
|..|-..+++++. +..+... ..++..+.+.-++...|++.|..
T Consensus 17 L~~i~~~~~~l~~~~~~~~~~~~~~l~~i~~~~~~l~~li~~ll~ 61 (68)
T PF00512_consen 17 LTAIRGYLELLERDSDLDPEQLREYLDRIRSAADRLNELINDLLD 61 (68)
T ss_dssp HHHHHHHHHHHHCSSCC-HHHCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3446667777777 6666654 77888888888888888888653
No 69
>COG2747 FlgM Negative regulator of flagellin synthesis (anti-sigma28 factor) [Transcription / Cell motility and secretion / Intracellular trafficking and secretion]
Probab=24.37 E-value=1.2e+02 Score=22.59 Aligned_cols=27 Identities=26% Similarity=0.401 Sum_probs=19.6
Q ss_pred HHHHHHHHHHHHhcCCCCcchHHHHHH
Q 032021 85 LLHLMENLADAIENGTRDQQSDALVNE 111 (148)
Q Consensus 85 L~~lve~Ladaie~GtRDQ~sDaLv~E 111 (148)
..-.||.|..|||+|+-==.+..|..-
T Consensus 59 ~~~kVeeiK~aI~~G~ykvD~~kiAd~ 85 (93)
T COG2747 59 REEKVEELKQAIENGEYKVDTEKIADK 85 (93)
T ss_pred hHHHHHHHHHHHHcCCeeecHHHHHHH
Confidence 567899999999999875544444333
No 70
>PF14966 DNA_repr_REX1B: DNA repair REX1-B
Probab=23.89 E-value=2.1e+02 Score=20.81 Aligned_cols=41 Identities=17% Similarity=0.342 Sum_probs=32.8
Q ss_pred HHHHHHHhcCCCCcchHHHHHHHHHhHHHHHHHHHHhhhhcc
Q 032021 90 ENLADAIENGTRDQQSDALVNELNNHFEKCQQLLSSISESLD 131 (148)
Q Consensus 90 e~Ladaie~GtRDQ~sDaLv~EL~s~FekcQQLLnSis~sl~ 131 (148)
+..++-..+|.- -....++.+++..|..|=.=+..|.+.|.
T Consensus 24 ~gf~~yl~~~~~-~~y~~~~~~iT~~f~~~S~ei~~ie~~L~ 64 (97)
T PF14966_consen 24 EGFKKYLRSGPE-EAYRQLCHEITQEFSAISKEILAIEAELR 64 (97)
T ss_pred HHHHHHHhcCCh-HHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 456666666666 66789999999999999888888888876
No 71
>PRK01885 greB transcription elongation factor GreB; Reviewed
Probab=23.82 E-value=90 Score=24.18 Aligned_cols=18 Identities=17% Similarity=0.289 Sum_probs=15.6
Q ss_pred HHHHHHHHHhcCCCCcch
Q 032021 88 LMENLADAIENGTRDQQS 105 (148)
Q Consensus 88 lve~Ladaie~GtRDQ~s 105 (148)
+++.|++|.+.|+++-|+
T Consensus 30 ~~~~i~~Ar~~GDl~ENa 47 (157)
T PRK01885 30 VTQKVSWAASLGDRSENA 47 (157)
T ss_pred HHHHHHHHHHcCCcchhh
Confidence 567899999999999887
No 72
>PF03127 GAT: GAT domain; InterPro: IPR004152 The GAT domain is responsible for binding of GGA proteins to several members of the ARF family including ARF1 [] and ARF3. The GAT domain stabilises membrane bound ARF1 in its GTP bound state, by interfering with GAP proteins [].; GO: 0006886 intracellular protein transport, 0005622 intracellular; PDB: 1YD8_H 1WR6_C 1WRD_A 1O3X_A 1J2J_B 1NWM_X 1X79_A 1OXZ_A 1NAF_A.
Probab=23.82 E-value=2.6e+02 Score=19.51 Aligned_cols=46 Identities=15% Similarity=0.380 Sum_probs=30.4
Q ss_pred HHHHHHHHHHhcCCCCcchHHHHHHHHHhHHHHHHHHHHhhhhccc
Q 032021 87 HLMENLADAIENGTRDQQSDALVNELNNHFEKCQQLLSSISESLDT 132 (148)
Q Consensus 87 ~lve~Ladaie~GtRDQ~sDaLv~EL~s~FekcQQLLnSis~sl~t 132 (148)
.|+..+-+....|......++|+.||...-.+.+..|..+...+..
T Consensus 21 ~lL~emL~~~~~~~~~~~~~el~~eL~~~ck~~r~~i~~li~~~~d 66 (100)
T PF03127_consen 21 KLLNEMLDNYDPGEESSSDNELIQELYESCKSMRPRIQRLIEEVED 66 (100)
T ss_dssp HHHHHHHHHTTTTTSTHHHHHHHHHHHHHHHHHHHHHHHHHHTSTT
T ss_pred HHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHHHHHHHhhcCc
Confidence 4555555666667777665689999977777777666665554433
No 73
>PF04212 MIT: MIT (microtubule interacting and transport) domain; InterPro: IPR007330 The MIT domain is found in vacuolar sorting proteins, spastin (probable ATPase involved in the assembly or function of nuclear protein complexes), and a sorting nexin, which may play a role in intracellular trafficking.; PDB: 2DL1_A 2JQK_A 1WR0_A 2CPT_A 2JQH_A 2V6Y_A 2JQ9_A 2K3W_A 1YXR_A 3EAB_E ....
Probab=23.74 E-value=2.1e+02 Score=18.40 Aligned_cols=39 Identities=18% Similarity=0.347 Sum_probs=27.0
Q ss_pred HHHHHHHHHHhcCCCCcchHHHHHHHHHhHHHHHHHHHH
Q 032021 87 HLMENLADAIENGTRDQQSDALVNELNNHFEKCQQLLSS 125 (148)
Q Consensus 87 ~lve~Ladaie~GtRDQ~sDaLv~EL~s~FekcQQLLnS 125 (148)
.-|+.|-.++..-+.+..-+.|-..+..-.+||+.|.+.
T Consensus 30 ~ai~~l~~~~~~~~~~~~~~~l~~k~~~yl~RAE~lk~~ 68 (69)
T PF04212_consen 30 EAIEYLMQALKSESNPERRQALRQKMKEYLERAEKLKEY 68 (69)
T ss_dssp HHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 345566666666666666666666778888898888764
No 74
>PF12806 Acyl-CoA_dh_C: Acetyl-CoA dehydrogenase C-terminal like
Probab=23.67 E-value=61 Score=23.38 Aligned_cols=18 Identities=39% Similarity=0.518 Sum_probs=16.5
Q ss_pred hHHHHHHHHHHHHhcCCC
Q 032021 84 HLLHLMENLADAIENGTR 101 (148)
Q Consensus 84 hL~~lve~Ladaie~GtR 101 (148)
++||-++.+..+|++|.+
T Consensus 106 ~~LP~~~~~~~~i~~g~~ 123 (130)
T PF12806_consen 106 RILPRADALAAAIEAGDD 123 (130)
T ss_pred HHHhhHHHHHHHHHccch
Confidence 689999999999999975
No 75
>PLN02372 violaxanthin de-epoxidase
Probab=23.59 E-value=64 Score=30.22 Aligned_cols=20 Identities=25% Similarity=0.501 Sum_probs=16.6
Q ss_pred HHHHHHHHHHhcCCCCcchH
Q 032021 87 HLMENLADAIENGTRDQQSD 106 (148)
Q Consensus 87 ~lve~Ladaie~GtRDQ~sD 106 (148)
||||+|.+.+|.|.++---|
T Consensus 361 ~l~~~l~~~~e~~e~~i~~e 380 (455)
T PLN02372 361 PLLERLEKDVEEGEKTIVKE 380 (455)
T ss_pred hHHHHHHHHHHHHHHHHHHH
Confidence 68999999999998876544
No 76
>PRK14145 heat shock protein GrpE; Provisional
Probab=23.53 E-value=2e+02 Score=23.62 Aligned_cols=28 Identities=25% Similarity=0.433 Sum_probs=19.1
Q ss_pred hHHHHHHHHHHHHhcCCCCcchHHHHHHHHH
Q 032021 84 HLLHLMENLADAIENGTRDQQSDALVNELNN 114 (148)
Q Consensus 84 hL~~lve~Ladaie~GtRDQ~sDaLv~EL~s 114 (148)
-|||++++|..|++.. .| .++|+.-+.-
T Consensus 100 ~LLpV~DnLerAl~~~-~~--~~~l~~Gv~m 127 (196)
T PRK14145 100 ELLPVMDNFERALASS-GD--YNSLKEGIEL 127 (196)
T ss_pred HHHhHHhHHHHHHhcc-cc--HHHHHHHHHH
Confidence 4999999999999882 22 3455544433
No 77
>PF08649 DASH_Dad1: DASH complex subunit Dad1; InterPro: IPR013958 The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis []. In Saccharomyces cerevisiae (Baker's yeast) DASH forms both rings and spiral structures on microtubules in vitro [, ]. Components of the DASH complex, including Dam1, Duo1, Spc34, Dad1 and Ask1, are essential and connect the centromere to the plus end of spindle microtubules []. Throughout the cell cycle Dad1 remains bound to kinetochores and its association is dependent on the Mis6 and Mal2 [].
Probab=23.50 E-value=1.3e+02 Score=20.80 Aligned_cols=28 Identities=29% Similarity=0.510 Sum_probs=23.1
Q ss_pred chHHHHHHHHHhHHHHHHHHHHhhhhcc
Q 032021 104 QSDALVNELNNHFEKCQQLLSSISESLD 131 (148)
Q Consensus 104 ~sDaLv~EL~s~FekcQQLLnSis~sl~ 131 (148)
.-|.|+.|+.+.++++-.-||.+-.+|.
T Consensus 6 qR~~Li~eI~~~~e~vl~nlN~LNRsLE 33 (58)
T PF08649_consen 6 QRDRLIQEISESMESVLNNLNALNRSLE 33 (58)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhHH
Confidence 3489999999999999988888766654
No 78
>PF06580 His_kinase: Histidine kinase; InterPro: IPR010559 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. Signal transducing histidine kinases are the key elements in two-component signal transduction systems, which control complex processes such as the initiation of development in microorganisms [, ]. Examples of histidine kinases are EnvZ, which plays a central role in osmoregulation [], and CheA, which plays a central role in the chemotaxis system []. Histidine kinases usually have an N-terminal ligand-binding domain and a C-terminal kinase domain, but other domains may also be present. The kinase domain is responsible for the autophosphorylation of the histidine with ATP, the phosphotransfer from the kinase to an aspartate of the response regulator, and (with bifunctional enzymes) the phosphotransfer from aspartyl phosphate back to ADP or to water []. The kinase core has a unique fold, distinct from that of the Ser/Thr/Tyr kinase superfamily. HKs can be roughly divided into two classes: orthodox and hybrid kinases [, ]. Most orthodox HKs, typified by the Escherichia coli EnvZ protein, function as periplasmic membrane receptors and have a signal peptide and transmembrane segment(s) that separate the protein into a periplasmic N-terminal sensing domain and a highly conserved cytoplasmic C-terminal kinase core. Members of this family, however, have an integral membrane sensor domain. Not all orthodox kinases are membrane bound, e.g., the nitrogen regulatory kinase NtrB (GlnL) is a soluble cytoplasmic HK []. Hybrid kinases contain multiple phosphodonor and phosphoacceptor sites and use multi-step phospho-relay schemes instead of promoting a single phosphoryl transfer. In addition to the sensor domain and kinase core, they contain a CheY-like receiver domain and a His-containing phosphotransfer (HPt) domain. This family represents a region within bacterial histidine kinase enzymes. Two-component signal transduction systems such as those mediated by histidine kinase are integral parts of bacterial cellular regulatory processes, and are used to regulate the expression of genes involved in virulence. Members of this family often contain IPR003594 from INTERPRO and/or IPR003660 from INTERPRO.; GO: 0000155 two-component sensor activity, 0000160 two-component signal transduction system (phosphorelay), 0016021 integral to membrane
Probab=23.17 E-value=2.3e+02 Score=19.18 Aligned_cols=56 Identities=13% Similarity=0.214 Sum_probs=34.9
Q ss_pred hhhhhhHHHHHHHHHHHHhcCCCCcchHHHHHHHHHhHHHHHHHHHHhhhhcccccceehhhhhhhh
Q 032021 79 LASNFHLLHLMENLADAIENGTRDQQSDALVNELNNHFEKCQQLLSSISESLDTKAMTVEGQRRKLE 145 (148)
Q Consensus 79 LAShFhL~~lve~Ladaie~GtRDQ~sDaLv~EL~s~FekcQQLLnSis~sl~tk~~TVegQk~kLE 145 (148)
+-.|| ||..+..+...+..+ .+.- ..+|..|..-|. -.. .-..+.++|+....-++
T Consensus 9 InPHF-l~NtLn~I~~l~~~~-~~~~-~~~i~~ls~~lR-------y~l-~~~~~~v~l~~El~~i~ 64 (82)
T PF06580_consen 9 INPHF-LFNTLNSISWLARID-PEKA-SEMILSLSDLLR-------YSL-SSKEEFVTLEEELEFIE 64 (82)
T ss_pred cChHH-HHHHHHHHHHHHHcC-HHHH-HHHHHHHHHHHH-------HHh-CCCCCeeeHHHHHHHHH
Confidence 44577 888888888888888 5554 455666666554 222 22355667766555443
No 79
>PRK07192 flgL flagellar hook-associated protein FlgL; Reviewed
Probab=23.04 E-value=2.2e+02 Score=23.14 Aligned_cols=62 Identities=13% Similarity=0.185 Sum_probs=37.8
Q ss_pred hHHHHHHHHHHHHhcCCCC---cchHHHHHHHHHhHHHHHHHHHHhhhhcccccceehhhhhhhh
Q 032021 84 HLLHLMENLADAIENGTRD---QQSDALVNELNNHFEKCQQLLSSISESLDTKAMTVEGQRRKLE 145 (148)
Q Consensus 84 hL~~lve~Ladaie~GtRD---Q~sDaLv~EL~s~FekcQQLLnSis~sl~tk~~TVegQk~kLE 145 (148)
.++..+..+.++++.+.-+ ....+.+.+....++++..-|...-+.|++....||..+..++
T Consensus 190 ~~~~~l~~~~~~l~~~~~~~~~~~~~~~~~~~l~~ld~a~~~l~~~ra~iGa~~~rle~~~~~~~ 254 (305)
T PRK07192 190 DVFNTLDKLIDLLETPALPAADAALTAAVDEALGAIDDALDNVLTVRTELGSRQNELDLLDGNHE 254 (305)
T ss_pred hHHHHHHHHHHHhcCCCCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 5677777778888776532 2223445555556666666666666777776666665555444
No 80
>PRK14158 heat shock protein GrpE; Provisional
Probab=23.03 E-value=2.2e+02 Score=23.26 Aligned_cols=47 Identities=13% Similarity=0.274 Sum_probs=26.7
Q ss_pred hHHHHHHHHHHHHhcCCCCcchHHHHHHHHHhHHHHHHHHHHhhhhcccccc
Q 032021 84 HLLHLMENLADAIENGTRDQQSDALVNELNNHFEKCQQLLSSISESLDTKAM 135 (148)
Q Consensus 84 hL~~lve~Ladaie~GtRDQ~sDaLv~EL~s~FekcQQLLnSis~sl~tk~~ 135 (148)
-|||+++||..|++..+ +...+++ ..-|+-....|.++-...+=+.|
T Consensus 95 ~lLpV~DnLerAl~~~~-~~~~~~i----~~Gv~mi~k~l~~vLek~Gv~~I 141 (194)
T PRK14158 95 EILPAVDNMERALDHAD-EESMSAI----IEGIRMTLSMLLSTLKKFGVTPV 141 (194)
T ss_pred HHHhHHhHHHHHHhccC-cchHHHH----HHHHHHHHHHHHHHHHHCCCEEe
Confidence 39999999999999865 2222333 33344333334444444444444
No 81
>PF14461 Prok-E2_B: Prokaryotic E2 family B
Probab=22.98 E-value=1.5e+02 Score=21.82 Aligned_cols=33 Identities=15% Similarity=0.380 Sum_probs=26.2
Q ss_pred HHHHHHHHHHHHhcCCCCcchHHHHHHHHHhHH
Q 032021 85 LLHLMENLADAIENGTRDQQSDALVNELNNHFE 117 (148)
Q Consensus 85 L~~lve~Ladaie~GtRDQ~sDaLv~EL~s~Fe 117 (148)
+.-++++....++.|-.+.+.+++..|..+-..
T Consensus 93 ~~~~l~~a~~lL~~~~~~~~~~d~~~Ef~sYW~ 125 (133)
T PF14461_consen 93 IADCLERAIRLLEDGLSGDNEDDFADEFQSYWN 125 (133)
T ss_pred HHHHHHHHHHHHHHhhcCCchHHHHHHHHHHHh
Confidence 455678888888999988889999999876544
No 82
>KOG3182 consensus Predicted cation transporter [Inorganic ion transport and metabolism]
Probab=22.94 E-value=95 Score=26.56 Aligned_cols=41 Identities=20% Similarity=0.365 Sum_probs=31.8
Q ss_pred HHHHHHHHHHHHhcCCCCcchHHHHHHHHHhHHHHHHHHHHh
Q 032021 85 LLHLMENLADAIENGTRDQQSDALVNELNNHFEKCQQLLSSI 126 (148)
Q Consensus 85 L~~lve~Ladaie~GtRDQ~sDaLv~EL~s~FekcQQLLnSi 126 (148)
|+.|.++|++..= |.+|.+.-+|++++.....+|+++...+
T Consensus 156 Lf~La~am~~l~p-~~~D~hl~eL~~~Vrk~l~~~~~~~~al 196 (212)
T KOG3182|consen 156 LFNLAKAMRQLFP-GAEDEHLFELENEVRKYLVESRPLVHAL 196 (212)
T ss_pred HHHHHHHHHHcCC-CchhHHHHHHHHHHHHHHhccchhhhhh
Confidence 6666666666543 8999999999999988888887666554
No 83
>KOG3661 consensus Uncharacterized conserved protein [Function unknown]
Probab=22.77 E-value=88 Score=31.60 Aligned_cols=47 Identities=30% Similarity=0.541 Sum_probs=38.3
Q ss_pred cCCCCcchHHHHHHHH---HhHHHHHHHHHHhhhhcccccceehhhhhhh
Q 032021 98 NGTRDQQSDALVNELN---NHFEKCQQLLSSISESLDTKAMTVEGQRRKL 144 (148)
Q Consensus 98 ~GtRDQ~sDaLv~EL~---s~FekcQQLLnSis~sl~tk~~TVegQk~kL 144 (148)
.|+-|+.-|+-|.||+ ..++|-..||+|+++.+++.+..+.|=|-+|
T Consensus 577 TgdLdtkIDekvaEisrrl~~yA~~kkll~SmaS~lns~~~Sl~~Sr~Sl 626 (1019)
T KOG3661|consen 577 TGDLDTKIDEKVAEISRRLHKYAKLKKLLDSMASTLNSGAFSLAGSRFSL 626 (1019)
T ss_pred ccchhhhhhHHHHHHHHHHHHHHHHHHHHHHHhhccCCcccccccceecc
Confidence 5888999999999995 4577888899999999999888777665544
No 84
>PF01903 CbiX: CbiX; InterPro: IPR002762 Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt. Cobalamin is usually found in one of two biologically active forms: methylcobalamin and adocobalamin. Most prokaryotes, as well as animals, have cobalamin-dependent enzymes, whereas plants and fungi do not appear to use it. In bacteria and archaea, these include methionine synthase, ribonucleotide reductase, glutamate and methylmalonyl-CoA mutases, ethanolamine ammonia lyase, and diol dehydratase []. In mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase []. There are at least two distinct cobalamin biosynthetic pathways in bacteria []: Aerobic pathway that requires oxygen and in which cobalt is inserted late in the pathway []; found in Pseudomonas denitrificans and Rhodobacter capsulatus. Anaerobic pathway in which cobalt insertion is the first committed step towards cobalamin synthesis []; found in Salmonella typhimurium, Bacillus megaterium, and Propionibacterium freudenreichii subsp. shermanii. Either pathway can be divided into two parts: (1) corrin ring synthesis (differs in aerobic and anaerobic pathways) and (2) adenosylation of corrin ring, attachment of aminopropanol arm, and assembly of the nucleotide loop (common to both pathways) []. There are about 30 enzymes involved in either pathway, where those involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Several of these enzymes are pathway-specific: CbiD, CbiG, and CbiK are specific to the anaerobic route of S. typhimurium, whereas CobE, CobF, CobG, CobN, CobS, CobT, and CobW are unique to the aerobic pathway of P. denitrificans. This entry represents the CbiX protein, which functions as a cobalt-chelatase in the anaerobic biosynthesis of cobalamin. It catalyses the insertion of cobalt into sirohydrochlorin. The structure of CbiX from Archaeoglobus fulgidus consists of a central mixed beta-sheet flanked by four alpha-helices, although it is about half the size of other Class II tetrapyrrole chelatases []. The CbiX proteins found in archaea appear to be shorter than those found in eubacteria [].; GO: 0016829 lyase activity, 0046872 metal ion binding, 0009236 cobalamin biosynthetic process; PDB: 2XWQ_C 2DJ5_A 1TJN_A 2XWS_A 3LYH_B 2JH3_D.
Probab=22.35 E-value=1.1e+02 Score=20.54 Aligned_cols=21 Identities=24% Similarity=0.613 Sum_probs=16.6
Q ss_pred cCCCCcchHHHHHHHHHhHHH
Q 032021 98 NGTRDQQSDALVNELNNHFEK 118 (148)
Q Consensus 98 ~GtRDQ~sDaLv~EL~s~Fek 118 (148)
+|+||-.+.+-++++...+.+
T Consensus 1 HGSr~~~~~~~~~~la~~l~~ 21 (105)
T PF01903_consen 1 HGSRDPEANAELEDLADRLRE 21 (105)
T ss_dssp -STSSCHHHHHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHHHh
Confidence 699999988888888777664
No 85
>PF01920 Prefoldin_2: Prefoldin subunit; InterPro: IPR002777 Prefoldin (PFD) is a chaperone that interacts exclusively with type II chaperonins, hetero-oligomers lacking an obligate co-chaperonin that are found only in eukaryotes (chaperonin-containing T-complex polypeptide-1 (CCT)) and archaea. Eukaryotic PFD is a multi-subunit complex containing six polypeptides in the molecular mass range of 14-23 kDa. In archaea, on the other hand, PFD is composed of two types of subunits, two alpha and four beta. The six subunits associate to form two back-to-back up-and-down eight-stranded barrels, from which hang six coiled coils. Each subunit contributes one (beta subunits) or two (alpha subunits) beta hairpin turns to the barrels. The coiled coils are formed by the N and C termini of an individual subunit. Overall, this unique arrangement resembles a jellyfish. The eukaryotic PFD hexamer is composed of six different subunits; however, these can be grouped into two alpha-like (PFD3 and -5) and four beta-like (PFD1, -2, -4, and -6) subunits based on amino acid sequence similarity with their archaeal counterparts. Eukaryotic PFD has a six-legged structure similar to that seen in the archaeal homologue [, ]. This family contains the archaeal beta subunit, eukaryotic prefoldin subunits 1, 2, 4 and 6. Eukaryotic PFD has been shown to bind both actin and tubulin co-translationally. The chaperone then delivers the target protein to CCT, interacting with the chaperonin through the tips of the coiled coils. No authentic target proteins of any archaeal PFD have been identified, to date.; GO: 0051082 unfolded protein binding, 0006457 protein folding, 0016272 prefoldin complex; PDB: 2ZDI_B 3AEI_B 2ZQM_A 1FXK_A.
Probab=22.26 E-value=1.2e+02 Score=20.39 Aligned_cols=44 Identities=20% Similarity=0.354 Sum_probs=36.1
Q ss_pred cchHHHHHHHHHhHHHHHHHHHHhhhhcccccceehhhhhhhhh
Q 032021 103 QQSDALVNELNNHFEKCQQLLSSISESLDTKAMTVEGQRRKLEE 146 (148)
Q Consensus 103 Q~sDaLv~EL~s~FekcQQLLnSis~sl~tk~~TVegQk~kLEE 146 (148)
...+.++.+|...-++|+.-+..+...+....-.++.-+.+|.+
T Consensus 58 ~~~~~~~~~L~~~~~~~~~~i~~l~~~~~~l~~~l~~~~~~l~~ 101 (106)
T PF01920_consen 58 QDKEEAIEELEERIEKLEKEIKKLEKQLKYLEKKLKELKKKLYE 101 (106)
T ss_dssp EEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46789999999999999999999998887777777666666654
No 86
>PF01497 Peripla_BP_2: Periplasmic binding protein; InterPro: IPR002491 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energise diverse biological systems. ABC transporters minimally consist of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain []. The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyse ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarise the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site [, , ]. The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis [, , , , , ]. The ATP-Binding Cassette (ABC) superfamily forms one of the largest of all protein families with a diversity of physiological functions []. Several studies have shown that there is a correlation between the functional characterisation and the phylogenetic classification of the ABC cassette [, ]. More than 50 subfamilies have been described based on a phylogenetic and functional classification [, , ]; (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). Most bacterial importers employ a periplasmic substrate-binding protein (PBP) that delivers the ligand to the extracellular gate of the TM domains. These proteins bind their substrates selectively and with high affinity, which is thought to ensure the specificity of the transport reaction. Binding proteins in Gram-negative bacteria are present within the periplasm, whereas those in Gram-positive bacteria are tethered to the cell membrane via the acylation of a cysteine residue that is an integral component of a lipoprotein signal sequence. In planta expression of a high-affinity iron-uptake system involving the siderophore chrysobactin in Erwinia chrysanthemi 3937 contributes greatly to invasive growth of this pathogen on its natural host, African violets []. The cobalamin (vitamin B12) and the iron transport systems share many common attributes and probably evolved from the same origin [, ]. The periplasmic-binding domain is composed of two subdomains, each consisting of a central beta-sheet and surrounding alpha-helices, linked by a rigid alpha-helix. The substrate binding site is located in a cleft between the two alpha/beta subdomains [].; GO: 0005488 binding; PDB: 2X4L_A 1N4A_B 1N2Z_B 1N4D_B 4DBL_J 2QI9_F 3EIW_A 3EIX_A 3MWG_A 3MWF_A ....
Probab=22.20 E-value=2.6e+02 Score=20.51 Aligned_cols=39 Identities=21% Similarity=0.399 Sum_probs=31.9
Q ss_pred HHHHHHHHHHHHhcCCCCcchHHHHHHHHHhHHHHHHHHHHh
Q 032021 85 LLHLMENLADAIENGTRDQQSDALVNELNNHFEKCQQLLSSI 126 (148)
Q Consensus 85 L~~lve~Ladaie~GtRDQ~sDaLv~EL~s~FekcQQLLnSi 126 (148)
+...++.||+++.+. ..-++++.++..+++++...+..+
T Consensus 98 ~~~~i~~lg~~~g~~---~~a~~~~~~~~~~~~~~~~~~~~~ 136 (238)
T PF01497_consen 98 WKEQIRQLGKALGKE---DQAEALIAEYDARLDEIRKRLAKI 136 (238)
T ss_dssp HHHHHHHHHHHHTSH---HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhcccH---HHHHHHHHHHHHHHHHHHHhhhcc
Confidence 566788889888543 455999999999999999988887
No 87
>PF07445 priB_priC: Primosomal replication protein priB and priC; InterPro: IPR010890 This family contains the bacterial primosomal replication proteins priB and priC (approximately 180 residues long). In Escherichia coli, these function in the assembly of the primosome [].
Probab=22.09 E-value=3.9e+02 Score=20.97 Aligned_cols=63 Identities=21% Similarity=0.373 Sum_probs=40.8
Q ss_pred hhhHHHHHhhhhhhh----HHHHHHHHHHHHhcCCCCcchHHHH---HHHHHhHHHHHHHHHHhhhhcccc
Q 032021 70 QQQNQHHQSLASNFH----LLHLMENLADAIENGTRDQQSDALV---NELNNHFEKCQQLLSSISESLDTK 133 (148)
Q Consensus 70 ~~~~~~hqsLAShFh----L~~lve~Ladaie~GtRDQ~sDaLv---~EL~s~FekcQQLLnSis~sl~tk 133 (148)
++-...++.|+-|.. |+-+|+...+..+.-+.+ .--.|- ..+..|..||.+-|..|...|.-+
T Consensus 102 ~~~~~Lyq~L~~hqe~erRL~~mi~~~e~~l~~~~~~-~~~~lq~ei~a~e~RL~RCr~Ai~~iE~~I~~~ 171 (173)
T PF07445_consen 102 KPIHQLYQRLAQHQEYERRLLAMIQEREQQLEQAQSF-EQQQLQQEILALEQRLQRCRQAIEKIEEQIQRR 171 (173)
T ss_pred CchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCChH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455556888988865 344555544455544444 223443 445889999999999999887543
No 88
>PF08388 GIIM: Group II intron, maturase-specific domain; InterPro: IPR013597 This region is found mainly in various bacterial and archaeal species, but a few members of this family are expressed by fungal and chlamydomonal species. It has been implicated in the binding of intron RNA during reverse transcription and splicing [].
Probab=22.07 E-value=1.8e+02 Score=18.82 Aligned_cols=28 Identities=14% Similarity=0.315 Sum_probs=21.6
Q ss_pred HHHHHHHHHhcCCCCcchHHHHHHHHHh
Q 032021 88 LMENLADAIENGTRDQQSDALVNELNNH 115 (148)
Q Consensus 88 lve~Ladaie~GtRDQ~sDaLv~EL~s~ 115 (148)
+.+.|.+.+.+..+....+++|.+|+.-
T Consensus 4 ~~~kik~~~~~~~~~~~~~~~i~~LN~~ 31 (80)
T PF08388_consen 4 FRRKIKEITRRRNRGKSLEELIKKLNPI 31 (80)
T ss_pred HHHHHHHHHhCCCCCCCHHHHHHHHHHH
Confidence 4567788887777778889999998753
No 89
>PF08780 NTase_sub_bind: Nucleotidyltransferase substrate binding protein like; InterPro: IPR010235 The member of this family from Haemophilus influenzae, HI0074, has been shown by crystal structure to resemble nucleotidyltransferase substrate binding proteins []. It forms a complex with HI0073 (P43933 from SWISSPROT), encoded by the adjacent gene, which contains a nucleotidyltransferase nucleotide binding domain (IPR002934 from INTERPRO). Double- and single-stranded DNA binding assays showed no evidence of DNA binding to HI0074 or to HI0073/HI0074 complex despite the suggestive shape of the putative binding cleft formed by the HI0074 dimer []. ; PDB: 1WWP_A 1JOG_A 1WTY_C 2YWA_B.
Probab=22.00 E-value=2.5e+02 Score=20.72 Aligned_cols=39 Identities=21% Similarity=0.209 Sum_probs=27.6
Q ss_pred HHHHHHHHHHHHhcCCCCcchHHHHHHHHHhHHHHHHHHH
Q 032021 85 LLHLMENLADAIENGTRDQQSDALVNELNNHFEKCQQLLS 124 (148)
Q Consensus 85 L~~lve~Ladaie~GtRDQ~sDaLv~EL~s~FekcQQLLn 124 (148)
|---+.+|.+|++.. .|.-+|-+..-+..+||.|-.|.=
T Consensus 6 ~~kAl~~L~ea~~~~-~~~~~~~~~dg~IqrFE~t~ElaW 44 (124)
T PF08780_consen 6 FKKALSRLEEALEKY-EDPLSELERDGVIQRFEFTFELAW 44 (124)
T ss_dssp HHHHHHHHHHHHHHH--SCHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHhc-cCcchHHHHHHHHHHHHHHHHHHH
Confidence 445678888888876 455556666667999999877643
No 90
>PRK07701 flgL flagellar hook-associated protein FlgL; Validated
Probab=21.87 E-value=2.6e+02 Score=22.71 Aligned_cols=58 Identities=17% Similarity=0.370 Sum_probs=40.7
Q ss_pred hHHHHHHHHHHHHhcCCCCcchHHHHHHHHHhHHHHHHHHHHhhhhcccccceehhhhhhhhh
Q 032021 84 HLLHLMENLADAIENGTRDQQSDALVNELNNHFEKCQQLLSSISESLDTKAMTVEGQRRKLEE 146 (148)
Q Consensus 84 hL~~lve~Ladaie~GtRDQ~sDaLv~EL~s~FekcQQLLnSis~sl~tk~~TVegQk~kLEE 146 (148)
-++-.+.++..+++.|+++--+ ..-..++++..-|...-+.|+++...||..+..+++
T Consensus 190 ~v~~~l~~~~~~l~~~~~~~~~-----~al~~l~~a~~~v~~~~a~iG~~~~~l~~~~~~~~~ 247 (298)
T PRK07701 190 NLFEMLDNLENALDSGDTQGVS-----NLLSDIDQHIDNVLAVRAELGARSNRLELIENRLSD 247 (298)
T ss_pred hHHHHHHHHHHHHHCCChhHHH-----HHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHH
Confidence 4677778888889988765433 233456777766777777888888877777766654
No 91
>PRK14144 heat shock protein GrpE; Provisional
Probab=21.64 E-value=1.9e+02 Score=23.94 Aligned_cols=47 Identities=15% Similarity=0.328 Sum_probs=27.4
Q ss_pred hHHHHHHHHHHHHhcCCCCcchHHHHHHHHHhHHHHHHHHHHhhhhcccccc
Q 032021 84 HLLHLMENLADAIENGTRDQQSDALVNELNNHFEKCQQLLSSISESLDTKAM 135 (148)
Q Consensus 84 hL~~lve~Ladaie~GtRDQ~sDaLv~EL~s~FekcQQLLnSis~sl~tk~~ 135 (148)
-|||+++||..|++....+.. .+++. -|+-....|.++-...+=+.|
T Consensus 100 ~LLpV~DnLerAl~~~~~~~~-~~i~~----Gv~mi~k~l~~~L~k~GV~~I 146 (199)
T PRK14144 100 ALLPVVDSLEQALQLADKNSD-PSMHE----GLELTMKLFLDALQKFDVEQI 146 (199)
T ss_pred HHhhHHhHHHHHHHcccccch-hHHHH----HHHHHHHHHHHHHHHCCCEEe
Confidence 499999999999998754432 33443 333333334444444444444
No 92
>cd03416 CbiX_SirB_N Sirohydrochlorin cobalt chelatase (CbiX) and sirohydrochlorin iron chelatase (SirB), N-terminal domain. SirB catalyzes the ferro-chelation of sirohydrochlorin to siroheme, the prosthetic group of sulfite and nitrite reductases. CbiX is a cobaltochelatase, responsible for the chelation of Co2+ into sirohydrochlorin, an important step in the vitamin B12 biosynthetic pathway. CbiX often contains a C-terminal histidine-rich region that may be important for metal delivery and/or storage, and may also contain an iron-sulfur center. Both are found in a wide range of bacteria. This subgroup also contains single domain proteins from archaea and bacteria which may represent the ancestral form of class II chelatases before domain duplication occurred.
Probab=21.63 E-value=78 Score=21.32 Aligned_cols=23 Identities=17% Similarity=0.485 Sum_probs=16.9
Q ss_pred HhcCCCCcchHHHHHHHHHhHHH
Q 032021 96 IENGTRDQQSDALVNELNNHFEK 118 (148)
Q Consensus 96 ie~GtRDQ~sDaLv~EL~s~Fek 118 (148)
|.+|+|+....+-+++|...+.+
T Consensus 5 v~hGS~~~~~~~~~~~l~~~l~~ 27 (101)
T cd03416 5 VGHGSRDPRAAEALEALAERLRE 27 (101)
T ss_pred EEcCCCCHHHHHHHHHHHHHHHh
Confidence 46789988777777777776654
No 93
>cd00632 Prefoldin_beta Prefoldin beta; Prefoldin is a hexameric molecular chaperone complex, composed of two evolutionarily related subunits (alpha and beta), which are found in both eukaryotes and archaea. Prefoldin binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The hexameric structure consists of a double beta barrel assembly with six protruding coiled-coils. The alpha prefoldin subunits have two beta hairpin structures while the beta prefoldin subunits (this CD) have only one hairpin that is most similar to the second hairpin of the alpha subunit. The prefoldin hexamer consists of two alpha and four beta subunits and is assembled from the beta hairpins of all six subunits. The alpha subunits initially dimerize providing a structural nucleus for the assembly of the beta subunits. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the st
Probab=21.55 E-value=1.2e+02 Score=21.40 Aligned_cols=44 Identities=9% Similarity=0.210 Sum_probs=34.7
Q ss_pred chHHHHHHHHHhHHHHHHHHHHhhhhcccccceehhhhhhhhhc
Q 032021 104 QSDALVNELNNHFEKCQQLLSSISESLDTKAMTVEGQRRKLEER 147 (148)
Q Consensus 104 ~sDaLv~EL~s~FekcQQLLnSis~sl~tk~~TVegQk~kLEE~ 147 (148)
..|.++..|..+-+.+..-+..+.+.+....-.+..-+.+|+|.
T Consensus 60 ~~~ea~~~Le~~~e~le~~i~~l~~~~~~l~~~~~elk~~l~~~ 103 (105)
T cd00632 60 EKEEARTELKERLETIELRIKRLERQEEDLQEKLKELQEKIQQA 103 (105)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45778888888888888888888888877777777777777663
No 94
>PTZ00332 paraflagellar rod protein; Provisional
Probab=21.45 E-value=90 Score=30.10 Aligned_cols=24 Identities=29% Similarity=0.421 Sum_probs=19.7
Q ss_pred chHHHHHHHHHhHHHHHHHHHHhh
Q 032021 104 QSDALVNELNNHFEKCQQLLSSIS 127 (148)
Q Consensus 104 ~sDaLv~EL~s~FekcQQLLnSis 127 (148)
-||.-+..|.-.||||++||.|..
T Consensus 42 W~et~~~kl~~~~e~~~ellasVe 65 (589)
T PTZ00332 42 WSETQRQKLRGAHEKAEELLASVE 65 (589)
T ss_pred hHHHHHHHHHhHHHHHHHHHHhcc
Confidence 356677788899999999999754
No 95
>PRK09772 transcriptional antiterminator BglG; Provisional
Probab=21.36 E-value=2.5e+02 Score=22.78 Aligned_cols=50 Identities=18% Similarity=0.193 Sum_probs=33.3
Q ss_pred HHHhhhhhhhHHHHHHHHHHHHhcCCCCcchH-HHHHHHHHhHHHHHHHHHHhhhhc
Q 032021 75 HHQSLASNFHLLHLMENLADAIENGTRDQQSD-ALVNELNNHFEKCQQLLSSISESL 130 (148)
Q Consensus 75 ~hqsLAShFhL~~lve~Ladaie~GtRDQ~sD-aLv~EL~s~FekcQQLLnSis~sl 130 (148)
.+..|..| |-+++.++. .|....+.| .|+.++...|-++=.+...|+.-|
T Consensus 201 ~y~rl~~H--Lk~~~~R~~----~~~~~~n~~~~l~~~Ik~~Yp~~y~~a~~i~~~i 251 (278)
T PRK09772 201 SYQRLVTH--LKFLSWRIL----EHASINDSDESLQQAVKQNYPQAWQCAERIAIFI 251 (278)
T ss_pred cHHHHHHH--HHHHHHHHH----cCCCCccchHHHHHHHHHHChHHHHHHHHHHHHH
Confidence 45567776 888888886 455544544 588888888776666666555544
No 96
>PF09577 Spore_YpjB: Sporulation protein YpjB (SpoYpjB); InterPro: IPR014231 Proteins in thie entry, typified by YpjB, are restricted to a subset of the endospore-forming bacteria which includes Bacillus species, but not species. In Bacillus subtilis, ypjB was found to be part of the sigma-E regulon []. Sigma-E is a sporulation sigma factor that regulates expression in the mother cell compartment. Null mutants of ypjB show a sporulation defect, but this gene is not, however, a part of the endospore formation minimal gene set.
Probab=20.98 E-value=81 Score=26.53 Aligned_cols=30 Identities=33% Similarity=0.496 Sum_probs=23.9
Q ss_pred CcchHHHHHHH-HHhHHHHHHHHHHhhhhcc
Q 032021 102 DQQSDALVNEL-NNHFEKCQQLLSSISESLD 131 (148)
Q Consensus 102 DQ~sDaLv~EL-~s~FekcQQLLnSis~sl~ 131 (148)
|+-||.++.-+ ..+||+|.++|+-+|..+.
T Consensus 6 d~~sd~~lqlvk~~~yeeA~q~l~~fs~~f~ 36 (232)
T PF09577_consen 6 DQLSDEALQLVKQGKYEEAKQLLEYFSEQFT 36 (232)
T ss_pred HHHHHHHHHHHHcccHHHHHHHHHHHHHHHh
Confidence 45678888777 7889999999999887643
No 97
>KOG0992 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.86 E-value=1.6e+02 Score=28.66 Aligned_cols=60 Identities=30% Similarity=0.436 Sum_probs=48.7
Q ss_pred HHHHHHHHHHhcCCCCcchHHHHHH---HHHhHHHHHHHHHHhhhhcccccceehhhhhhhhh
Q 032021 87 HLMENLADAIENGTRDQQSDALVNE---LNNHFEKCQQLLSSISESLDTKAMTVEGQRRKLEE 146 (148)
Q Consensus 87 ~lve~Ladaie~GtRDQ~sDaLv~E---L~s~FekcQQLLnSis~sl~tk~~TVegQk~kLEE 146 (148)
+.++.-+++.+.-++.|.--++++| |..++++.--++++|.||.+..-.-.+-++-.|||
T Consensus 215 ~~~~s~~e~l~kl~~EqQlq~~~~ehkllee~~~rl~~~~s~VegS~S~~~l~~ek~r~~lee 277 (613)
T KOG0992|consen 215 IVEESRLESLGKLNSEQQLQALIREHKLLEEHLERLHLQLSDVEGSWSGQNLALEKQRSRLEE 277 (613)
T ss_pred HHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccchhHHHHHHHHHHHHH
Confidence 4445556667777888888888887 48999999999999999999988888888877776
No 98
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=20.78 E-value=49 Score=23.99 Aligned_cols=18 Identities=28% Similarity=0.351 Sum_probs=13.9
Q ss_pred cccccceehhhhhhhhhc
Q 032021 130 LDTKAMTVEGQRRKLEER 147 (148)
Q Consensus 130 l~tk~~TVegQk~kLEE~ 147 (148)
|+-.+=||++++.+|||.
T Consensus 33 l~~s~aTIRN~M~~Le~l 50 (78)
T PF03444_consen 33 LGRSPATIRNEMADLEEL 50 (78)
T ss_pred HCCChHHHHHHHHHHHHC
Confidence 344456999999999984
No 99
>PRK13276 cell wall biosynthesis protein ScdA; Provisional
Probab=20.72 E-value=2.2e+02 Score=23.79 Aligned_cols=45 Identities=9% Similarity=0.047 Sum_probs=34.8
Q ss_pred HHHHHHHHHHHHhcCCCCcc---------hHHHHHHHHHhHHHHHHHHHHhhhh
Q 032021 85 LLHLMENLADAIENGTRDQQ---------SDALVNELNNHFEKCQQLLSSISES 129 (148)
Q Consensus 85 L~~lve~Ladaie~GtRDQ~---------sDaLv~EL~s~FekcQQLLnSis~s 129 (148)
-+|.+..|+.-|++=-.|.+ ..+|..||..|+.|=+++|=..-..
T Consensus 93 ~lp~l~~l~~kV~~VHg~~~p~l~~l~~lf~~l~~eL~~H~~KEE~ilFP~i~~ 146 (224)
T PRK13276 93 EFKNLTPYVTKLSKVHGPNHPYLVELKETYDTFKNGMLEHMQKEDDVDFPKLIK 146 (224)
T ss_pred HHHHHHHHHHHHHHHhCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHH
Confidence 46777777777777666766 7888899999999999998775433
No 100
>TIGR02550 flagell_flgL flagellar hook-associated protein 3. This protein family consists of flagellar hook-associated proteins designated FlgL (or HAP3) encoded in bacterial flagellar operons. A N-terminal region of about 150 residues and a C-terminal region of about 85 residues are conserved. Members show considerable length heterogeneity between these two well-conserved terminal regions; members of the family vary between 287 to over 500 residues in length. This model distinguishes FlgL from the flagellin gene product FliC.
Probab=20.70 E-value=1.1e+02 Score=24.50 Aligned_cols=40 Identities=18% Similarity=0.217 Sum_probs=29.1
Q ss_pred HHHHHHHHhHHHHHHHHHHhhhhcccccceehhhhhhhhh
Q 032021 107 ALVNELNNHFEKCQQLLSSISESLDTKAMTVEGQRRKLEE 146 (148)
Q Consensus 107 aLv~EL~s~FekcQQLLnSis~sl~tk~~TVegQk~kLEE 146 (148)
+.+.+....++++..=|...-+.|+++...||..+..++.
T Consensus 217 ~~~~~al~~l~~a~~~l~~~~a~lG~~~~rle~~~~~~~~ 256 (306)
T TIGR02550 217 AALSASLNELDKALDNVLSARAEVGARLNRLENLENRLSE 256 (306)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHhhhh
Confidence 5566666677777777777788888888888777766654
No 101
>PF14357 DUF4404: Domain of unknown function (DUF4404)
Probab=20.50 E-value=3.2e+02 Score=19.32 Aligned_cols=48 Identities=21% Similarity=0.392 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHHhc-CCCCcchHHHHHH---HHHhHHH----HHHHHHHhhhhccc
Q 032021 85 LLHLMENLADAIEN-GTRDQQSDALVNE---LNNHFEK----CQQLLSSISESLDT 132 (148)
Q Consensus 85 L~~lve~Ladaie~-GtRDQ~sDaLv~E---L~s~Fek----cQQLLnSis~sl~t 132 (148)
|--|++.|..++.. +..+-....|+.. ...+||. .-.+|+.|..+|++
T Consensus 27 L~~l~~dIe~~L~~~~~~~~~~~~l~d~l~~av~~FE~~HP~l~~~lr~i~~sLa~ 82 (85)
T PF14357_consen 27 LSSLDDDIEAQLAEEDEAEAEDESLVDRLNEAVERFEASHPKLAGILRNIMDSLAN 82 (85)
T ss_pred HHHHHHHHHHHHhcCCcccccchhHHHHHHHHHHHHHHhCCcHHHHHHHHHHHHHH
Confidence 45566666666666 2333444556544 4778984 45666666666553
No 102
>COG1937 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.25 E-value=1.2e+02 Score=22.23 Aligned_cols=27 Identities=33% Similarity=0.612 Sum_probs=19.4
Q ss_pred HHHHHHHHHHhcCCCCcchHHHHHHHH
Q 032021 87 HLMENLADAIENGTRDQQSDALVNELN 113 (148)
Q Consensus 87 ~lve~Ladaie~GtRDQ~sDaLv~EL~ 113 (148)
||-+-++++++.|..++..|+|+..+.
T Consensus 60 hl~~cv~~a~~~~~~~~~i~el~~~~~ 86 (89)
T COG1937 60 HLKECVKRAVEDGDEEESIDELIKALR 86 (89)
T ss_pred HHHHHHHHHhhccchHhHHHHHHHHHH
Confidence 455667788888888777777776653
No 103
>PRK11677 hypothetical protein; Provisional
Probab=20.20 E-value=1.5e+02 Score=23.10 Aligned_cols=6 Identities=50% Similarity=0.816 Sum_probs=3.0
Q ss_pred hhhhhh
Q 032021 78 SLASNF 83 (148)
Q Consensus 78 sLAShF 83 (148)
.++.||
T Consensus 51 eV~~HF 56 (134)
T PRK11677 51 ELVSHF 56 (134)
T ss_pred HHHHHH
Confidence 445554
Done!