Query 028075
Match_columns 214
No_of_seqs 18 out of 20
Neff 2.2
Searched_HMMs 46136
Date Fri Mar 29 05:51:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028075.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028075hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF10158 LOH1CR12: Tumour supp 97.4 0.0019 4.1E-08 52.1 9.5 106 72-183 22-127 (131)
2 KOG4515 Uncharacterized conser 83.6 15 0.00033 32.9 10.1 165 10-188 27-196 (217)
3 PF14523 Syntaxin_2: Syntaxin- 76.9 4.9 0.00011 29.1 4.2 49 117-169 3-51 (102)
4 PF10805 DUF2730: Protein of u 75.7 2.5 5.5E-05 32.5 2.5 39 125-163 50-91 (106)
5 cd04766 HTH_HspR Helix-Turn-He 72.2 5.3 0.00012 29.0 3.4 47 108-154 42-89 (91)
6 cd00176 SPEC Spectrin repeats, 70.9 41 0.0009 25.1 8.8 74 75-168 137-210 (213)
7 PF09789 DUF2353: Uncharacteri 69.4 30 0.00065 32.2 8.3 99 80-182 18-124 (319)
8 PF10168 Nup88: Nuclear pore c 68.0 77 0.0017 32.1 11.4 90 69-168 527-617 (717)
9 cd00176 SPEC Spectrin repeats, 64.8 56 0.0012 24.4 8.1 41 75-123 31-71 (213)
10 PF05130 FlgN: FlgN protein; 63.3 55 0.0012 23.7 9.4 72 90-166 35-106 (143)
11 PF04156 IncA: IncA protein; 62.3 80 0.0017 25.3 9.1 50 119-168 132-182 (191)
12 PF10226 DUF2216: Uncharacteri 62.0 6.3 0.00014 34.8 2.4 52 119-176 95-150 (195)
13 PF05478 Prominin: Prominin; 60.0 35 0.00076 34.2 7.4 94 76-169 193-301 (806)
14 PF11780 DUF3318: Protein of u 59.4 4 8.6E-05 33.7 0.7 33 82-124 114-146 (146)
15 cd08637 DNA_pol_A_pol_I_C Poly 57.9 63 0.0014 29.6 8.1 86 112-202 37-132 (377)
16 PRK09646 RNA polymerase sigma 57.2 38 0.00083 26.8 5.9 66 47-122 7-72 (194)
17 PF10241 KxDL: Uncharacterized 57.2 80 0.0017 23.6 9.7 82 71-173 5-86 (88)
18 PF13935 Ead_Ea22: Ead/Ea22-li 55.3 74 0.0016 25.4 7.2 10 75-84 65-74 (139)
19 PF12443 AKNA: AT-hook-contain 54.8 10 0.00022 30.6 2.2 46 131-176 39-84 (106)
20 PF02403 Seryl_tRNA_N: Seryl-t 54.6 57 0.0012 24.1 6.1 20 74-93 23-42 (108)
21 PRK05755 DNA polymerase I; Pro 53.8 99 0.0021 31.3 9.4 104 95-202 510-632 (880)
22 cd04786 HTH_MerR-like_sg7 Heli 53.3 25 0.00055 27.8 4.3 33 129-161 80-112 (131)
23 KOG4460 Nuclear pore complex, 51.4 47 0.001 34.2 6.6 68 95-162 612-687 (741)
24 COG0177 Nth Predicted EndoIII- 50.2 15 0.00033 32.1 2.8 85 56-140 28-118 (211)
25 cd07677 F-BAR_FCHSD2 The F-BAR 49.8 96 0.0021 28.2 7.8 86 75-168 58-148 (260)
26 PRK13752 putative transcriptio 49.8 31 0.00068 27.8 4.3 29 133-161 90-118 (144)
27 PHA00781 hypothetical protein 48.9 16 0.00034 27.0 2.3 21 147-167 17-40 (59)
28 PF13514 AAA_27: AAA domain 48.8 2.4E+02 0.0052 29.2 11.3 106 72-177 721-848 (1111)
29 PF01895 PhoU: PhoU domain; I 48.2 79 0.0017 20.9 6.7 45 78-122 11-55 (88)
30 smart00150 SPEC Spectrin repea 47.4 83 0.0018 20.9 9.3 69 74-170 28-96 (101)
31 cd09236 V_AnPalA_UmRIM20_like 47.0 1.4E+02 0.003 27.0 8.4 48 76-129 1-48 (353)
32 cd04776 HTH_GnyR Helix-Turn-He 45.8 49 0.0011 25.6 4.7 15 116-130 48-62 (118)
33 PRK09514 zntR zinc-responsive 44.5 28 0.00061 27.6 3.3 18 114-131 49-66 (140)
34 PF14931 IFT20: Intraflagellar 44.3 1.6E+02 0.0034 23.8 7.5 79 91-170 30-112 (120)
35 cd01107 HTH_BmrR Helix-Turn-He 44.2 83 0.0018 23.6 5.6 27 109-135 44-70 (108)
36 PRK00286 xseA exodeoxyribonucl 43.9 2.6E+02 0.0056 25.6 10.0 155 17-174 193-395 (438)
37 PLN02678 seryl-tRNA synthetase 42.9 1.3E+02 0.0029 28.8 8.0 81 75-167 28-108 (448)
38 PF13887 MRF_C1: Myelin gene r 42.4 18 0.00039 24.6 1.6 21 93-113 15-35 (36)
39 PF05384 DegS: Sensor protein 42.1 22 0.00048 29.9 2.5 30 137-166 27-56 (159)
40 PRK10265 chaperone-modulator p 41.4 28 0.00061 26.5 2.7 39 118-156 59-97 (101)
41 PF10168 Nup88: Nuclear pore c 41.2 1.1E+02 0.0024 31.0 7.5 27 97-123 591-617 (717)
42 PF05615 THOC7: Tho complex su 40.0 1.8E+02 0.0039 22.7 8.4 32 140-171 91-128 (139)
43 cd04773 HTH_TioE_rpt2 Second H 39.3 1.6E+02 0.0034 22.3 6.5 30 108-137 42-71 (108)
44 PF15035 Rootletin: Ciliary ro 39.3 1.9E+02 0.0042 24.5 7.7 77 83-165 4-81 (182)
45 PTZ00332 paraflagellar rod pro 38.9 1E+02 0.0023 31.2 6.8 62 79-162 323-384 (589)
46 PF00435 Spectrin: Spectrin re 38.3 1.2E+02 0.0026 20.1 9.9 69 73-169 30-98 (105)
47 PF04210 MtrG: Tetrahydrometha 38.2 51 0.0011 25.2 3.6 28 95-125 15-42 (70)
48 PF08928 DUF1910: Domain of un 38.2 54 0.0012 24.6 3.8 73 86-162 10-82 (117)
49 PF11594 Med28: Mediator compl 37.7 54 0.0012 26.5 3.9 46 113-158 52-98 (106)
50 TIGR02047 CadR-PbrR Cd(II)/Pb( 37.7 49 0.0011 25.7 3.6 18 115-132 49-66 (127)
51 PRK15330 cell invasion protein 37.6 1.4E+02 0.003 28.6 7.1 74 85-161 130-206 (343)
52 cd01279 HTH_HspR-like Helix-Tu 37.1 47 0.001 24.8 3.3 47 109-155 43-90 (98)
53 PF10473 CENP-F_leu_zip: Leuci 36.7 1.4E+02 0.0031 24.7 6.3 53 84-137 87-139 (140)
54 cd04787 HTH_HMRTR_unk Helix-Tu 34.5 65 0.0014 25.1 3.8 20 114-133 48-67 (133)
55 PF08400 phage_tail_N: Prophag 34.1 1.2E+02 0.0025 25.2 5.4 40 53-101 82-121 (134)
56 cd00592 HTH_MerR-like Helix-Tu 34.1 1.6E+02 0.0034 21.2 5.6 34 108-141 41-74 (100)
57 COG4064 MtrG Tetrahydromethano 33.6 61 0.0013 25.1 3.5 28 95-125 18-45 (75)
58 smart00150 SPEC Spectrin repea 33.5 1.2E+02 0.0027 20.1 4.6 37 130-166 31-67 (101)
59 TIGR02043 ZntR Zn(II)-responsi 32.9 79 0.0017 24.7 4.1 16 116-131 51-66 (131)
60 PF08114 PMP1_2: ATPase proteo 32.9 30 0.00066 24.3 1.6 10 85-94 29-38 (43)
61 TIGR00414 serS seryl-tRNA synt 32.8 2.7E+02 0.0059 26.0 8.2 77 78-167 28-106 (418)
62 PRK11924 RNA polymerase sigma 32.3 2E+02 0.0044 21.4 6.1 47 73-122 9-55 (179)
63 cd01282 HTH_MerR-like_sg3 Heli 31.8 1.6E+02 0.0035 22.3 5.5 27 109-135 42-68 (112)
64 PF13591 MerR_2: MerR HTH fami 31.4 41 0.00088 24.7 2.1 37 115-151 48-84 (84)
65 TIGR02044 CueR Cu(I)-responsiv 31.3 92 0.002 24.0 4.2 17 115-131 49-65 (127)
66 PF10147 CR6_interact: Growth 30.8 2.4E+02 0.0052 25.1 7.2 53 76-128 98-175 (217)
67 PF04156 IncA: IncA protein; 30.6 2.8E+02 0.0061 22.2 9.7 38 130-167 151-191 (191)
68 PF11348 DUF3150: Protein of u 30.5 1.3E+02 0.0029 26.6 5.5 90 77-167 85-187 (257)
69 cd01111 HTH_MerD Helix-Turn-He 30.0 2.5E+02 0.0054 21.4 6.5 58 110-167 44-103 (107)
70 PF09537 DUF2383: Domain of un 29.9 1.7E+02 0.0037 21.4 5.3 50 110-168 2-51 (111)
71 cd04784 HTH_CadR-PbrR Helix-Tu 29.9 84 0.0018 24.1 3.7 17 115-131 49-65 (127)
72 KOG4302 Microtubule-associated 29.9 4.6E+02 0.0099 27.1 9.7 92 78-169 40-142 (660)
73 PF01086 Clathrin_lg_ch: Clath 29.5 69 0.0015 27.6 3.5 53 84-136 112-166 (225)
74 PRK10755 sensor protein BasS/P 29.4 3.4E+02 0.0075 22.8 8.2 17 120-136 146-162 (356)
75 PRK01026 tetrahydromethanopter 29.2 81 0.0018 24.4 3.5 29 95-126 18-46 (77)
76 cd08915 V_Alix_like Protein-in 28.9 4.1E+02 0.0089 23.5 9.6 46 76-127 1-46 (342)
77 PF11472 DUF3206: Protein of u 28.7 44 0.00095 27.9 2.1 29 145-173 76-104 (128)
78 KOG4052 Uncharacterized conser 28.7 66 0.0014 28.5 3.3 83 91-176 18-109 (190)
79 PF04012 PspA_IM30: PspA/IM30 28.4 3.4E+02 0.0073 22.4 7.8 95 73-167 21-142 (221)
80 cd01108 HTH_CueR Helix-Turn-He 27.9 89 0.0019 24.1 3.6 18 115-132 49-66 (127)
81 PF03938 OmpH: Outer membrane 27.1 2.4E+02 0.0051 21.8 5.8 47 71-117 19-65 (158)
82 PRK11115 transcriptional regul 27.0 3E+02 0.0066 22.4 6.7 42 79-120 36-77 (236)
83 TIGR01149 mtrG N5-methyltetrah 26.8 97 0.0021 23.7 3.5 29 95-126 15-43 (70)
84 PF09447 Cnl2_NKP2: Cnl2/NKP2 26.0 1.2E+02 0.0025 22.6 3.7 25 83-107 40-64 (67)
85 PF09731 Mitofilin: Mitochondr 25.9 5.2E+02 0.011 24.5 8.9 87 88-174 311-428 (582)
86 PF06401 Alpha-2-MRAP_C: Alpha 25.7 1E+02 0.0022 27.5 4.0 32 142-174 74-105 (214)
87 PF05529 Bap31: B-cell recepto 25.6 3.7E+02 0.008 21.9 9.3 35 135-169 152-186 (192)
88 PRK10869 recombination and rep 25.5 6.3E+02 0.014 24.5 9.7 95 75-169 152-286 (553)
89 TIGR02051 MerR Hg(II)-responsi 25.4 2.8E+02 0.0062 21.3 6.0 22 114-135 47-68 (124)
90 cd04779 HTH_MerR-like_sg4 Heli 25.2 3.4E+02 0.0073 21.8 6.5 26 112-137 45-70 (134)
91 PRK05431 seryl-tRNA synthetase 24.9 3.1E+02 0.0066 25.8 7.1 83 79-179 27-111 (425)
92 PRK14096 pgi glucose-6-phospha 24.9 1.8E+02 0.0039 28.7 5.9 44 65-108 409-472 (528)
93 cd04765 HTH_MlrA-like_sg2 Heli 24.4 78 0.0017 23.8 2.7 21 115-135 49-70 (99)
94 PRK03692 putative UDP-N-acetyl 24.4 77 0.0017 27.8 3.0 51 104-175 111-161 (243)
95 PRK09413 IS2 repressor TnpA; R 23.8 3.3E+02 0.0072 20.8 6.0 28 141-168 75-102 (121)
96 PF10157 DUF2365: Uncharacteri 23.5 4.4E+02 0.0096 22.0 10.6 80 71-154 46-143 (149)
97 cd04785 HTH_CadR-PbrR-like Hel 23.0 1.6E+02 0.0035 22.7 4.2 19 114-132 48-66 (126)
98 TIGR00593 pola DNA polymerase 22.9 6.1E+02 0.013 26.5 9.4 85 113-202 545-639 (887)
99 PF11172 DUF2959: Protein of u 22.8 3.9E+02 0.0084 23.9 6.9 49 121-169 127-188 (201)
100 TIGR00153 conserved hypothetic 22.7 4.4E+02 0.0096 21.8 9.4 46 78-126 29-74 (216)
101 cd07603 BAR_ACAPs The Bin/Amph 22.1 73 0.0016 27.1 2.3 28 138-165 3-30 (200)
102 TIGR02105 III_needle type III 21.9 2.1E+02 0.0046 21.3 4.5 23 75-97 33-61 (72)
103 KOG2391 Vacuolar sorting prote 21.9 7.4E+02 0.016 24.1 9.9 102 43-169 171-278 (365)
104 cd07637 BAR_ACAP3 The Bin/Amph 21.7 78 0.0017 27.1 2.4 29 138-166 3-31 (200)
105 PF02601 Exonuc_VII_L: Exonucl 21.6 5.4E+02 0.012 22.4 9.5 46 16-64 75-129 (319)
106 cd07665 BAR_SNX1 The Bin/Amphi 21.5 5.7E+02 0.012 22.6 7.8 33 138-170 160-192 (234)
107 PRK10227 DNA-binding transcrip 21.3 1.7E+02 0.0038 23.2 4.2 16 116-131 50-65 (135)
108 cd01109 HTH_YyaN Helix-Turn-He 21.2 3.5E+02 0.0076 20.2 5.6 20 115-134 49-68 (113)
109 cd07653 F-BAR_CIP4-like The F- 21.1 4.9E+02 0.011 21.7 7.7 79 84-168 62-143 (251)
110 TIGR00608 radc DNA repair prot 21.1 1.9E+02 0.004 25.1 4.6 56 110-172 33-91 (218)
111 PRK06285 chorismate mutase; Pr 20.9 3.3E+02 0.0072 20.3 5.4 34 98-131 6-40 (96)
112 PF08900 DUF1845: Domain of un 20.8 2.3E+02 0.005 24.4 5.1 32 137-168 102-136 (217)
113 PHA02557 22 prohead core prote 20.5 5.2E+02 0.011 24.1 7.5 74 86-169 97-173 (271)
114 PF08614 ATG16: Autophagy prot 20.4 75 0.0016 26.2 2.0 31 137-167 151-181 (194)
115 TIGR02553 SipD_IpaD_SspD type 20.2 4.6E+02 0.01 24.8 7.2 73 86-161 103-178 (308)
116 PF04508 Pox_A_type_inc: Viral 20.1 69 0.0015 19.8 1.3 21 138-158 2-22 (23)
No 1
>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=97.37 E-value=0.0019 Score=52.13 Aligned_cols=106 Identities=17% Similarity=0.321 Sum_probs=92.9
Q ss_pred CCCChHHHHHHHHHhHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHhccchhhhhhhhhhhccccchhhhHhhhhh
Q 028075 72 GTVNPKVLLELFSMYRDWQEEKAKQISKRQEEIENKIEVADALATKLLQRFGYSVSAMKTSSQHLSEVHALQVEIGELKG 151 (214)
Q Consensus 72 ~~~np~v~~ELfS~YreWQe~~a~~isk~QeeienkIE~adalA~KLlQR~n~S~S~Mktts~hL~~V~~LqvevgElKg 151 (214)
.-+|+.-++-|-+-|++--...|+.|...|..|.+||.-+|..-.++++-+.---..+..-+.+|+.|+.|...+....-
T Consensus 22 eklds~~~l~Lc~R~Q~HL~~cA~~Va~~Q~~L~~riKevd~~~~~l~~~~~erqk~~~k~ae~L~kv~els~~L~~~~~ 101 (131)
T PF10158_consen 22 EKLDSRPVLRLCSRYQEHLNQCAEAVAFDQNALAKRIKEVDQEIAKLLQQMVERQKRFAKFAEQLEKVNELSQQLSRCQS 101 (131)
T ss_pred HccChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46999999999999999999999999999999999999999999999999998888899999999999999999999999
Q ss_pred HHHHHHhhhHHHHHHHHhcCCcccccccCccc
Q 028075 152 RLTEVISNCDALCKRIAAEGPDSLKASIKPLA 183 (214)
Q Consensus 152 rLteVisncdaLCKRI~~eGPesLr~sv~pfs 183 (214)
-|++++..++ +++.-=|+.-| .-||.
T Consensus 102 lL~~~v~~ie----~LN~~LP~~~R--Lep~~ 127 (131)
T PF10158_consen 102 LLNQTVPSIE----TLNEILPEEER--LEPFV 127 (131)
T ss_pred HHHHHHHHHH----HHHhhCChhhc--CCCCC
Confidence 9999887665 45555566544 44553
No 2
>KOG4515 consensus Uncharacterized conserved protein [Function unknown]
Probab=83.57 E-value=15 Score=32.89 Aligned_cols=165 Identities=11% Similarity=0.143 Sum_probs=103.5
Q ss_pred CCCCCCCCcceeeeecCc-----cCcchHHHhhhcccccCccccCCCCCCCcccceeeccCCCCCCCCCCChHHHHHHHH
Q 028075 10 SPQSQRPIDDITTVSYKS-----ESVDPILENIKSLKITTPILTSPPPTESSLTDILVRRSSTSSASGTVNPKVLLELFS 84 (214)
Q Consensus 10 ~~~~q~~~DeITTVse~~-----e~~DP~LErLkSLkIa~PiL~spp~~EssLtDILvrk~ssSs~S~~~np~v~~ELfS 84 (214)
.+++..--|.|-||..|. ++.||.+.||+.+----|+|+..-.+-.+-+|-- .---+|-.-++.|--
T Consensus 27 ~~~sta~s~~IV~V~~G~i~~~~~~~D~d~~rl~eIP~FlPvl~~~i~~qTn~~~a~--------~lekl~Sq~~~~lct 98 (217)
T KOG4515|consen 27 TRASTARSKGIVTVKDGNIPQEKLEDDEDYKRLTEIPRFLPVLPAVIGKQTNQGAAY--------TLEKLSSQPFFRLCT 98 (217)
T ss_pred ChhhhcccCCeEEecCCCcccccccccHHHHHHhccchhhhhhHHHhcCCCCcchHH--------HHHHhcchHHHHHHH
Confidence 445555678999999887 6789999999998777777764331100000000 001345556777888
Q ss_pred HhHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHhccchhhhhhhhhhhccccchhhhHhhhhhHHHHHHhhhHHHH
Q 028075 85 MYRDWQEEKAKQISKRQEEIENKIEVADALATKLLQRFGYSVSAMKTSSQHLSEVHALQVEIGELKGRLTEVISNCDALC 164 (214)
Q Consensus 85 ~YreWQe~~a~~isk~QeeienkIE~adalA~KLlQR~n~S~S~Mktts~hL~~V~~LqvevgElKgrLteVisncdaLC 164 (214)
-|++---..|+-+.--|..|-.++.++|+=-+.|+--|-----.--.-+..|+.|..|--.+ .|....|+.--++-
T Consensus 99 R~Q~Hl~~cA~aVA~dQn~lv~r~K~v~~s~~tLf~~~~~~qk~ya~yaeq~~k~n~ls~~l----~riq~~l~~~Vp~l 174 (217)
T KOG4515|consen 99 RLQEHLAVCAKAVAADQNKLVARCKSVEASMITLFEETRAHQKQYAGYAEQLSKLNQLSDDL----CRIQIILEDIVPML 174 (217)
T ss_pred HHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHhHHHH
Confidence 88888889999999999999999999999999888655321111111233445554444333 34555555555666
Q ss_pred HHHHhcCCcccccccCccccccCC
Q 028075 165 KRIAAEGPDSLKASIKPLAVTTTR 188 (214)
Q Consensus 165 KRI~~eGPesLr~sv~pfs~a~~~ 188 (214)
.+|+.-=|+-= ..-||..-+.+
T Consensus 175 e~lN~~L~~~e--RLePf~~~~d~ 196 (217)
T KOG4515|consen 175 ETLNEILTPDE--RLEPFNLGSDL 196 (217)
T ss_pred HHHHhcCCccc--ccCCcccCccc
Confidence 66665444432 46788766553
No 3
>PF14523 Syntaxin_2: Syntaxin-like protein; PDB: 2DNX_A.
Probab=76.93 E-value=4.9 Score=29.07 Aligned_cols=49 Identities=20% Similarity=0.320 Sum_probs=37.5
Q ss_pred HHHHHhccchhhhhhhhhhhccccchhhhHhhhhhHHHHHHhhhHHHHHHHHh
Q 028075 117 KLLQRFGYSVSAMKTSSQHLSEVHALQVEIGELKGRLTEVISNCDALCKRIAA 169 (214)
Q Consensus 117 KLlQR~n~S~S~Mktts~hL~~V~~LqvevgElKgrLteVisncdaLCKRI~~ 169 (214)
..|+++|-.++.++-...+|..- -+-.++..++..++..|..|||.|..
T Consensus 3 ~~l~~in~~v~~l~k~~~~lGt~----~Ds~~lR~~i~~~~~~~~~l~k~~~~ 51 (102)
T PF14523_consen 3 SNLFKINQNVSQLEKLVNQLGTP----RDSQELREKIHQLIQKTNQLIKEISE 51 (102)
T ss_dssp HHHHHHHHHHHHHHHHHHHH-SS----S--HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHHHhCCc----cccHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46788888888888777777633 56678889999999999999999876
No 4
>PF10805 DUF2730: Protein of unknown function (DUF2730); InterPro: IPR020269 This entry represents a family of various hypothetical proteins. The proteins, which include HI1498 and Gp25, from phage Mu, are currently uncharacterised.
Probab=75.66 E-value=2.5 Score=32.54 Aligned_cols=39 Identities=36% Similarity=0.652 Sum_probs=31.5
Q ss_pred chhhhhhhhhhh---ccccchhhhHhhhhhHHHHHHhhhHHH
Q 028075 125 SVSAMKTSSQHL---SEVHALQVEIGELKGRLTEVISNCDAL 163 (214)
Q Consensus 125 S~S~Mktts~hL---~~V~~LqvevgElKgrLteVisncdaL 163 (214)
.++.+.+.-.|| ++||.|+++|.||+|++.++=..-+++
T Consensus 50 Rl~~lE~~l~~LPt~~dv~~L~l~l~el~G~~~~l~~~l~~v 91 (106)
T PF10805_consen 50 RLQALETKLEHLPTRDDVHDLQLELAELRGELKELSARLQGV 91 (106)
T ss_pred HHHHHHHHHHhCCCHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Confidence 345666777788 789999999999999998887766665
No 5
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=72.19 E-value=5.3 Score=29.03 Aligned_cols=47 Identities=21% Similarity=0.349 Sum_probs=39.3
Q ss_pred HHHHHHHHHHHHHH-hccchhhhhhhhhhhccccchhhhHhhhhhHHH
Q 028075 108 IEVADALATKLLQR-FGYSVSAMKTSSQHLSEVHALQVEIGELKGRLT 154 (214)
Q Consensus 108 IE~adalA~KLlQR-~n~S~S~Mktts~hL~~V~~LqvevgElKgrLt 154 (214)
.++.-.-.++-|++ +|++...++.--..+.+.+.||-++.+|+..|.
T Consensus 42 ~dv~~l~~i~~L~~d~g~~l~~i~~~l~l~~~~~~l~~~l~~l~~~~~ 89 (91)
T cd04766 42 RDIERLRRIQRLTQELGVNLAGVKRILELEEELAELRAELDELRARLR 89 (91)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 35555666777888 999999999999999999999999999987763
No 6
>cd00176 SPEC Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here
Probab=70.85 E-value=41 Score=25.09 Aligned_cols=74 Identities=19% Similarity=0.287 Sum_probs=49.9
Q ss_pred ChHHHHHHHHHhHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHhccchhhhhhhhhhhccccchhhhHhhhhhHHH
Q 028075 75 NPKVLLELFSMYRDWQEEKAKQISKRQEEIENKIEVADALATKLLQRFGYSVSAMKTSSQHLSEVHALQVEIGELKGRLT 154 (214)
Q Consensus 75 np~v~~ELfS~YreWQe~~a~~isk~QeeienkIE~adalA~KLlQR~n~S~S~Mktts~hL~~V~~LqvevgElKgrLt 154 (214)
++..+-+++.-+.+++++.+ .....|+.+...+-.|+...++... ..++..+.+++.+..
T Consensus 137 ~~~~~~~~l~~~~~~~~~~~--------~~~~~~~~~~~~~~~l~~~~~~~~~------------~~~~~~l~~l~~~~~ 196 (213)
T cd00176 137 DLESVEELLKKHKELEEELE--------AHEPRLKSLNELAEELLEEGHPDAD------------EEIEEKLEELNERWE 196 (213)
T ss_pred CHHHHHHHHHHHHHHHHHHH--------hchHHHHHHHHHHHHHHHcCCCCcH------------HHHHHHHHHHHHHHH
Confidence 88889899988888888766 3466777778888888877665432 445555555565555
Q ss_pred HHHhhhHHHHHHHH
Q 028075 155 EVISNCDALCKRIA 168 (214)
Q Consensus 155 eVisncdaLCKRI~ 168 (214)
.|..-++...+++.
T Consensus 197 ~l~~~~~~~~~~L~ 210 (213)
T cd00176 197 ELLELAEERQKKLE 210 (213)
T ss_pred HHHHHHHHHHHHHH
Confidence 55555555555544
No 7
>PF09789 DUF2353: Uncharacterized coiled-coil protein (DUF2353); InterPro: IPR019179 Members of this family have been annotated as being coiled-coil domain-containing protein 149, however they currently have no known function.
Probab=69.38 E-value=30 Score=32.21 Aligned_cols=99 Identities=18% Similarity=0.198 Sum_probs=66.2
Q ss_pred HHHHHHhHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHhccchhhhhhhh--------hhhccccchhhhHhhhhh
Q 028075 80 LELFSMYRDWQEEKAKQISKRQEEIENKIEVADALATKLLQRFGYSVSAMKTSS--------QHLSEVHALQVEIGELKG 151 (214)
Q Consensus 80 ~ELfS~YreWQe~~a~~isk~QeeienkIE~adalA~KLlQR~n~S~S~Mktts--------~hL~~V~~LqvevgElKg 151 (214)
+|-+..=||=-+.+|.++-++...+..++.-.+.. ..+||.+-..+.+.. .-=.+...|+.||.+|++
T Consensus 18 Le~cq~ErDqyKlMAEqLqer~q~LKkk~~el~~~----~~~~~d~~~~~~~~~~~La~lL~~sre~Nk~L~~Ev~~Lrq 93 (319)
T PF09789_consen 18 LEKCQSERDQYKLMAEQLQERYQALKKKYRELIQE----AAGFGDPSIPPEKENKNLAQLLSESREQNKKLKEEVEELRQ 93 (319)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh----hcccCCccCCcccchhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34455556666778999998888888888765533 235553322222222 222456789999999999
Q ss_pred HHHHHHhhhHHHHHHHHhcCCcccccccCcc
Q 028075 152 RLTEVISNCDALCKRIAAEGPDSLKASIKPL 182 (214)
Q Consensus 152 rLteVisncdaLCKRI~~eGPesLr~sv~pf 182 (214)
+|.|+-+.|..|=+.++..-...-..-.++|
T Consensus 94 kl~E~qGD~KlLR~~la~~r~~~~~~~~~~~ 124 (319)
T PF09789_consen 94 KLNEAQGDIKLLREKLARQRVGDEGIGARHF 124 (319)
T ss_pred HHHHHhchHHHHHHHHHhhhhhhcccccccc
Confidence 9999999999999988876444333333444
No 8
>PF10168 Nup88: Nuclear pore component; InterPro: IPR019321 Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein have no obvious structural motifs. It is, however, where it binds to Nup98; one of the components of the nuclear pore. The C-terminal end is a predicted coiled-coil domain []. Nup88 is over expressed in tumour cells [].
Probab=67.97 E-value=77 Score=32.07 Aligned_cols=90 Identities=22% Similarity=0.288 Sum_probs=54.0
Q ss_pred CCCCCCChHHHHHHHHHhHH-HHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHhccchhhhhhhhhhhccccchhhhHh
Q 028075 69 SASGTVNPKVLLELFSMYRD-WQEEKAKQISKRQEEIENKIEVADALATKLLQRFGYSVSAMKTSSQHLSEVHALQVEIG 147 (214)
Q Consensus 69 s~S~~~np~v~~ELfS~Yre-WQe~~a~~isk~QeeienkIE~adalA~KLlQR~n~S~S~Mktts~hL~~V~~Lqvevg 147 (214)
..+.+.+|...+|+|+-+-+ ..++-.++.-+-+++|+.++....+..-+-+++++.--.-.+. |+-.-.
T Consensus 527 ~k~~~p~~~E~l~lL~~a~~vlreeYi~~~~~ar~ei~~rv~~Lk~~~e~Ql~~L~~l~e~~~~----------l~~~ae 596 (717)
T PF10168_consen 527 DKSSSPSPQECLELLSQATKVLREEYIEKQDLAREEIQRRVKLLKQQKEQQLKELQELQEERKS----------LRESAE 596 (717)
T ss_pred ccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----------HHHHHH
Confidence 34566789999999987743 3444467777788888888887777666666555433222111 111122
Q ss_pred hhhhHHHHHHhhhHHHHHHHH
Q 028075 148 ELKGRLTEVISNCDALCKRIA 168 (214)
Q Consensus 148 ElKgrLteVisncdaLCKRI~ 168 (214)
.|..|+.++..+.+.|-+|+.
T Consensus 597 ~LaeR~e~a~d~Qe~L~~R~~ 617 (717)
T PF10168_consen 597 KLAERYEEAKDKQEKLMKRVD 617 (717)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 234456666666666666554
No 9
>cd00176 SPEC Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here
Probab=64.75 E-value=56 Score=24.36 Aligned_cols=41 Identities=17% Similarity=0.226 Sum_probs=23.0
Q ss_pred ChHHHHHHHHHhHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHhc
Q 028075 75 NPKVLLELFSMYRDWQEEKAKQISKRQEEIENKIEVADALATKLLQRFG 123 (214)
Q Consensus 75 np~v~~ELfS~YreWQe~~a~~isk~QeeienkIE~adalA~KLlQR~n 123 (214)
|+..+-+++.-|+..+++.. ....+++-+...|-+|+....
T Consensus 31 d~~~~~~~l~~~~~~~~e~~--------~~~~~~~~l~~~~~~L~~~~~ 71 (213)
T cd00176 31 DLESVEALLKKHEALEAELA--------AHEERVEALNELGEQLIEEGH 71 (213)
T ss_pred CHHHHHHHHHHHHHHHHHHH--------HCHHHHHHHHHHHHHHHhcCC
Confidence 66666666666655554432 224455556666666666544
No 10
>PF05130 FlgN: FlgN protein; InterPro: IPR007809 Flagella synthesis protein FlgN is an export chaperone involved in flagellar synthesis []. This entry represents a FlgN-like domain, consisting of a 4 long helices bundle, where the last helix is shorter than the three others.; GO: 0009296 flagellum assembly, 0019861 flagellum; PDB: 2FUP_A 3OPC_A.
Probab=63.28 E-value=55 Score=23.72 Aligned_cols=72 Identities=18% Similarity=0.312 Sum_probs=51.8
Q ss_pred HHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHhccchhhhhhhhhhhccccchhhhHhhhhhHHHHHHhhhHHHHHH
Q 028075 90 QEEKAKQISKRQEEIENKIEVADALATKLLQRFGYSVSAMKTSSQHLSEVHALQVEIGELKGRLTEVISNCDALCKR 166 (214)
Q Consensus 90 Qe~~a~~isk~QeeienkIE~adalA~KLlQR~n~S~S~Mktts~hL~~V~~LqvevgElKgrLteVisncdaLCKR 166 (214)
.-+....+....+++=.+|+..+.--..++++++.. ..-.+|+++-..+-++.++...|.+.+..|..+-++
T Consensus 35 d~~~l~~~~~~k~~l~~~l~~le~~r~~~~~~~~~~-----~~~~~l~~~~~~~~~l~~~~~~l~~~~~~~~~~n~~ 106 (143)
T PF05130_consen 35 DIDELEELVEEKQELLEELRELEKQRQQLLAKLGAE-----PEEATLSELIEEREELQALWRELRELLEELQELNER 106 (143)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-------SCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCc-----cccccHHHHHhccHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334556677778888888888888888999999887 334445555447788888888888888888776543
No 11
>PF04156 IncA: IncA protein; InterPro: IPR007285 Chlamydia trachomatis is an obligate intracellular bacterium that develops within a parasitophorous vacuole termed an inclusion. The inclusion is nonfusogenic with lysosomes but intercepts lipids from a host cell exocytic pathway. Initiation of chlamydial development is concurrent with modification of the inclusion membrane by a set of C. trachomatis-encoded proteins collectively designated Incs. One of these Incs, IncA (Inclusion membrane protein A), is functionally associated with the homotypic fusion of inclusions [].
Probab=62.29 E-value=80 Score=25.28 Aligned_cols=50 Identities=22% Similarity=0.374 Sum_probs=24.8
Q ss_pred HHHhccchhhhhhhhhhhc-cccchhhhHhhhhhHHHHHHhhhHHHHHHHH
Q 028075 119 LQRFGYSVSAMKTSSQHLS-EVHALQVEIGELKGRLTEVISNCDALCKRIA 168 (214)
Q Consensus 119 lQR~n~S~S~Mktts~hL~-~V~~LqvevgElKgrLteVisncdaLCKRI~ 168 (214)
++.|+.+...|.....-|. .+.-++-++.+++..+...-.+.+.|+..++
T Consensus 132 l~~l~~~~~~~~~e~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~ 182 (191)
T PF04156_consen 132 LDSLDESIKELEKEIRELQKELQDSREEVQELRSQLERLQENLQQLEEKIQ 182 (191)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4455555555555555554 3334444444444444444444555544443
No 12
>PF10226 DUF2216: Uncharacterized conserved proteins (DUF2216); InterPro: IPR019359 Proteins in this entry are found in Metazoa and contain a coiled-coil domain. Some annotation suggests it might be PKR, the Hepatitis delta antigen-interacting protein A, but this could not be confirmed.
Probab=62.01 E-value=6.3 Score=34.77 Aligned_cols=52 Identities=37% Similarity=0.566 Sum_probs=41.2
Q ss_pred HHHhc-cchhhhhhhhhhhccccchhhhHhhhhhHHHHHHhhhH---HHHHHHHhcCCcccc
Q 028075 119 LQRFG-YSVSAMKTSSQHLSEVHALQVEIGELKGRLTEVISNCD---ALCKRIAAEGPDSLK 176 (214)
Q Consensus 119 lQR~n-~S~S~Mktts~hL~~V~~LqvevgElKgrLteVisncd---aLCKRI~~eGPesLr 176 (214)
-|||| |.+++|+. +|..-+-.+.||-++..+++.+-. .||=.+..+.|..-+
T Consensus 95 WQrFGryta~vmr~------eV~~Y~~KL~eLE~kq~~L~rEN~eLKElcl~LDeer~~~~~ 150 (195)
T PF10226_consen 95 WQRFGRYTASVMRQ------EVAQYQQKLKELEDKQEELIRENLELKELCLYLDEERPGSGR 150 (195)
T ss_pred HHHhhhHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHhccccCCCC
Confidence 69999 56889984 788888899999999999987654 578888888864433
No 13
>PF05478 Prominin: Prominin; InterPro: IPR008795 The prominins are an emerging family of proteins that, among the multispan membrane proteins, display a novel topology. Mouse and Homo sapiens prominin and (Mus musculus) prominin-like 1 (PROML1) are predicted to contain five membrane spanning domains, with an N-terminal domain exposed to the extracellular space followed by four, alternating small cytoplasmic and large extracellular, loops and a cytoplasmic C-terminal domain []. The exact function of prominin is unknown although in humans defects in PROM1, the gene coding for prominin, cause retinal degeneration [].; GO: 0016021 integral to membrane
Probab=60.01 E-value=35 Score=34.19 Aligned_cols=94 Identities=15% Similarity=0.268 Sum_probs=61.0
Q ss_pred hHHHHHHHHH-hHHHHHHHHHHHHHHHHHHhHHHHH-HHHHHHHHHHHhccchhhhhhhhhhhccccch-----------
Q 028075 76 PKVLLELFSM-YRDWQEEKAKQISKRQEEIENKIEV-ADALATKLLQRFGYSVSAMKTSSQHLSEVHAL----------- 142 (214)
Q Consensus 76 p~v~~ELfS~-YreWQe~~a~~isk~QeeienkIE~-adalA~KLlQR~n~S~S~Mktts~hL~~V~~L----------- 142 (214)
|+.+-.|+.- |++=++.-..++..--.-|+..|.. .++-+...|.+.---..+|+.+..+|.+|+..
T Consensus 193 ~~qi~~l~~~ny~~~~~~v~~~L~~~~~~lg~~i~~~l~~~~~~~L~~i~~l~~~~~~~~~~L~~v~~~~~~L~~~~~qL 272 (806)
T PF05478_consen 193 PQQIDHLLVQNYSELKDHVSSDLDNIGSLLGGDIQDQLGSNVYPALDSILDLAQAMQETKELLQNVNSSLKDLQEYQSQL 272 (806)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhccchhhHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444556666 7766666666666666666666543 34444444554444444788888888777654
Q ss_pred hhhHhhhhhHHHHHHhh-hHH-HHHHHHh
Q 028075 143 QVEIGELKGRLTEVISN-CDA-LCKRIAA 169 (214)
Q Consensus 143 qvevgElKgrLteVisn-cda-LCKRI~~ 169 (214)
+-.+.++|.+|+..+.+ |.. .|..|..
T Consensus 273 ~~~L~~vK~~L~~~l~~~C~~~~C~~i~~ 301 (806)
T PF05478_consen 273 RDGLRGVKRDLNNTLQDLCTNRECNSILS 301 (806)
T ss_pred HHHHHHHHHHHHHHHHhhCCChhhHHHHH
Confidence 44566778888999999 888 8988743
No 14
>PF11780 DUF3318: Protein of unknown function (DUF3318); InterPro: IPR021751 This is a bacterial family of uncharacterised proteins.
Probab=59.44 E-value=4 Score=33.71 Aligned_cols=33 Identities=36% Similarity=0.640 Sum_probs=25.8
Q ss_pred HHHHhHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHhcc
Q 028075 82 LFSMYRDWQEEKAKQISKRQEEIENKIEVADALATKLLQRFGY 124 (214)
Q Consensus 82 LfS~YreWQe~~a~~isk~QeeienkIE~adalA~KLlQR~n~ 124 (214)
-++.||=||..+. .|.++ .||+-|++.-+|+||
T Consensus 114 ~~~~~riwq~~~~-----~~~~~-----~Ad~~A~~~A~~~Gy 146 (146)
T PF11780_consen 114 AWAAYRIWQQNRS-----PQREL-----DADEAAIRPATRRGY 146 (146)
T ss_pred HHHHHHHHHHccC-----ccccc-----CcchhhhhhHHhcCC
Confidence 4679999998876 23333 378899999999998
No 15
>cd08637 DNA_pol_A_pol_I_C Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. Family A polymerase (polymerase I) functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified in six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerase are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I (pol I) ,mitochondrial polymerase delta, and several bacteriphage polymerases including those from odd-numbered phage (T3, T5, and T7). Prokaryotic Pol Is have two functional domains located on the same polypeptide; a 5'-3' polymerase and 5'-3' exonuc
Probab=57.88 E-value=63 Score=29.58 Aligned_cols=86 Identities=27% Similarity=0.340 Sum_probs=53.1
Q ss_pred HHHHHHHHHHhccchh--------hhhhhhhhhccccchhhhHhhhhhHHHHHHhh-hHHHHHHHHh-cCCcccccccCc
Q 028075 112 DALATKLLQRFGYSVS--------AMKTSSQHLSEVHALQVEIGELKGRLTEVISN-CDALCKRIAA-EGPDSLKASIKP 181 (214)
Q Consensus 112 dalA~KLlQR~n~S~S--------~Mktts~hL~~V~~LqvevgElKgrLteVisn-cdaLCKRI~~-eGPesLr~sv~p 181 (214)
+.+|.-|+.++|+... +.+..-.+|.+-|++=--|.|.+. |+..++. ++.+.+-+.. .| .+++.+.+
T Consensus 37 ~qv~~~L~~~lgl~~~~~t~~~~~t~~~~L~~l~~~~p~~~~lle~r~-l~k~~~t~~~~l~~~~~~~dg--rih~~~~~ 113 (377)
T cd08637 37 KQLGEVLFEKLGLPVGKKTKTGYSTDAEVLEKLADEHPIVELILEYRE-LTKLKSTYVDALPKLINPKTG--RIHTSFNQ 113 (377)
T ss_pred HHHHHHHHHhCCCCCCCcCCCCCCchHHHHHhhhhcChHHHHHHHHHH-HHHHHHHHHHHHHHHcCCCCC--ceeeeeee
Confidence 4667777788887653 222233455556765555555554 5555544 6778877765 44 58899988
Q ss_pred cccccCCCcccccCCcccccC
Q 028075 182 LAVTTTRSEVSCSSSSLQKDD 202 (214)
Q Consensus 182 fs~a~~~~~~~~~~~~~~~~~ 202 (214)
+.+++ .+.+++...+|...
T Consensus 114 ~gt~T--GRlS~~~PNlQniP 132 (377)
T cd08637 114 TVTAT--GRLSSSDPNLQNIP 132 (377)
T ss_pred ccccc--cchhcccCccccCC
Confidence 86654 44555555666654
No 16
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=57.23 E-value=38 Score=26.84 Aligned_cols=66 Identities=17% Similarity=0.273 Sum_probs=47.1
Q ss_pred ccCCCCCCCcccceeeccCCCCCCCCCCChHHHHHHHHHhHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHh
Q 028075 47 LTSPPPTESSLTDILVRRSSTSSASGTVNPKVLLELFSMYRDWQEEKAKQISKRQEEIENKIEVADALATKLLQRF 122 (214)
Q Consensus 47 L~spp~~EssLtDILvrk~ssSs~S~~~np~v~~ELfS~YreWQe~~a~~isk~QeeienkIE~adalA~KLlQR~ 122 (214)
+|+||..+.++.+++ +.-.. -|...+-+||.-|+.|-...+..+....++.+ +++-..=+++.++.
T Consensus 7 ~~~~~~~~~~~~~li-~~~~~------g~~~a~~~l~~~y~~~l~~~~~~~~~~~~dAe---DivQe~fi~l~~~~ 72 (194)
T PRK09646 7 MTGPPAESPDLDALL-RRVAR------GDQDAFAELYDRTSSRVYGLVRRVLRDPGYSE---ETTQEVYLEVWRTA 72 (194)
T ss_pred ccCCCCCcccHHHHH-HHHHc------cCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHH---HHHHHHHHHHHHhh
Confidence 478884555555554 33222 27999999999999999999999988777653 56666667776553
No 17
>PF10241 KxDL: Uncharacterized conserved protein; InterPro: IPR019371 This entry represents a conserved region of 80 residues which defines a family of short proteins. There is a characteristic KxDL motif towards the C terminus. The function is unknown.
Probab=57.21 E-value=80 Score=23.63 Aligned_cols=82 Identities=21% Similarity=0.351 Sum_probs=63.8
Q ss_pred CCCCChHHHHHHHHHhHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHhccchhhhhhhhhhhccccchhhhHhhhh
Q 028075 71 SGTVNPKVLLELFSMYRDWQEEKAKQISKRQEEIENKIEVADALATKLLQRFGYSVSAMKTSSQHLSEVHALQVEIGELK 150 (214)
Q Consensus 71 S~~~np~v~~ELfS~YreWQe~~a~~isk~QeeienkIE~adalA~KLlQR~n~S~S~Mktts~hL~~V~~LqvevgElK 150 (214)
+..+||..+-+.+.+ |...-.++.++++++.+-++.+..==.++-.||.--.-+ +.+||
T Consensus 5 ~~~~d~~d~~~~l~~----Q~~~l~~ln~tn~~L~~~n~~s~~rl~~~~~~f~~~~~~-----------------l~~mK 63 (88)
T PF10241_consen 5 TQAVDPEDLDEILAL----QAQTLGRLNKTNEELLNLNDLSQQRLAEARERFARHTKL-----------------LKEMK 63 (88)
T ss_pred HhcCCHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----------------HHHHH
Confidence 356888888777654 888999999999999999998888777777787433222 45688
Q ss_pred hHHHHHHhhhHHHHHHHHhcCCc
Q 028075 151 GRLTEVISNCDALCKRIAAEGPD 173 (214)
Q Consensus 151 grLteVisncdaLCKRI~~eGPe 173 (214)
.-|.-+-.+-.+|=.+++..=|+
T Consensus 64 ~DLd~i~krir~lk~kl~~~yP~ 86 (88)
T PF10241_consen 64 KDLDYIFKRIRSLKAKLAKQYPE 86 (88)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCC
Confidence 88888888888888888777776
No 18
>PF13935 Ead_Ea22: Ead/Ea22-like protein
Probab=55.30 E-value=74 Score=25.43 Aligned_cols=10 Identities=40% Similarity=0.776 Sum_probs=8.7
Q ss_pred ChHHHHHHHH
Q 028075 75 NPKVLLELFS 84 (214)
Q Consensus 75 np~v~~ELfS 84 (214)
||++++.|+.
T Consensus 65 nP~tvLALLD 74 (139)
T PF13935_consen 65 NPATVLALLD 74 (139)
T ss_pred cchHHHHHHH
Confidence 8999999885
No 19
>PF12443 AKNA: AT-hook-containing transcription factor; InterPro: IPR022150 This domain family is found in eukaryotes, and is approximately 110 amino acids in length. This family contains a transcription factor which regulates the expression of the costimulatory molecules on lymphocytes.
Probab=54.81 E-value=10 Score=30.60 Aligned_cols=46 Identities=22% Similarity=0.334 Sum_probs=42.1
Q ss_pred hhhhhhccccchhhhHhhhhhHHHHHHhhhHHHHHHHHhcCCcccc
Q 028075 131 TSSQHLSEVHALQVEIGELKGRLTEVISNCDALCKRIAAEGPDSLK 176 (214)
Q Consensus 131 tts~hL~~V~~LqvevgElKgrLteVisncdaLCKRI~~eGPesLr 176 (214)
.++.-|+-..-+.-||-.||.++.+.--+-|..-|||+..||+.+.
T Consensus 39 ~sp~~f~~~~ege~~~qkL~eqteeLK~kvqe~sk~i~~~~~~~~q 84 (106)
T PF12443_consen 39 GSPGIFDKIREGEQMIQKLGEQTEELKDKVQEFSKRIEQDSPDHLQ 84 (106)
T ss_pred CCccccCcchHHHHHHHHHHHHHHHHHHHHHHHhcCcCCCCccccc
Confidence 6677788888899999999999999999999999999999999665
No 20
>PF02403 Seryl_tRNA_N: Seryl-tRNA synthetase N-terminal domain; InterPro: IPR015866 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 N-terminal domain of Seryl-tRNA synthetase, which consists of two helices in a long alpha-hairpin. Seryl-tRNA synthetase (6.1.1.11 from EC) exists as monomer and belongs to class IIa [].; GO: 0000166 nucleotide binding, 0004828 serine-tRNA ligase activity, 0005524 ATP binding, 0006434 seryl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 3QO8_A 3QO5_A 3QO7_A 3QNE_A 3LSQ_A 3LSS_A 2DQ3_B 1SET_A 1SER_A 1SRY_B ....
Probab=54.62 E-value=57 Score=24.13 Aligned_cols=20 Identities=10% Similarity=0.144 Sum_probs=15.7
Q ss_pred CChHHHHHHHHHhHHHHHHH
Q 028075 74 VNPKVLLELFSMYRDWQEEK 93 (214)
Q Consensus 74 ~np~v~~ELfS~YreWQe~~ 93 (214)
.++..+-++..+|.+|....
T Consensus 23 ~~~~~vd~i~~ld~~~r~l~ 42 (108)
T PF02403_consen 23 GDEEDVDEIIELDQERRELQ 42 (108)
T ss_dssp CCCHHHHHHHHHHHHHHHHH
T ss_pred CCHhhHHHHHHHHHHHHHHH
Confidence 45677889999999997654
No 21
>PRK05755 DNA polymerase I; Provisional
Probab=53.80 E-value=99 Score=31.31 Aligned_cols=104 Identities=25% Similarity=0.344 Sum_probs=57.5
Q ss_pred HHHHHHHHHHhHHHHH----------HHHHHHHHHHHhccchhhh-----hhhhhhhcc---ccchhhhHhhhhhHHHHH
Q 028075 95 KQISKRQEEIENKIEV----------ADALATKLLQRFGYSVSAM-----KTSSQHLSE---VHALQVEIGELKGRLTEV 156 (214)
Q Consensus 95 ~~isk~QeeienkIE~----------adalA~KLlQR~n~S~S~M-----ktts~hL~~---V~~LqvevgElKgrLteV 156 (214)
.++.+++++|+.+|-- ...|+--|+.++|+-..-. .|....|.. .|++=-.|.|.+. ++..
T Consensus 510 ~~~~~~~~~l~~~~~~~~g~~fn~~S~~ql~~~L~~~lgl~~~~kt~~g~st~~~~L~~l~~~~p~~~~lle~r~-~~kl 588 (880)
T PRK05755 510 AELAQRLAELEQEIYELAGEEFNINSPKQLGEILFEKLGLPVGKKTKTGYSTDAEVLEKLADDHPIPDKILEYRQ-LSKL 588 (880)
T ss_pred HHHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhcCCCCCCCCCCCCCCcHHHHHHHHhcChHHHHHHHHHH-HHHH
Confidence 3344455555555532 1345556667888754111 233344443 3666555666655 5566
Q ss_pred Hhh-hHHHHHHHHhcCCcccccccCccccccCCCcccccCCcccccC
Q 028075 157 ISN-CDALCKRIAAEGPDSLKASIKPLAVTTTRSEVSCSSSSLQKDD 202 (214)
Q Consensus 157 isn-cdaLCKRI~~eGPesLr~sv~pfs~a~~~~~~~~~~~~~~~~~ 202 (214)
++. ++.|.+-+...|- .+++.+.++.++| .+.+++...+|...
T Consensus 589 ~sty~~~l~~~~~~~~~-rih~~~~~~~t~T--GRlss~~PnlQniP 632 (880)
T PRK05755 589 KSTYTDALPKLINPDTG-RIHTSFNQTVTAT--GRLSSSDPNLQNIP 632 (880)
T ss_pred HHHHHHHHHHHhccCCC-eecceEeecccce--eeeeccCCCcccCC
Confidence 655 6778777764432 6888877776543 34555555566554
No 22
>cd04786 HTH_MerR-like_sg7 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 7) with a conserved cysteine present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic su
Probab=53.31 E-value=25 Score=27.78 Aligned_cols=33 Identities=15% Similarity=0.343 Sum_probs=19.0
Q ss_pred hhhhhhhhccccchhhhHhhhhhHHHHHHhhhH
Q 028075 129 MKTSSQHLSEVHALQVEIGELKGRLTEVISNCD 161 (214)
Q Consensus 129 Mktts~hL~~V~~LqvevgElKgrLteVisncd 161 (214)
+.....++.++.....|+.+++..|...++.|+
T Consensus 80 ~~~l~~k~~~i~~~i~~L~~~~~~L~~~i~~~~ 112 (131)
T cd04786 80 LAALERKVADIEALEARLAQNKAQLLVLIDLIE 112 (131)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 334445555666666666666666666665553
No 23
>KOG4460 consensus Nuclear pore complex, Nup88/rNup84 component [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=51.39 E-value=47 Score=34.17 Aligned_cols=68 Identities=18% Similarity=0.270 Sum_probs=38.0
Q ss_pred HHHHHHHHHHhHHHHHH-------HHHHHHHHHHhccchhhhhhhhhh-hccccchhhhHhhhhhHHHHHHhhhHH
Q 028075 95 KQISKRQEEIENKIEVA-------DALATKLLQRFGYSVSAMKTSSQH-LSEVHALQVEIGELKGRLTEVISNCDA 162 (214)
Q Consensus 95 ~~isk~QeeienkIE~a-------dalA~KLlQR~n~S~S~Mktts~h-L~~V~~LqvevgElKgrLteVisncda 162 (214)
..|+++|+-++.|||-| ..-..+|+||||-+.-..--+-.- =++|+++-+++.-|-..++.+=...|.
T Consensus 612 ~~i~e~a~~La~R~eea~e~qe~L~~~~~~L~~~~~~~lp~l~~AErdFk~Elq~~~~~~~~L~~~iET~~~~~~K 687 (741)
T KOG4460|consen 612 KSLREMAERLADRYEEAKEKQEDLMNRMKKLLHSFHSELPVLSDAERDFKKELQLIPDQLRHLGNAIETVTMKKDK 687 (741)
T ss_pred HHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhcccccCCcchhHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHH
Confidence 34445555444444433 334567888888765543222222 246677777777777766665544443
No 24
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=50.23 E-value=15 Score=32.14 Aligned_cols=85 Identities=24% Similarity=0.238 Sum_probs=60.6
Q ss_pred cccceeeccCCCCCCCCCCChHHHHHHHHHhHHHHHHHHHHHHHHHHHH------hHHHHHHHHHHHHHHHHhccchhhh
Q 028075 56 SLTDILVRRSSTSSASGTVNPKVLLELFSMYRDWQEEKAKQISKRQEEI------ENKIEVADALATKLLQRFGYSVSAM 129 (214)
Q Consensus 56 sLtDILvrk~ssSs~S~~~np~v~~ELfS~YreWQe~~a~~isk~Qeei------enkIE~adalA~KLlQR~n~S~S~M 129 (214)
.--..||..--|++++-.+=-.++.+||.-|..||.--........+-| .+|-.-.-++|..|+.+||-.+.--
T Consensus 28 ~pf~lLva~iLSaqttD~~vn~at~~Lf~~~~t~e~l~~a~~~~l~~~I~~iGlyr~KAk~I~~~~~~l~e~~~g~vP~~ 107 (211)
T COG0177 28 DPFELLVAVILSAQTTDEVVNKATPALFKRYPTPEDLLNADEEELEELIKSIGLYRNKAKNIKELARILLEKFGGEVPDT 107 (211)
T ss_pred CcHHHHHHHHHhccCchHHHHHHHHHHHHHcCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHcCCCCCch
Confidence 3445677777777777655557899999999999987666665555555 4788888999999999999865543
Q ss_pred hhhhhhhcccc
Q 028075 130 KTSSQHLSEVH 140 (214)
Q Consensus 130 ktts~hL~~V~ 140 (214)
+-.-.-|-+|+
T Consensus 108 ~~eL~~LPGVG 118 (211)
T COG0177 108 REELLSLPGVG 118 (211)
T ss_pred HHHHHhCCCcc
Confidence 33333344443
No 25
>cd07677 F-BAR_FCHSD2 The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of FCH and double SH3 domains 2 (FCHSD2). F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. FCH and double SH3 domains 2 (FCHSD2) contains an N-terminal F-BAR domain and two SH3 domains at the C-terminus. It has been characterized only in silico, and its biological function is still unknown. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They can induce membrane deformation in the form of long tubules.
Probab=49.84 E-value=96 Score=28.23 Aligned_cols=86 Identities=12% Similarity=0.143 Sum_probs=58.9
Q ss_pred ChHHHHHHHHHhHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHhccchhhhhhh-----hhhhccccchhhhHhhh
Q 028075 75 NPKVLLELFSMYRDWQEEKAKQISKRQEEIENKIEVADALATKLLQRFGYSVSAMKTS-----SQHLSEVHALQVEIGEL 149 (214)
Q Consensus 75 np~v~~ELfS~YreWQe~~a~~isk~QeeienkIE~adalA~KLlQR~n~S~S~Mktt-----s~hL~~V~~LqvevgEl 149 (214)
-|.-+-...|+|.-|..--.+-.+--++ ++.++|.+...+-.++- +.++. =.|......||-|+.+.
T Consensus 58 tpgsle~~~S~~~~W~~~L~~Te~~A~~----~~~~ae~l~~~~a~~~k----~~r~~ke~~~Kk~~e~~~~lq~El~~~ 129 (260)
T cd07677 58 KADERADYRSMYTVWKSFLEGTMQVAQS----RINICENYKNLISEPAR----TVRLYKEQQLKRCVDQLTKIQAELQET 129 (260)
T ss_pred CCCcchhhhhHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHhhhHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3333334899999998765544333333 66677776665555443 33333 45777888899999888
Q ss_pred hhHHHHHHhhhHHHHHHHH
Q 028075 150 KGRLTEVISNCDALCKRIA 168 (214)
Q Consensus 150 KgrLteVisncdaLCKRI~ 168 (214)
=.-|..+-..||..|.-.+
T Consensus 130 ~~EL~KaKK~Y~~~cq~~e 148 (260)
T cd07677 130 VKDLAKGKKKYFETEQMAH 148 (260)
T ss_pred HHHHHHHHhhhhHHHHHHH
Confidence 8888889999999997665
No 26
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=49.81 E-value=31 Score=27.77 Aligned_cols=29 Identities=17% Similarity=0.511 Sum_probs=16.2
Q ss_pred hhhhccccchhhhHhhhhhHHHHHHhhhH
Q 028075 133 SQHLSEVHALQVEIGELKGRLTEVISNCD 161 (214)
Q Consensus 133 s~hL~~V~~LqvevgElKgrLteVisncd 161 (214)
.+|+.+|..-.-++..++..|...+..|+
T Consensus 90 ~~k~~~l~~~i~~L~~~~~~L~~~~~~~~ 118 (144)
T PRK13752 90 EHKLKDVREKMADLARMEAVLSELVCACH 118 (144)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 34455555545555556666666666555
No 27
>PHA00781 hypothetical protein
Probab=48.95 E-value=16 Score=27.04 Aligned_cols=21 Identities=48% Similarity=0.751 Sum_probs=17.9
Q ss_pred hhhhhHHHHHHhhhH---HHHHHH
Q 028075 147 GELKGRLTEVISNCD---ALCKRI 167 (214)
Q Consensus 147 gElKgrLteVisncd---aLCKRI 167 (214)
+||-.||.+||+.|| .||.-|
T Consensus 17 ~EL~eRl~svIH~YDGEISl~EAv 40 (59)
T PHA00781 17 QELYERLESVIHDYDGEISLCEAI 40 (59)
T ss_pred HHHHHHHHHHHHHhcccchHHHHH
Confidence 789999999999997 577655
No 28
>PF13514 AAA_27: AAA domain
Probab=48.83 E-value=2.4e+02 Score=29.25 Aligned_cols=106 Identities=17% Similarity=0.338 Sum_probs=66.4
Q ss_pred CCCChHHHHHHHHHhHHHHHHH--HHHHHHHHHHHhHHHHHHHHHHHHHHHHhccchhhh------hhhhhhh-------
Q 028075 72 GTVNPKVLLELFSMYRDWQEEK--AKQISKRQEEIENKIEVADALATKLLQRFGYSVSAM------KTSSQHL------- 136 (214)
Q Consensus 72 ~~~np~v~~ELfS~YreWQe~~--a~~isk~QeeienkIE~adalA~KLlQR~n~S~S~M------ktts~hL------- 136 (214)
..+.|..+.+.|..+++|++.. ..++.++-+.|+..++..+.-+..|+++++..+... ..-..-|
T Consensus 721 ~~~~~~~~~~~l~~l~~l~~~~~~~~~~~~ri~~~~~~~~~f~~~~~~L~~~l~~~~~~~~~~~~~~~L~~~l~~a~~~~ 800 (1111)
T PF13514_consen 721 ADASPEEALEALELLEELREALAEIRELRRRIEQMEADLAAFEEQVAALAERLGPDLPEDPAEEALEALRARLEEAREAQ 800 (1111)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcccccCcHHHHHHHHHHHHHHHHHHH
Confidence 4567889999999999988643 345566667788888888887888888888743221 1111111
Q ss_pred c-------cccchhhhHhhhhhHHHHHHhhhHHHHHHHHhcCCccccc
Q 028075 137 S-------EVHALQVEIGELKGRLTEVISNCDALCKRIAAEGPDSLKA 177 (214)
Q Consensus 137 ~-------~V~~LqvevgElKgrLteVisncdaLCKRI~~eGPesLr~ 177 (214)
. ++..++-++.++...|...-...+.||........+.|+.
T Consensus 801 ~~~~~l~~~~~~~~~~~~~~~~~l~~~~~~l~~L~~~a~~~~~e~l~~ 848 (1111)
T PF13514_consen 801 EERERLQEQLEELEEELEQAEEELEELEAELAELLEQAGVEDEEELRE 848 (1111)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCHHHHHH
Confidence 1 1223444455555555666666677777766666665543
No 29
>PF01895 PhoU: PhoU domain; InterPro: IPR008170 This family contains phosphate regulatory proteins including PhoU. PhoU proteins are known to play a role in the regulation of phosphate uptake. The PhoU domain is composed of a three helix bundle []. The PhoU protein contains two copies of this domain. The domain binds to an iron cluster via its conserved E/DXXXD motif. Deletion of PhoU activates constitutive expression of the phosphate ABC transporter and allows phosphate transport, but causes a growth defect; suggesting that the protein has some secondary function []. ; PDB: 2I0M_A 1T72_B 1T8B_A 1SUM_B 1VCT_A 2BKN_A 2BKP_A 2BKO_A.
Probab=48.21 E-value=79 Score=20.92 Aligned_cols=45 Identities=20% Similarity=0.268 Sum_probs=32.4
Q ss_pred HHHHHHHHhHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHh
Q 028075 78 VLLELFSMYRDWQEEKAKQISKRQEEIENKIEVADALATKLLQRF 122 (214)
Q Consensus 78 v~~ELfS~YreWQe~~a~~isk~QeeienkIE~adalA~KLlQR~ 122 (214)
.+-..+..|.++..+.|+++-++.++|.+.-.-+..-.++.+++.
T Consensus 11 ~l~~~~~~~~~~d~~~a~~i~~~e~~id~~~~~~~~~~~~~~~~~ 55 (88)
T PF01895_consen 11 MLDDAIEAFEERDSELAQEIIQLEEEIDELYREIRRQILKILKNQ 55 (88)
T ss_dssp HHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCHHHHHHHHHhHHHHHHHHHHHHHHHHHHHhhC
Confidence 345677889999999999999988888776666655555665553
No 30
>smart00150 SPEC Spectrin repeats.
Probab=47.42 E-value=83 Score=20.93 Aligned_cols=69 Identities=19% Similarity=0.279 Sum_probs=43.3
Q ss_pred CChHHHHHHHHHhHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHhccchhhhhhhhhhhccccchhhhHhhhhhHH
Q 028075 74 VNPKVLLELFSMYRDWQEEKAKQISKRQEEIENKIEVADALATKLLQRFGYSVSAMKTSSQHLSEVHALQVEIGELKGRL 153 (214)
Q Consensus 74 ~np~v~~ELfS~YreWQe~~a~~isk~QeeienkIE~adalA~KLlQR~n~S~S~Mktts~hL~~V~~LqvevgElKgrL 153 (214)
-|+..+-.+..-+...+++. +..+.+++.+..+|-+|++. |+ -+..+++.++
T Consensus 28 ~d~~~~~~~~~~~~~~~~e~--------~~~~~~v~~~~~~~~~L~~~-~~-------------------~~~~~i~~~~ 79 (101)
T smart00150 28 KDLESVEALLKKHEALEAEL--------EAHEERVEALNELGEQLIEE-GH-------------------PDAEEIEERL 79 (101)
T ss_pred CCHHHHHHHHHHHHHHHHHH--------HHhHHHHHHHHHHHHHHHHc-CC-------------------CcHHHHHHHH
Confidence 46666666666555555443 23445566666667677665 21 1244667778
Q ss_pred HHHHhhhHHHHHHHHhc
Q 028075 154 TEVISNCDALCKRIAAE 170 (214)
Q Consensus 154 teVisncdaLCKRI~~e 170 (214)
.++-..|+.||.++...
T Consensus 80 ~~l~~~w~~l~~~~~~r 96 (101)
T smart00150 80 EELNERWEELKELAEER 96 (101)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 88888888998887754
No 31
>cd09236 V_AnPalA_UmRIM20_like Protein-interacting V-domains of Aspergillus nidulans PalA/RIM20, Ustilago maydis RIM20, and related proteins. This family belongs to the V_Alix_like superfamily which includes the V-shaped (V) domains of Bro1 and Rim20 from Saccharomyces cerevisiae, mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), and related domains. Aspergillus nidulas PalA/RIM20 and Ustilago maydis RIM20, like Saccharomyces cerevisiae Rim20, participate in the response to the external pH via the Pal/Rim101 pathway; however, Saccharomyces cerevisiae Rim20 does not belong to this family. This pathway is a signaling cascade resulting in the activation of the transcription factor PacC/Rim101. The mammalian Alix V-domain (belonging to a different family) contains a binding site, partially conserved in the superfamily, for the retroviral late assembly (L) domain YPXnL motif. Aspergillus nidulas Pa
Probab=47.05 E-value=1.4e+02 Score=27.01 Aligned_cols=48 Identities=21% Similarity=0.221 Sum_probs=37.1
Q ss_pred hHHHHHHHHHhHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHhccchhhh
Q 028075 76 PKVLLELFSMYRDWQEEKAKQISKRQEEIENKIEVADALATKLLQRFGYSVSAM 129 (214)
Q Consensus 76 p~v~~ELfS~YreWQe~~a~~isk~QeeienkIE~adalA~KLlQR~n~S~S~M 129 (214)
|-.+.|-.|+|.|=|..-+. ++|..++|.+...+...|.-+|...+.=
T Consensus 1 P~~v~ea~s~Y~erk~~lVr------~~~~~~le~~~~~l~~~L~slnLP~sl~ 48 (353)
T cd09236 1 PFGVHLAISIYDDRKDRLVN------ESIIDELEELTNRAHSTLRSLNLPGSLQ 48 (353)
T ss_pred ChhHHHHHHHHHHHHHHHHH------HHHHhHHHHHHHHHHHHHHhCCCcHHHH
Confidence 44567888999986655543 4567899999999999999999876643
No 32
>cd04776 HTH_GnyR Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR. Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=45.78 E-value=49 Score=25.55 Aligned_cols=15 Identities=20% Similarity=0.445 Sum_probs=7.5
Q ss_pred HHHHHHhccchhhhh
Q 028075 116 TKLLQRFGYSVSAMK 130 (214)
Q Consensus 116 ~KLlQR~n~S~S~Mk 130 (214)
++.|+++|+|+.-||
T Consensus 48 I~~lr~~G~~L~~I~ 62 (118)
T cd04776 48 ILRGKRLGFSLEEIR 62 (118)
T ss_pred HHHHHHCCCCHHHHH
Confidence 344555555554444
No 33
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=44.49 E-value=28 Score=27.62 Aligned_cols=18 Identities=6% Similarity=0.362 Sum_probs=10.6
Q ss_pred HHHHHHHHhccchhhhhh
Q 028075 114 LATKLLQRFGYSVSAMKT 131 (214)
Q Consensus 114 lA~KLlQR~n~S~S~Mkt 131 (214)
..++.|+.+|+|+.-|+.
T Consensus 49 ~~I~~lr~~G~sL~eI~~ 66 (140)
T PRK09514 49 RFIRRAKQLGFTLEEIRE 66 (140)
T ss_pred HHHHHHHHcCCCHHHHHH
Confidence 345556666666666654
No 34
>PF14931 IFT20: Intraflagellar transport complex B, subunit 20
Probab=44.33 E-value=1.6e+02 Score=23.78 Aligned_cols=79 Identities=27% Similarity=0.286 Sum_probs=54.2
Q ss_pred HHHHHHHHHHHHHHhHHHHHHHHHHHHHHH----HhccchhhhhhhhhhhccccchhhhHhhhhhHHHHHHhhhHHHHHH
Q 028075 91 EEKAKQISKRQEEIENKIEVADALATKLLQ----RFGYSVSAMKTSSQHLSEVHALQVEIGELKGRLTEVISNCDALCKR 166 (214)
Q Consensus 91 e~~a~~isk~QeeienkIE~adalA~KLlQ----R~n~S~S~Mktts~hL~~V~~LqvevgElKgrLteVisncdaLCKR 166 (214)
.+-..+|..-|.=++.=|++++.+|-..=+ -.|-.-.+=-.+-++-.+...||..|.|-|--|...-..|++|+|
T Consensus 30 ~~F~~ki~~F~~iv~~~~~~~~~~A~~VE~eKlkAIG~RN~l~s~~k~R~~~~q~lq~~I~Ek~~eLERl~~E~~sL~k- 108 (120)
T PF14931_consen 30 KEFVEKISEFQKIVKGFIEILDELAKRVENEKLKAIGARNLLKSEAKQREAQQQQLQALIAEKKMELERLRSEYESLQK- 108 (120)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-
Confidence 344567777788888888888888765422 122211111113346677888999999999999999999999986
Q ss_pred HHhc
Q 028075 167 IAAE 170 (214)
Q Consensus 167 I~~e 170 (214)
|+++
T Consensus 109 ve~e 112 (120)
T PF14931_consen 109 VEQE 112 (120)
T ss_pred HHHH
Confidence 4443
No 35
>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=44.17 E-value=83 Score=23.64 Aligned_cols=27 Identities=15% Similarity=0.299 Sum_probs=20.8
Q ss_pred HHHHHHHHHHHHHhccchhhhhhhhhh
Q 028075 109 EVADALATKLLQRFGYSVSAMKTSSQH 135 (214)
Q Consensus 109 E~adalA~KLlQR~n~S~S~Mktts~h 135 (214)
++...-.++.|+++|+|++.|+.--..
T Consensus 44 ~i~~l~~I~~lr~~G~sl~~i~~l~~~ 70 (108)
T cd01107 44 QLERLNRIKYLRDLGFPLEEIKEILDA 70 (108)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHhc
Confidence 455556789999999999999875443
No 36
>PRK00286 xseA exodeoxyribonuclease VII large subunit; Reviewed
Probab=43.87 E-value=2.6e+02 Score=25.65 Aligned_cols=155 Identities=15% Similarity=0.272 Sum_probs=78.0
Q ss_pred CcceeeeecCc--cCcch-----HHHhhhcccccCcccc--CCCCCCCcccceeecc--CCCCCCCC--CCChHHHH-HH
Q 028075 17 IDDITTVSYKS--ESVDP-----ILENIKSLKITTPILT--SPPPTESSLTDILVRR--SSTSSASG--TVNPKVLL-EL 82 (214)
Q Consensus 17 ~DeITTVse~~--e~~DP-----~LErLkSLkIa~PiL~--spp~~EssLtDILvrk--~ssSs~S~--~~np~v~~-EL 82 (214)
.|.|--+++|- |++.| +.+.+-..+ -||++ +++ +..+|.|..--. +-||.+.. ..|-.... +|
T Consensus 193 ~Dviii~RGGGS~eDL~~Fn~e~v~~ai~~~~--~Pvis~IGHE-~D~tl~D~vAd~ra~TPtaaae~~~~~~~e~~q~L 269 (438)
T PRK00286 193 EDVLIVARGGGSLEDLWAFNDEAVARAIAASR--IPVISAVGHE-TDFTIADFVADLRAPTPTAAAELAVPDRAELLQRL 269 (438)
T ss_pred CCEEEEecCCCCHHHhhccCcHHHHHHHHcCC--CCEEEeccCC-CCccHHHHhhhccCCChHHHHHHhCccHHHHHHHH
Confidence 58898888877 66633 344555443 47888 788 899999987533 33333221 11212221 22
Q ss_pred HHHhHHHHHHHHHHHHHHHHHHhH----------------HHHHHHHHHHHHHHHhccchhhhh----hhhhhhccccch
Q 028075 83 FSMYRDWQEEKAKQISKRQEEIEN----------------KIEVADALATKLLQRFGYSVSAMK----TSSQHLSEVHAL 142 (214)
Q Consensus 83 fS~YreWQe~~a~~isk~Qeeien----------------kIE~adalA~KLlQR~n~S~S~Mk----tts~hL~~V~~L 142 (214)
=.+++..+......+...+..+++ .-+-.+.+...|.+.+.+-+...+ ...+.|..++++
T Consensus 270 d~l~~rL~~a~~~~L~~~~~~L~~L~~rL~~~~P~~~l~~~~q~L~~l~~rL~~a~~~~L~~~~~~L~~l~~rL~~lsP~ 349 (438)
T PRK00286 270 QQLQQRLARAMRRRLEQKRQRLDQLARRLKFQSPERLLAQQQQRLDRLQQRLQRALERRLRLAKQRLERLSQRLQQQNPQ 349 (438)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCHH
Confidence 222333333333344433333322 112233333333333332222222 223334445554
Q ss_pred hh------hHhhhhhHHHHHH--------hhhHHHHHHHHhcCCcc
Q 028075 143 QV------EIGELKGRLTEVI--------SNCDALCKRIAAEGPDS 174 (214)
Q Consensus 143 qv------evgElKgrLteVi--------sncdaLCKRI~~eGPes 174 (214)
++ .+.+|..||...+ .+.+.|..|+..-.|..
T Consensus 350 ~~L~r~~qrL~~L~~rL~~a~~~~L~~~~~rL~~l~~rL~~lsP~~ 395 (438)
T PRK00286 350 RRIERAQQRLEQLEQRLRRAMRRQLKRKRQRLEALAQQLEALSPLA 395 (438)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCChh
Confidence 43 4555666665554 55678899999998874
No 37
>PLN02678 seryl-tRNA synthetase
Probab=42.90 E-value=1.3e+02 Score=28.82 Aligned_cols=81 Identities=17% Similarity=0.316 Sum_probs=46.3
Q ss_pred ChHHHHHHHHHhHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHhccchhhhhhhhhhhccccchhhhHhhhhhHHH
Q 028075 75 NPKVLLELFSMYRDWQEEKAKQISKRQEEIENKIEVADALATKLLQRFGYSVSAMKTSSQHLSEVHALQVEIGELKGRLT 154 (214)
Q Consensus 75 np~v~~ELfS~YreWQe~~a~~isk~QeeienkIE~adalA~KLlQR~n~S~S~Mktts~hL~~V~~LqvevgElKgrLt 154 (214)
|...+-++.++|++|.+.. +++...+.+.. ++..+++.+ .+=+-. ...-..++..|..||.+|...+.
T Consensus 28 ~~~~id~il~ld~~~r~l~-~~~e~lr~erN---~~sk~I~~~--k~~~~~------~~~l~~~~~~Lk~ei~~le~~~~ 95 (448)
T PLN02678 28 SVELVDEVIALDKEWRQRQ-FELDSLRKEFN---KLNKEVAKL--KIAKED------ATELIAETKELKKEITEKEAEVQ 95 (448)
T ss_pred CHHHHHHHHHHHHHHHHHH-HHHHHHHHHHH---HHHHHHHHH--hhCCCc------HHHHHHHHHHHHHHHHHHHHHHH
Confidence 4446788999999998764 23333332221 122222221 111111 12223456667778888888888
Q ss_pred HHHhhhHHHHHHH
Q 028075 155 EVISNCDALCKRI 167 (214)
Q Consensus 155 eVisncdaLCKRI 167 (214)
++-..-+.++.+|
T Consensus 96 ~~~~~l~~~~~~i 108 (448)
T PLN02678 96 EAKAALDAKLKTI 108 (448)
T ss_pred HHHHHHHHHHHhC
Confidence 8888888777776
No 38
>PF13887 MRF_C1: Myelin gene regulatory factor -C-terminal domain 1
Probab=42.42 E-value=18 Score=24.61 Aligned_cols=21 Identities=14% Similarity=0.409 Sum_probs=18.2
Q ss_pred HHHHHHHHHHHHhHHHHHHHH
Q 028075 93 KAKQISKRQEEIENKIEVADA 113 (214)
Q Consensus 93 ~a~~isk~QeeienkIE~ada 113 (214)
-+|++||.-..+|+||+-++.
T Consensus 15 AvqeLck~t~~Le~rI~ele~ 35 (36)
T PF13887_consen 15 AVQELCKLTDNLETRIDELER 35 (36)
T ss_pred HHHHHHHHhccHHHHHHHHhh
Confidence 478999999999999997653
No 39
>PF05384 DegS: Sensor protein DegS; InterPro: IPR008595 This is a group of Bacillus DegS proteins. The DegS-DegU two-component regulatory system of Bacillus subtilis controls various processes that characterise the transition from the exponential to the stationary growth phase, including the induction of extracellular degradative enzymes, expression of late competence genes and down-regulation of the sigma D regulon []. The entry also contains one sequence Q8R9D3 from SWISSPROT from Thermoanaerobacter tengcongensis which is described as a sensory transduction histidine kinase.; GO: 0016301 kinase activity, 0007165 signal transduction
Probab=42.11 E-value=22 Score=29.86 Aligned_cols=30 Identities=40% Similarity=0.542 Sum_probs=25.6
Q ss_pred ccccchhhhHhhhhhHHHHHHhhhHHHHHH
Q 028075 137 SEVHALQVEIGELKGRLTEVISNCDALCKR 166 (214)
Q Consensus 137 ~~V~~LqvevgElKgrLteVisncdaLCKR 166 (214)
.++..|+-|+.++|..+.+||..+|.|-++
T Consensus 27 ~E~~~l~~EL~evk~~v~~~I~evD~Le~~ 56 (159)
T PF05384_consen 27 QEYERLRKELEEVKEEVSEVIEEVDKLEKR 56 (159)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 466778899999999999999999998765
No 40
>PRK10265 chaperone-modulator protein CbpM; Provisional
Probab=41.36 E-value=28 Score=26.46 Aligned_cols=39 Identities=21% Similarity=0.266 Sum_probs=25.4
Q ss_pred HHHHhccchhhhhhhhhhhccccchhhhHhhhhhHHHHH
Q 028075 118 LLQRFGYSVSAMKTSSQHLSEVHALQVEIGELKGRLTEV 156 (214)
Q Consensus 118 LlQR~n~S~S~Mktts~hL~~V~~LqvevgElKgrLteV 156 (214)
|-.-|+.....+--.-.=|++++.|+-|+.+||+||.-.
T Consensus 59 L~~dl~in~~gialvl~LLd~i~~Lr~el~~L~~~l~~~ 97 (101)
T PRK10265 59 LRHELALDWPGIAVALTLLDEIAHLKQENRLLRQRLSRF 97 (101)
T ss_pred HHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333344444444444455677899999999999988643
No 41
>PF10168 Nup88: Nuclear pore component; InterPro: IPR019321 Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein have no obvious structural motifs. It is, however, where it binds to Nup98; one of the components of the nuclear pore. The C-terminal end is a predicted coiled-coil domain []. Nup88 is over expressed in tumour cells [].
Probab=41.17 E-value=1.1e+02 Score=31.00 Aligned_cols=27 Identities=22% Similarity=0.399 Sum_probs=14.6
Q ss_pred HHHHHHHHhHHHHHHHHHHHHHHHHhc
Q 028075 97 ISKRQEEIENKIEVADALATKLLQRFG 123 (214)
Q Consensus 97 isk~QeeienkIE~adalA~KLlQR~n 123 (214)
|+.+++.+..|||-|..-=-+|.+|..
T Consensus 591 l~~~ae~LaeR~e~a~d~Qe~L~~R~~ 617 (717)
T PF10168_consen 591 LRESAEKLAERYEEAKDKQEKLMKRVD 617 (717)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344445555566655555555666654
No 42
>PF05615 THOC7: Tho complex subunit 7; InterPro: IPR008501 The Tho complex (THOC) is involved in transcription elongation and mRNA export from the nucleus []. This entry represents the subunit THOC7, which is found in higher eukaryotes, and the non-homologous subunit Mft1p found in yeast. The funtions of these subunits are unknown, and it is not known if these subunits are functionally equivalent.
Probab=40.01 E-value=1.8e+02 Score=22.66 Aligned_cols=32 Identities=38% Similarity=0.465 Sum_probs=19.6
Q ss_pred cchhhhHhhhhhHHHHH------HhhhHHHHHHHHhcC
Q 028075 140 HALQVEIGELKGRLTEV------ISNCDALCKRIAAEG 171 (214)
Q Consensus 140 ~~LqvevgElKgrLteV------isncdaLCKRI~~eG 171 (214)
...+-+|.+||..|.+. -..||+|++-|....
T Consensus 91 ~~~k~~ie~lk~~L~~ak~~r~~k~eyd~La~~I~~~p 128 (139)
T PF05615_consen 91 EQAKKEIEELKEELEEAKRVRQNKEEYDALAKKINSQP 128 (139)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Confidence 34444455555544321 238999999998765
No 43
>cd04773 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.
Probab=39.32 E-value=1.6e+02 Score=22.26 Aligned_cols=30 Identities=33% Similarity=0.443 Sum_probs=23.4
Q ss_pred HHHHHHHHHHHHHHhccchhhhhhhhhhhc
Q 028075 108 IEVADALATKLLQRFGYSVSAMKTSSQHLS 137 (214)
Q Consensus 108 IE~adalA~KLlQR~n~S~S~Mktts~hL~ 137 (214)
-++.....++.|+++|+++..+|.--..+.
T Consensus 42 ~dl~~l~~I~~lr~~G~~l~~I~~~l~~~~ 71 (108)
T cd04773 42 SDVRDARLIHLLRRGGYLLEQIATVVEQLR 71 (108)
T ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHHHhh
Confidence 356666778899999999999998766553
No 44
>PF15035 Rootletin: Ciliary rootlet component, centrosome cohesion
Probab=39.31 E-value=1.9e+02 Score=24.50 Aligned_cols=77 Identities=18% Similarity=0.262 Sum_probs=45.0
Q ss_pred HHHhHHHHHHHHHHHHHHHHHHh-HHHHHHHHHHHHHHHHhccchhhhhhhhhhhccccchhhhHhhhhhHHHHHHhhhH
Q 028075 83 FSMYRDWQEEKAKQISKRQEEIE-NKIEVADALATKLLQRFGYSVSAMKTSSQHLSEVHALQVEIGELKGRLTEVISNCD 161 (214)
Q Consensus 83 fS~YreWQe~~a~~isk~Qeeie-nkIE~adalA~KLlQR~n~S~S~Mktts~hL~~V~~LqvevgElKgrLteVisncd 161 (214)
+..|+|+|..-|+-|++.|-.+. +|-..+| |.-+| +. -.+.-+.+.+=.....--.++.++-.||.|=--.|+
T Consensus 4 l~a~qe~Qq~qa~Lv~~LQ~KV~qYr~rc~e-le~~l----~~-~~~l~~~~~~~~~~~e~s~dLe~~l~rLeEEqqR~~ 77 (182)
T PF15035_consen 4 LDAYQEEQQRQAQLVQRLQAKVLQYRKRCAE-LEQQL----SA-SQVLESPSQRRRSEEEHSPDLEEALIRLEEEQQRSE 77 (182)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHH----hc-ccCcCcccccccccccCcccHHHHHHHHHHHHHhHH
Confidence 36799999999999999998753 3433332 33333 11 112222222211122234567778888888888888
Q ss_pred HHHH
Q 028075 162 ALCK 165 (214)
Q Consensus 162 aLCK 165 (214)
.|+.
T Consensus 78 ~L~q 81 (182)
T PF15035_consen 78 ELAQ 81 (182)
T ss_pred HHHH
Confidence 8653
No 45
>PTZ00332 paraflagellar rod protein; Provisional
Probab=38.94 E-value=1e+02 Score=31.21 Aligned_cols=62 Identities=27% Similarity=0.402 Sum_probs=42.9
Q ss_pred HHHHHHHhHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHhccchhhhhhhhhhhccccchhhhHhhhhhHHHHHHh
Q 028075 79 LLELFSMYRDWQEEKAKQISKRQEEIENKIEVADALATKLLQRFGYSVSAMKTSSQHLSEVHALQVEIGELKGRLTEVIS 158 (214)
Q Consensus 79 ~~ELfS~YreWQe~~a~~isk~QeeienkIE~adalA~KLlQR~n~S~S~Mktts~hL~~V~~LqvevgElKgrLteVis 158 (214)
.--+|.|||+-|... .+|-+|++.+||.+|+=+-. |-+| .+-|.-+++| |++|.-.|-
T Consensus 323 wnrI~eLer~Lq~l~----~eR~~eV~rRIe~~~rEekR---r~~y-eqFl~~asQH--------------kqrL~~tv~ 380 (589)
T PTZ00332 323 WNKIQDLERQLQRLG----TERFEEVKRRIEENDREEKR---RVEY-QQFLEVAGQH--------------KKLLELTVY 380 (589)
T ss_pred HHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHh---HhHH-HHHHHHHHHH--------------HHHHHHHHH
Confidence 345677778877766 56778999999998887642 2233 4567777777 567777777
Q ss_pred hhHH
Q 028075 159 NCDA 162 (214)
Q Consensus 159 ncda 162 (214)
|||.
T Consensus 381 Ncd~ 384 (589)
T PTZ00332 381 NCDL 384 (589)
T ss_pred HHHH
Confidence 7763
No 46
>PF00435 Spectrin: Spectrin repeat; InterPro: IPR002017 Spectrin repeats [] are found in several proteins involved in cytoskeletal structure. These include spectrin alpha and beta subunits [, ], alpha-actinin [] and dystrophin. The spectrin repeat forms a three-helix bundle. The second helix is interrupted by proline in some sequences. The repeats are defined by a characteristic tryptophan (W) residue at position 17 in helix A and a leucine (L) at 2 residues from the carboxyl end of helix C.; GO: 0005515 protein binding; PDB: 1HCI_A 1QUU_A 3FB2_B 1S35_A 1U5P_A 1U4Q_A 1CUN_B 1YDI_B 3EDV_A 1AJ3_A ....
Probab=38.29 E-value=1.2e+02 Score=20.13 Aligned_cols=69 Identities=26% Similarity=0.368 Sum_probs=38.9
Q ss_pred CCChHHHHHHHHHhHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHhccchhhhhhhhhhhccccchhhhHhhhhhH
Q 028075 73 TVNPKVLLELFSMYRDWQEEKAKQISKRQEEIENKIEVADALATKLLQRFGYSVSAMKTSSQHLSEVHALQVEIGELKGR 152 (214)
Q Consensus 73 ~~np~v~~ELfS~YreWQe~~a~~isk~QeeienkIE~adalA~KLlQR~n~S~S~Mktts~hL~~V~~LqvevgElKgr 152 (214)
.-|+..+-+++.-|++++.+.. .++. +++.+.+.|-.| ..-++. +..+++.+
T Consensus 30 ~~~~~~~~~~~~~~~~~~~ei~----~~~~----~l~~l~~~~~~L-~~~~~~-------------------~~~~i~~~ 81 (105)
T PF00435_consen 30 GSDLEELEEQLKKHKELQEEIE----SRQE----RLESLNEQAQQL-IDSGPE-------------------DSDEIQEK 81 (105)
T ss_dssp SSSHHHHHHHHHHHHHHHHHHH----HHHH----HHHHHHHHHHHH-HHTTHT-------------------THHHHHHH
T ss_pred CCCHHHHHHHHHHHhhhhhHHH----HHHH----HHHHHHHHHHHH-HHcCCC-------------------cHHHHHHH
Confidence 5577777777777777665433 3333 344444555555 222211 12455666
Q ss_pred HHHHHhhhHHHHHHHHh
Q 028075 153 LTEVISNCDALCKRIAA 169 (214)
Q Consensus 153 LteVisncdaLCKRI~~ 169 (214)
+..+-.++++||.++..
T Consensus 82 ~~~l~~~w~~l~~~~~~ 98 (105)
T PF00435_consen 82 LEELNQRWEALCELVEE 98 (105)
T ss_dssp HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 66677777777777654
No 47
>PF04210 MtrG: Tetrahydromethanopterin S-methyltransferase, subunit G ; InterPro: IPR005866 This model describes the N5-methyltetrahydromethanopterin: coenzyme M methyltransferase subunit G in methanogenic archaea. This methyltranferase is a membrane-associated enzyme complex that uses methyl-transfer reaction to drive a sodium-ion pump. Archaea have evolved energy-yielding pathways marked by one-carbon biochemistry featuring novel cofactors and enzymes. This transferase is involved in the transfer of a methyl group from N5-methyltetrahydromethanopterin to coenzyme M. In an accompanying reaction, methane is produced by two-electron reduction of the methyl moiety in methyl-coenzyme M by another enzyme methyl-coenzyme M reductase.; GO: 0030269 tetrahydromethanopterin S-methyltransferase activity, 0015948 methanogenesis, 0016021 integral to membrane
Probab=38.20 E-value=51 Score=25.18 Aligned_cols=28 Identities=43% Similarity=0.642 Sum_probs=21.4
Q ss_pred HHHHHHHHHHhHHHHHHHHHHHHHHHHhccc
Q 028075 95 KQISKRQEEIENKIEVADALATKLLQRFGYS 125 (214)
Q Consensus 95 ~~isk~QeeienkIE~adalA~KLlQR~n~S 125 (214)
.++.+|-.+||.|+|-+.+ .+.||.|-.
T Consensus 15 ~~i~~rLd~iEeKvEf~~~---Ei~Qr~Gkk 42 (70)
T PF04210_consen 15 NEIMKRLDEIEEKVEFTNA---EIAQRAGKK 42 (70)
T ss_pred HHHHHHHHHHHHHHHhHHH---HHHHHHhHH
Confidence 3566788999999998765 677887754
No 48
>PF08928 DUF1910: Domain of unknown function (DUF1910); InterPro: IPR015024 This domain is found in hypothetical bacterial proteins.
Probab=38.20 E-value=54 Score=24.58 Aligned_cols=73 Identities=19% Similarity=0.211 Sum_probs=39.4
Q ss_pred hHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHhccchhhhhhhhhhhccccchhhhHhhhhhHHHHHHhhhHH
Q 028075 86 YRDWQEEKAKQISKRQEEIENKIEVADALATKLLQRFGYSVSAMKTSSQHLSEVHALQVEIGELKGRLTEVISNCDA 162 (214)
Q Consensus 86 YreWQe~~a~~isk~QeeienkIE~adalA~KLlQR~n~S~S~Mktts~hL~~V~~LqvevgElKgrLteVisncda 162 (214)
|++|-+..-+.|.+.. .+|...+.-..+-.||+|++-+.-...-..+---++.=..|.+||.-+-.+|....-
T Consensus 10 f~~~i~~~~e~i~~~~----~~i~~~~~~~~~~~~r~~~~~~~~~~~~~~l~~~YS~G~~i~~l~~~~~~~l~~~e~ 82 (117)
T PF08928_consen 10 FEKWIEFYEESIEEFE----EKIIELKEDEDNGIQRYNYYWSIFDYYLELLIAKYSAGDSIEELKPYYPNILDYFEE 82 (117)
T ss_pred HHHHHHHHHHHHHHHH----HHHHhcccccccchhhHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHH
Confidence 4455544444444442 234444444445556655444444443444444455666788888888888775443
No 49
>PF11594 Med28: Mediator complex subunit 28; InterPro: IPR021640 Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species [],[]. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function []. Subunit Med28 of the Mediator may function as a scaffolding protein within Mediator by maintaining the stability of a submodule within the head module, and components of this submodule act together in a gene-regulatory programme to suppress smooth muscle cell differentiation. Thus, mammalian Mediator subunit Med28 functions as a repressor of smooth muscle-cell differentiation, which could have implications for disorders associated with abnormalities in smooth muscle cell growth and differentiation, including atherosclerosis, asthma, hypertension, and smooth muscle tumours [].
Probab=37.73 E-value=54 Score=26.55 Aligned_cols=46 Identities=20% Similarity=0.224 Sum_probs=38.8
Q ss_pred HHHHHHHHHhccchhhhhhhhhhhccccchhhhHh-hhhhHHHHHHh
Q 028075 113 ALATKLLQRFGYSVSAMKTSSQHLSEVHALQVEIG-ELKGRLTEVIS 158 (214)
Q Consensus 113 alA~KLlQR~n~S~S~Mktts~hL~~V~~Lqvevg-ElKgrLteVis 158 (214)
+..-.|+|+++--++.-...-+-+++||...-||- |+.+|+-+.-+
T Consensus 52 qRKe~Ll~Kh~~kI~~w~~lL~d~~~~~k~~~evp~e~~~~~~e~~~ 98 (106)
T PF11594_consen 52 QRKEQLLQKHYEKIDYWEKLLSDAQNQHKVPDEVPPEARQRLAELAT 98 (106)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhccCchhccchHHHHHHhhcc
Confidence 55667788888888888888899999999999998 99999987654
No 50
>TIGR02047 CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional regulator. This model represents the cadmium(II) and/or lead(II) responsive transcriptional activator of the proteobacterial metal efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(6-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=37.71 E-value=49 Score=25.68 Aligned_cols=18 Identities=6% Similarity=0.126 Sum_probs=12.0
Q ss_pred HHHHHHHhccchhhhhhh
Q 028075 115 ATKLLQRFGYSVSAMKTS 132 (214)
Q Consensus 115 A~KLlQR~n~S~S~Mktt 132 (214)
.++.|+.+|+|+..+|.-
T Consensus 49 ~I~~lr~lG~sL~eI~~~ 66 (127)
T TIGR02047 49 FIRNCRTLDMSLAEIRQL 66 (127)
T ss_pred HHHHHHHcCCCHHHHHHH
Confidence 456667777777777654
No 51
>PRK15330 cell invasion protein SipD; Provisional
Probab=37.64 E-value=1.4e+02 Score=28.58 Aligned_cols=74 Identities=18% Similarity=0.212 Sum_probs=59.6
Q ss_pred HhHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHhccchhhhhhhhhhh---ccccchhhhHhhhhhHHHHHHhhhH
Q 028075 85 MYRDWQEEKAKQISKRQEEIENKIEVADALATKLLQRFGYSVSAMKTSSQHL---SEVHALQVEIGELKGRLTEVISNCD 161 (214)
Q Consensus 85 ~YreWQe~~a~~isk~QeeienkIE~adalA~KLlQR~n~S~S~Mktts~hL---~~V~~LqvevgElKgrLteVisncd 161 (214)
-|+|---..++-|+...++--...+-+=.-.+...|-||--+|-|. .|+ ++=..++..+..||..|.+++.+|.
T Consensus 130 S~aELW~~Is~sIssIk~dYldvYa~vVk~YTd~yQsfne~lSkls---~~IsaGsDGntIkFd~~slk~~i~~lidKY~ 206 (343)
T PRK15330 130 SDAEIWDMVSQNISAIGDSYLGVYENVVAVYTDFYQAFSDILSKMG---GWLLPGKDGNTVKLDVTSLKNDLNSLVNKYN 206 (343)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh---hhcccCCCCCeeeecHHHHHHHHHHHHHhcc
Confidence 3777667788999999888777776666778899999999888884 443 4456689999999999999998885
No 52
>cd01279 HTH_HspR-like Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator HspR and related proteins, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=37.14 E-value=47 Score=24.78 Aligned_cols=47 Identities=17% Similarity=0.176 Sum_probs=33.8
Q ss_pred HHHHHHHHHHHHH-hccchhhhhhhhhhhccccchhhhHhhhhhHHHH
Q 028075 109 EVADALATKLLQR-FGYSVSAMKTSSQHLSEVHALQVEIGELKGRLTE 155 (214)
Q Consensus 109 E~adalA~KLlQR-~n~S~S~Mktts~hL~~V~~LqvevgElKgrLte 155 (214)
++...--++-|++ .|++...++..-.-+.++..|+-++.+++.++..
T Consensus 43 dv~~l~~I~~L~~~~G~~l~~i~~~l~l~~~~~~l~~~~~~~~~~~~~ 90 (98)
T cd01279 43 DLELLRQVQRLSQDEGFNLAGIKRIIELYPQVLLLQCRSCEHATELIG 90 (98)
T ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHHhhhHHHHHHHHHHHHHHHHHh
Confidence 5555556677787 9999999998777777777777666666655543
No 53
>PF10473 CENP-F_leu_zip: Leucine-rich repeats of kinetochore protein Cenp-F/LEK1; InterPro: IPR019513 Cenp-F, a centromeric kinetochore, microtubule-binding protein consisting of two 1,600-amino acid-long coils, is essential for the full functioning of the mitotic checkpoint pathway [, ]. There are several leucine-rich repeats along the sequence of LEK1 that are considered to be zippers, though they do not appear to be binding DNA directly in this instance []. ; GO: 0008134 transcription factor binding, 0042803 protein homodimerization activity, 0045502 dynein binding
Probab=36.72 E-value=1.4e+02 Score=24.74 Aligned_cols=53 Identities=15% Similarity=0.207 Sum_probs=43.0
Q ss_pred HHhHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHhccchhhhhhhhhhhc
Q 028075 84 SMYRDWQEEKAKQISKRQEEIENKIEVADALATKLLQRFGYSVSAMKTSSQHLS 137 (214)
Q Consensus 84 S~YreWQe~~a~~isk~QeeienkIE~adalA~KLlQR~n~S~S~Mktts~hL~ 137 (214)
-+-++||+ ++.++-..+.++.|.|+.+++=-+++.+.+.+.+..+.+--.||.
T Consensus 87 k~lq~~q~-kv~eLE~~~~~~~~~l~~~E~ek~q~~e~~~~~ve~L~~ql~~L~ 139 (140)
T PF10473_consen 87 KELQKKQE-KVSELESLNSSLENLLQEKEQEKVQLKEESKSAVEMLQKQLKELN 139 (140)
T ss_pred HHHHHHHH-HHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Confidence 34555653 578888889999999999999999999999999888877666654
No 54
>cd04787 HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription regulators. Putative helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR), unknown subgroup. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules, such as, metal ions, drugs, and organic substrates. This subgroup lacks one of the c
Probab=34.49 E-value=65 Score=25.08 Aligned_cols=20 Identities=15% Similarity=0.197 Sum_probs=12.2
Q ss_pred HHHHHHHHhccchhhhhhhh
Q 028075 114 LATKLLQRFGYSVSAMKTSS 133 (214)
Q Consensus 114 lA~KLlQR~n~S~S~Mktts 133 (214)
--++.|+.+|+|+.-||.--
T Consensus 48 ~~I~~lr~~G~sL~eI~~~l 67 (133)
T cd04787 48 RFILSARQLGFSLKDIKEIL 67 (133)
T ss_pred HHHHHHHHcCCCHHHHHHHH
Confidence 34556666777766666543
No 55
>PF08400 phage_tail_N: Prophage tail fibre N-terminal; InterPro: IPR013609 This entry represents the N terminus of phage 933W tail fibre protein. The characteristics of the protein distribution suggest prophage matches.
Probab=34.12 E-value=1.2e+02 Score=25.25 Aligned_cols=40 Identities=18% Similarity=0.355 Sum_probs=25.4
Q ss_pred CCCcccceeeccCCCCCCCCCCChHHHHHHHHHhHHHHHHHHHHHHHHH
Q 028075 53 TESSLTDILVRRSSTSSASGTVNPKVLLELFSMYRDWQEEKAKQISKRQ 101 (214)
Q Consensus 53 ~EssLtDILvrk~ssSs~S~~~np~v~~ELfS~YreWQe~~a~~isk~Q 101 (214)
..++|.|+| +.+ .-+.+-|.++.+ |++|+.+-++...+-+
T Consensus 82 ~pGTLN~fL-~~~----~e~dl~Pevlk~----fe~m~~~a~~~a~~a~ 121 (134)
T PF08400_consen 82 KPGTLNDFL-TAP----DEDDLRPEVLKR----FEEMVAQAARSAEAAA 121 (134)
T ss_pred CCCcHHHHh-hcc----ccccCCHHHHHH----HHHHHHHHHHHHHHHH
Confidence 458899988 332 236788888876 5666666555444433
No 56
>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators. Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=34.06 E-value=1.6e+02 Score=21.21 Aligned_cols=34 Identities=12% Similarity=0.155 Sum_probs=27.7
Q ss_pred HHHHHHHHHHHHHHhccchhhhhhhhhhhccccc
Q 028075 108 IEVADALATKLLQRFGYSVSAMKTSSQHLSEVHA 141 (214)
Q Consensus 108 IE~adalA~KLlQR~n~S~S~Mktts~hL~~V~~ 141 (214)
-++.....++-|+++|++...++...+++.+-+.
T Consensus 41 ~dv~~l~~i~~l~~~g~~~~~i~~~l~~~~~~~~ 74 (100)
T cd00592 41 EDLERLRLIRRLRELGLSLKEIRELLDARDEELS 74 (100)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHhcccccch
Confidence 4666667788899999999999999888877654
No 57
>COG4064 MtrG Tetrahydromethanopterin S-methyltransferase, subunit G [Coenzyme metabolism]
Probab=33.63 E-value=61 Score=25.10 Aligned_cols=28 Identities=39% Similarity=0.669 Sum_probs=21.9
Q ss_pred HHHHHHHHHHhHHHHHHHHHHHHHHHHhccc
Q 028075 95 KQISKRQEEIENKIEVADALATKLLQRFGYS 125 (214)
Q Consensus 95 ~~isk~QeeienkIE~adalA~KLlQR~n~S 125 (214)
.++.||-+|||.|.|.+-+ .+.||+|--
T Consensus 18 ne~~kRLdeieekvef~~~---Ev~Qr~Gkk 45 (75)
T COG4064 18 NEIHKRLDEIEEKVEFVNG---EVYQRIGKK 45 (75)
T ss_pred HHHHHHHHHHHHHHHhhHH---HHHHHHHHH
Confidence 4678899999999887654 678888843
No 58
>smart00150 SPEC Spectrin repeats.
Probab=33.48 E-value=1.2e+02 Score=20.09 Aligned_cols=37 Identities=16% Similarity=0.213 Sum_probs=25.3
Q ss_pred hhhhhhhccccchhhhHhhhhhHHHHHHhhhHHHHHH
Q 028075 130 KTSSQHLSEVHALQVEIGELKGRLTEVISNCDALCKR 166 (214)
Q Consensus 130 ktts~hL~~V~~LqvevgElKgrLteVisncdaLCKR 166 (214)
.+.-..+.....++.||...+.++..|..-++.|...
T Consensus 31 ~~~~~~~~~~~~~~~e~~~~~~~v~~~~~~~~~L~~~ 67 (101)
T smart00150 31 ESVEALLKKHEALEAELEAHEERVEALNELGEQLIEE 67 (101)
T ss_pred HHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHc
Confidence 3334445556778888888888888877766666654
No 59
>TIGR02043 ZntR Zn(II)-responsive transcriptional regulator. This model represents the zinc and cadmium (II) responsive transcriptional activator of the gamma proteobacterial zinc efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-Cys-X(8-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=32.95 E-value=79 Score=24.67 Aligned_cols=16 Identities=13% Similarity=0.397 Sum_probs=7.8
Q ss_pred HHHHHHhccchhhhhh
Q 028075 116 TKLLQRFGYSVSAMKT 131 (214)
Q Consensus 116 ~KLlQR~n~S~S~Mkt 131 (214)
++.|+.+|+|+..+|.
T Consensus 51 I~~lr~~G~sl~eI~~ 66 (131)
T TIGR02043 51 ILKAKELGFTLDEIKE 66 (131)
T ss_pred HHHHHHcCCCHHHHHH
Confidence 3444555555555443
No 60
>PF08114 PMP1_2: ATPase proteolipid family; InterPro: IPR012589 This family consists of small proteolipids associated with the plasma membrane H+ ATPase. Two proteolipids (PMP1 and PMP2) are associated with the ATPase and both genes are similarly expressed in the wild-type strain of yeast. No modification of the level of transcription of one PMP gene is detected in a strain deleted of the other. Though both proteolipids show similarity with other small proteolipids associated with other cation -transporting ATPases, their functions remain unclear [].
Probab=32.85 E-value=30 Score=24.34 Aligned_cols=10 Identities=50% Similarity=1.179 Sum_probs=8.3
Q ss_pred HhHHHHHHHH
Q 028075 85 MYRDWQEEKA 94 (214)
Q Consensus 85 ~YreWQe~~a 94 (214)
+||.||..+.
T Consensus 29 iYRKw~aRkr 38 (43)
T PF08114_consen 29 IYRKWQARKR 38 (43)
T ss_pred HHHHHHHHHH
Confidence 7999998764
No 61
>TIGR00414 serS seryl-tRNA synthetase. This model represents the seryl-tRNA synthetase found in most organisms. This protein is a class II tRNA synthetase, and is recognized by the pfam model tRNA-synt_2b. The seryl-tRNA synthetases of two archaeal species, Methanococcus jannaschii and Methanobacterium thermoautotrophicum, differ considerably and are included in a different model.
Probab=32.75 E-value=2.7e+02 Score=26.04 Aligned_cols=77 Identities=14% Similarity=0.199 Sum_probs=41.4
Q ss_pred HHHHHHHHhHHHHHHHH--HHHHHHHHHHhHHHHHHHHHHHHHHHHhccchhhhhhhhhhhccccchhhhHhhhhhHHHH
Q 028075 78 VLLELFSMYRDWQEEKA--KQISKRQEEIENKIEVADALATKLLQRFGYSVSAMKTSSQHLSEVHALQVEIGELKGRLTE 155 (214)
Q Consensus 78 v~~ELfS~YreWQe~~a--~~isk~QeeienkIE~adalA~KLlQR~n~S~S~Mktts~hL~~V~~LqvevgElKgrLte 155 (214)
.+-++.++|++|.+... +++...+..+..+| +.+. +. +-. -......++..|+-+|.+++..+.+
T Consensus 28 ~vd~i~~ld~~~r~~~~~~~~l~~erN~~sk~i------~~~~-~~-~~~-----~~~~l~~~~~~l~~~~~~~~~~~~~ 94 (418)
T TIGR00414 28 DLEKLIALDDERKKLLSEIEELQAKRNELSKQI------GKAK-GQ-KKD-----KIEEIKKELKELKEELTELSAALKA 94 (418)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------HHHh-cc-Ccc-----hHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46789999999987642 23333333333333 2110 00 000 0123344555666677777777777
Q ss_pred HHhhhHHHHHHH
Q 028075 156 VISNCDALCKRI 167 (214)
Q Consensus 156 VisncdaLCKRI 167 (214)
+-.+.+.++-+|
T Consensus 95 ~~~~~~~~~~~l 106 (418)
T TIGR00414 95 LEAELQDKLLSI 106 (418)
T ss_pred HHHHHHHHHHhC
Confidence 777777666665
No 62
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=32.33 E-value=2e+02 Score=21.42 Aligned_cols=47 Identities=13% Similarity=0.028 Sum_probs=39.3
Q ss_pred CCChHHHHHHHHHhHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHh
Q 028075 73 TVNPKVLLELFSMYRDWQEEKAKQISKRQEEIENKIEVADALATKLLQRF 122 (214)
Q Consensus 73 ~~np~v~~ELfS~YreWQe~~a~~isk~QeeienkIE~adalA~KLlQR~ 122 (214)
.-|+..+.+|+..|+..--..|......+++.+ +++...-++|++++
T Consensus 9 ~~~~~a~~~l~~~y~~~l~~~~~~~~~~~~~ae---Dl~qe~~~~l~~~~ 55 (179)
T PRK11924 9 TGDKEAFSELFRPHAPDLLRYARRQLGDRALAE---DAVQEAFLRAWRKA 55 (179)
T ss_pred ccCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHH---HHHHHHHHHHHHHH
Confidence 448899999999999988888988888887766 77888888888765
No 63
>cd01282 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=31.77 E-value=1.6e+02 Score=22.30 Aligned_cols=27 Identities=11% Similarity=0.110 Sum_probs=19.9
Q ss_pred HHHHHHHHHHHHHhccchhhhhhhhhh
Q 028075 109 EVADALATKLLQRFGYSVSAMKTSSQH 135 (214)
Q Consensus 109 E~adalA~KLlQR~n~S~S~Mktts~h 135 (214)
++.....++.|+++|+|+.-+|.--..
T Consensus 42 ~~~~l~~I~~lr~~G~sl~eI~~~l~~ 68 (112)
T cd01282 42 AVDRVRQIRRLLAAGLTLEEIREFLPC 68 (112)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 344556788889999999988876543
No 64
>PF13591 MerR_2: MerR HTH family regulatory protein
Probab=31.39 E-value=41 Score=24.66 Aligned_cols=37 Identities=19% Similarity=0.349 Sum_probs=26.8
Q ss_pred HHHHHHHhccchhhhhhhhhhhccccchhhhHhhhhh
Q 028075 115 ATKLLQRFGYSVSAMKTSSQHLSEVHALQVEIGELKG 151 (214)
Q Consensus 115 A~KLlQR~n~S~S~Mktts~hL~~V~~LqvevgElKg 151 (214)
+..|-+-|+.....+--.-+=|++|+.||-|+.+||+
T Consensus 48 ~~rL~~Dl~in~~gi~lil~LLd~i~~L~~el~~L~~ 84 (84)
T PF13591_consen 48 IRRLHRDLGINLEGIALILDLLDRIEQLRRELRELRR 84 (84)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 4455555666666666666777889999999988874
No 65
>TIGR02044 CueR Cu(I)-responsive transcriptional regulator. This model represents the copper-, silver- and gold- (I) responsive transcriptional activator of the gamma proteobacterial copper efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X7-Cys. This family also lacks a conserved cysteine at the N-terminal end of the dimerization helix which is required for the binding of divalent metals such as zinc; here it is replaced by a serine residue.
Probab=31.32 E-value=92 Score=23.99 Aligned_cols=17 Identities=18% Similarity=0.317 Sum_probs=10.6
Q ss_pred HHHHHHHhccchhhhhh
Q 028075 115 ATKLLQRFGYSVSAMKT 131 (214)
Q Consensus 115 A~KLlQR~n~S~S~Mkt 131 (214)
.++.|+++|+|+.-+|.
T Consensus 49 ~I~~lr~~G~sL~eI~~ 65 (127)
T TIGR02044 49 LISRARQVGFSLEECKE 65 (127)
T ss_pred HHHHHHHCCCCHHHHHH
Confidence 45566666666666664
No 66
>PF10147 CR6_interact: Growth arrest and DNA-damage-inducible proteins-interacting protein 1; InterPro: IPR018472 Members of this family of proteins act as negative regulators of G1 to S cell cycle phase progression by inhibiting cyclin-dependent kinases. Inhibitory effects are additive with GADD45 proteins but occur also in the absence of GADD45 proteins. Furthermore, they act as a repressor of the orphan nuclear receptor NR4A1 by inhibiting AB domain-mediated transcriptional activity []. They may be involved in the hormone-mediated regulation of NR4A1 transcriptional activity.; GO: 0007049 cell cycle, 0005634 nucleus
Probab=30.83 E-value=2.4e+02 Score=25.13 Aligned_cols=53 Identities=30% Similarity=0.523 Sum_probs=36.9
Q ss_pred hHHHHHHHHHhHHHHHHHHHHHHHHHHHHhHHH-------------------------HHHHHHHHHHHHHhccchhh
Q 028075 76 PKVLLELFSMYRDWQEEKAKQISKRQEEIENKI-------------------------EVADALATKLLQRFGYSVSA 128 (214)
Q Consensus 76 p~v~~ELfS~YreWQe~~a~~isk~QeeienkI-------------------------E~adalA~KLlQR~n~S~S~ 128 (214)
|..+.++.-.+++=++++.+.+..++++|..+. +.-+.|.-..-.+|||-++.
T Consensus 98 ~~sl~em~k~~~~~~~~k~~k~~~Rek~Ia~nM~Kmpk~i~e~~~~~~kk~~~~~~~k~rkerl~eEvre~fGy~vDp 175 (217)
T PF10147_consen 98 PPSLQEMLKELREKKEEKEEKRLAREKEIAKNMAKMPKWIAEWKAKIAKKEAKAQAAKERKERLIEEVREHFGYKVDP 175 (217)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcCCC
Confidence 456777777777777777777777777776543 23345556677899998764
No 67
>PF04156 IncA: IncA protein; InterPro: IPR007285 Chlamydia trachomatis is an obligate intracellular bacterium that develops within a parasitophorous vacuole termed an inclusion. The inclusion is nonfusogenic with lysosomes but intercepts lipids from a host cell exocytic pathway. Initiation of chlamydial development is concurrent with modification of the inclusion membrane by a set of C. trachomatis-encoded proteins collectively designated Incs. One of these Incs, IncA (Inclusion membrane protein A), is functionally associated with the homotypic fusion of inclusions [].
Probab=30.59 E-value=2.8e+02 Score=22.16 Aligned_cols=38 Identities=24% Similarity=0.330 Sum_probs=24.2
Q ss_pred hhhhhhhccccchhhhHhhh---hhHHHHHHhhhHHHHHHH
Q 028075 130 KTSSQHLSEVHALQVEIGEL---KGRLTEVISNCDALCKRI 167 (214)
Q Consensus 130 ktts~hL~~V~~LqvevgEl---KgrLteVisncdaLCKRI 167 (214)
+.-.+....|..+..++.++ +.+|.+.+.+..++.+|+
T Consensus 151 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~l~~~~ 191 (191)
T PF04156_consen 151 KELQDSREEVQELRSQLERLQENLQQLEEKIQELQELLEQL 191 (191)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 34445555566666666555 667777777777777763
No 68
>PF11348 DUF3150: Protein of unknown function (DUF3150); InterPro: IPR021496 This bacterial family of proteins with unknown function appears to be restricted to Proteobacteria.
Probab=30.51 E-value=1.3e+02 Score=26.56 Aligned_cols=90 Identities=18% Similarity=0.322 Sum_probs=54.4
Q ss_pred HHHHHHHHHhHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHH----------HH--Hhccchhhhhhhhhhhccccchhh
Q 028075 77 KVLLELFSMYRDWQEEKAKQISKRQEEIENKIEVADALATKL----------LQ--RFGYSVSAMKTSSQHLSEVHALQV 144 (214)
Q Consensus 77 ~v~~ELfS~YreWQe~~a~~isk~QeeienkIE~adalA~KL----------lQ--R~n~S~S~Mktts~hL~~V~~Lqv 144 (214)
.+..||=.+=.+|.+++..=+..-...|++-|.-.-..+--+ -. +|+|++-.+...+.| ..-+.|.-
T Consensus 85 ~l~~~L~~i~~eF~~~k~~Fl~~Yd~~i~~w~~~~pew~~~Ir~~~~~~~~v~~r~~F~~~~~~v~~~~~~-~~~~~l~~ 163 (257)
T PF11348_consen 85 ELAEELEDIKTEFEQEKQDFLANYDQAIEEWIDRHPEWADIIRRAAPPAEDVRSRFSFSWQAIKVQPPSDD-GQADGLEE 163 (257)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHChHHHHHHHhcCCCHHHHHhhccceeEEEEecCcccc-cccchHHH
Confidence 345566666667776666666655555555554432222211 12 466766556666556 55678888
Q ss_pred hHhhhhhHH-HHHHhhhHHHHHHH
Q 028075 145 EIGELKGRL-TEVISNCDALCKRI 167 (214)
Q Consensus 145 evgElKgrL-teVisncdaLCKRI 167 (214)
++..|-+.| .||-..|..+-++.
T Consensus 164 ~v~~L~~~l~~Eia~~A~~~~~~~ 187 (257)
T PF11348_consen 164 EVDGLGGQLFDEIAQEARDILEKS 187 (257)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhh
Confidence 888887664 67777787765554
No 69
>cd01111 HTH_MerD Helix-Turn-Helix DNA binding domain of the MerD transcription regulator. Helix-turn-helix (HTH) transcription regulator MerD. The putative secondary regulator of mercury resistance (mer) operons, MerD, has been shown to down-regulate the expression of this operon in gram-negative bacteria. It binds to the same operator DNA as MerR that activates transcription of the operon in the presence of mercury ions. The MerD protein shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily, which promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are conserved and contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules such as metal ions, drugs,
Probab=30.02 E-value=2.5e+02 Score=21.39 Aligned_cols=58 Identities=9% Similarity=0.121 Sum_probs=35.4
Q ss_pred HHHHHHHHHHHHhccchhhhhhhhhhhcc--ccchhhhHhhhhhHHHHHHhhhHHHHHHH
Q 028075 110 VADALATKLLQRFGYSVSAMKTSSQHLSE--VHALQVEIGELKGRLTEVISNCDALCKRI 167 (214)
Q Consensus 110 ~adalA~KLlQR~n~S~S~Mktts~hL~~--V~~LqvevgElKgrLteVisncdaLCKRI 167 (214)
+.....++.|+++|+++..++..-..++. .+.++..+..+..+|.+-+...+.+-..+
T Consensus 44 l~~l~~I~~lr~~G~~l~~I~~~l~~~~~~~~~~~~~~~~~~~~~l~~~~~~L~~l~~~L 103 (107)
T cd01111 44 LQRLRFVRAAFEAGIGLDELARLCRALDAGDGKQPEACLAQLRQKIEVRRAALNALTTQL 103 (107)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHHHhCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34445678888999999988876655432 22455455555556666555555544433
No 70
>PF09537 DUF2383: Domain of unknown function (DUF2383); InterPro: IPR019052 This entry represents a functionally uncharacterised ferritin like domain.; PDB: 3FSE_B.
Probab=29.94 E-value=1.7e+02 Score=21.41 Aligned_cols=50 Identities=16% Similarity=0.280 Sum_probs=34.9
Q ss_pred HHHHHHHHHHHHhccchhhhhhhhhhhccccchhhhHhhhhhHHHHHHhhhHHHHHHHH
Q 028075 110 VADALATKLLQRFGYSVSAMKTSSQHLSEVHALQVEIGELKGRLTEVISNCDALCKRIA 168 (214)
Q Consensus 110 ~adalA~KLlQR~n~S~S~Mktts~hL~~V~~LqvevgElKgrLteVisncdaLCKRI~ 168 (214)
++++| -+|++..+.+...-+.++.+..+ .++|..|++.+..+...+.++.
T Consensus 2 ~i~~L-n~Ll~~~~d~~~~Y~~a~~~~~~--------~~lk~~f~~~~~~~~~~~~~L~ 51 (111)
T PF09537_consen 2 TIEAL-NDLLKGLHDGIEGYEKAAEKAED--------PELKSLFQEFAQERQQHAEELQ 51 (111)
T ss_dssp HHHHH-HHHHHHHHHHHHHHHHHHHH--S--------HHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHH-HHHHHHHHHHHHHHHHHHHHCCC--------HHHHHHHHHHHHHHHHHHHHHH
Confidence 34444 36888889999999999988775 5677888888877766655543
No 71
>cd04784 HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators. Helix-turn-helix (HTH) CadR and PbrR transcription regulators including Pseudomonas aeruginosa CadR and Ralstonia metallidurans PbrR that regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which form a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=29.88 E-value=84 Score=24.06 Aligned_cols=17 Identities=12% Similarity=0.227 Sum_probs=11.2
Q ss_pred HHHHHHHhccchhhhhh
Q 028075 115 ATKLLQRFGYSVSAMKT 131 (214)
Q Consensus 115 A~KLlQR~n~S~S~Mkt 131 (214)
.++.|+.+|+|+.-+|.
T Consensus 49 ~I~~lr~~G~sL~eI~~ 65 (127)
T cd04784 49 FIRRCRSLDMSLDEIRT 65 (127)
T ss_pred HHHHHHHcCCCHHHHHH
Confidence 45666777777766665
No 72
>KOG4302 consensus Microtubule-associated protein essential for anaphase spindle elongation [Cell cycle control, cell division, chromosome partitioning; Cytoskeleton]
Probab=29.85 E-value=4.6e+02 Score=27.05 Aligned_cols=92 Identities=16% Similarity=0.245 Sum_probs=62.6
Q ss_pred HHHHHHHHhHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHhccchhhhh----hhhhhhccccchhhhHhhh----
Q 028075 78 VLLELFSMYRDWQEEKAKQISKRQEEIENKIEVADALATKLLQRFGYSVSAMK----TSSQHLSEVHALQVEIGEL---- 149 (214)
Q Consensus 78 v~~ELfS~YreWQe~~a~~isk~QeeienkIE~adalA~KLlQR~n~S~S~Mk----tts~hL~~V~~LqvevgEl---- 149 (214)
.+++|+--..+--..+..+.++.+..|.+.|.+++|=+.-|++.+|-....-. ....=.++...|...+++|
T Consensus 40 ~l~~le~e~~~~y~~kve~a~~~~~~L~~~ia~~eael~~l~s~l~~~~~~~~~~~k~e~tLke~l~~l~~~le~lr~qk 119 (660)
T KOG4302|consen 40 KLLRLEQECLEIYKRKVEEASESKARLLQEIAVIEAELNDLCSALGEPSIIGEISDKIEGTLKEQLESLKPYLEGLRKQK 119 (660)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccccccccccCccHHHHHHHHHHHHHHHHHHH
Confidence 34555554444445788999999999999999999999999999998765554 2222222222333333444
Q ss_pred ---hhHHHHHHhhhHHHHHHHHh
Q 028075 150 ---KGRLTEVISNCDALCKRIAA 169 (214)
Q Consensus 150 ---KgrLteVisncdaLCKRI~~ 169 (214)
+..+.+|++.-+.||..|.-
T Consensus 120 ~eR~~ef~el~~qie~l~~~l~g 142 (660)
T KOG4302|consen 120 DERRAEFKELYHQIEKLCEELGG 142 (660)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcC
Confidence 34456788888899999863
No 73
>PF01086 Clathrin_lg_ch: Clathrin light chain; InterPro: IPR000996 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. These vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transport []. Clathrin coats contain both clathrin (acts as a scaffold) and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors [, ]. Clathrin is a trimer composed of three heavy chains and three light chains, each monomer projecting outwards like a leg; this three-legged structure is known as a triskelion [, ]. The heavy chains form the legs, their N-terminal beta-propeller regions extending outwards, while their C-terminal alpha-alpha-superhelical regions form the central hub of the triskelion. Peptide motifs can bind between the beta-propeller blades. The light chains appear to have a regulatory role, and may help orient the assembly and disassembly of clathrin coats as they interact with hsc70 uncoating ATPase []. Clathrin triskelia self-polymerise into a curved lattice by twisting individual legs together. The clathrin lattice forms around a vesicle as it buds from the TGN, plasma membrane or endosomes, acting to stabilise the vesicle and facilitate the budding process []. The multiple blades created when the triskelia polymerise are involved in multiple protein interactions, enabling the recruitment of different cargo adaptors and membrane attachment proteins []. This entry represents clathrin light chains, which are more divergent in sequence than the heavy chains []. In higher eukaryotes, two genes encode distinct but related light chains, each of which can yield two separate forms via alternative splicing. In yeast there is a single light chain whose sequence is only distantly related to that of higher eukaryotes. Clathrin light chains have a conserved acidic N-terminal domain, a central coiled-coil domain and a conserved C-terminal domain. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030130 clathrin coat of trans-Golgi network vesicle, 0030132 clathrin coat of coated pit; PDB: 3LVG_E 3LVH_D.
Probab=29.54 E-value=69 Score=27.62 Aligned_cols=53 Identities=30% Similarity=0.391 Sum_probs=39.7
Q ss_pred HHhHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHhc--cchhhhhhhhhhh
Q 028075 84 SMYRDWQEEKAKQISKRQEEIENKIEVADALATKLLQRFG--YSVSAMKTSSQHL 136 (214)
Q Consensus 84 S~YreWQe~~a~~isk~QeeienkIE~adalA~KLlQR~n--~S~S~Mktts~hL 136 (214)
..-|+|+++..++|.+|.++-+.|.+-.-+-|.|=|.-|. |....=++..+|.
T Consensus 112 e~ireWre~~~~~i~ekD~~e~~kk~e~~~~A~k~lddfY~~~~~k~e~~k~~nr 166 (225)
T PF01086_consen 112 EAIREWREERDKRIEEKDAEEEEKKEEIKEKAKKELDDFYENRNEKKEKNKKQNR 166 (225)
T ss_dssp THHHHHHHHHTTTSTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3458999999999999999999888888888988888773 4444334444444
No 74
>PRK10755 sensor protein BasS/PmrB; Provisional
Probab=29.38 E-value=3.4e+02 Score=22.78 Aligned_cols=17 Identities=6% Similarity=0.196 Sum_probs=7.8
Q ss_pred HHhccchhhhhhhhhhh
Q 028075 120 QRFGYSVSAMKTSSQHL 136 (214)
Q Consensus 120 QR~n~S~S~Mktts~hL 136 (214)
..++-.+++|+...+.+
T Consensus 146 HelrtPL~~i~~~~e~l 162 (356)
T PRK10755 146 HELRTPLAGIRLHLELL 162 (356)
T ss_pred HhhcChHHHHHHHHHHH
Confidence 34444445555444443
No 75
>PRK01026 tetrahydromethanopterin S-methyltransferase subunit G; Provisional
Probab=29.21 E-value=81 Score=24.41 Aligned_cols=29 Identities=48% Similarity=0.779 Sum_probs=21.6
Q ss_pred HHHHHHHHHHhHHHHHHHHHHHHHHHHhccch
Q 028075 95 KQISKRQEEIENKIEVADALATKLLQRFGYSV 126 (214)
Q Consensus 95 ~~isk~QeeienkIE~adalA~KLlQR~n~S~ 126 (214)
.++-+|-.+||.|+|-+-+ .+.||+|-.+
T Consensus 18 ~~i~~rLD~iEeKVEftn~---Ei~Qr~Gkkv 46 (77)
T PRK01026 18 KEIQKRLDEIEEKVEFTNA---EIFQRIGKKV 46 (77)
T ss_pred HHHHHHHHHHHHHHHHHHH---HHHHHHhHHh
Confidence 3567888999999987654 6788887543
No 76
>cd08915 V_Alix_like Protein-interacting V-domain of mammalian Alix and related domains. This superfamily contains the V-shaped (V) domain of mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), Bro1 and Rim20 (also known as PalA) from Saccharomyces cerevisiae, and related domains. Alix, HD-PTP, Bro1, and Rim20 all interact with the ESCRT (Endosomal Sorting Complexes Required for Transport) system. Alix, also known as apoptosis-linked gene-2 interacting protein 1 (AIP1), participates in membrane remodeling processes during the budding of enveloped viruses, vesicle budding inside late endosomal multivesicular bodies (MVBs), and the abscission reactions of mammalian cell division. It also functions in apoptosis. HD-PTP functions in cell migration and endosomal trafficking, Bro1 in endosomal trafficking, and Rim20 in the response to the external pH via the Rim101 pathway. The Alix V-domain contains
Probab=28.90 E-value=4.1e+02 Score=23.52 Aligned_cols=46 Identities=26% Similarity=0.364 Sum_probs=35.7
Q ss_pred hHHHHHHHHHhHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHhccchh
Q 028075 76 PKVLLELFSMYRDWQEEKAKQISKRQEEIENKIEVADALATKLLQRFGYSVS 127 (214)
Q Consensus 76 p~v~~ELfS~YreWQe~~a~~isk~QeeienkIE~adalA~KLlQR~n~S~S 127 (214)
|-.+.|.-|+|.|=+..-+. .+|-.++|.++..+...|..+|...+
T Consensus 1 P~~V~ea~s~Y~E~k~~lvr------~e~~~~~e~~~~~l~~~L~slnLP~s 46 (342)
T cd08915 1 PYDVIESASAYNERQDDYVR------EHIVEPIEALNKLLNSFLAERNLPAS 46 (342)
T ss_pred CHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHcCCChH
Confidence 55678999999975544332 34668899999999999999998766
No 77
>PF11472 DUF3206: Protein of unknown function (DUF3206); InterPro: IPR021571 This bacterial family of proteins has no known function. ; PDB: 2AU5_A.
Probab=28.73 E-value=44 Score=27.86 Aligned_cols=29 Identities=14% Similarity=0.068 Sum_probs=21.9
Q ss_pred hHhhhhhHHHHHHhhhHHHHHHHHhcCCc
Q 028075 145 EIGELKGRLTEVISNCDALCKRIAAEGPD 173 (214)
Q Consensus 145 evgElKgrLteVisncdaLCKRI~~eGPe 173 (214)
.+|+|||.++-.|.-|+++.||=-.+.-|
T Consensus 76 ~~~~L~~E~~~Li~LY~~~~~~~LT~N~~ 104 (128)
T PF11472_consen 76 STEQLMDEFNCLINLYFRARQRNLTSNQD 104 (128)
T ss_dssp SHHHHHHHHHHHHHHHHHHHTT---HHHH
T ss_pred cHHHHHHHHHHHHHHHHHHHHhhccccch
Confidence 47899999999999999999985444333
No 78
>KOG4052 consensus Uncharacterized conserved protein [Function unknown]
Probab=28.71 E-value=66 Score=28.48 Aligned_cols=83 Identities=24% Similarity=0.284 Sum_probs=51.1
Q ss_pred HHHHHHHHHHHH-HHhHHHHHHHHHHHHHHHHh---ccchhhhhhhhhhhccccchhhhHhhhhhHHHHHHhhhHHHHHH
Q 028075 91 EEKAKQISKRQE-EIENKIEVADALATKLLQRF---GYSVSAMKTSSQHLSEVHALQVEIGELKGRLTEVISNCDALCKR 166 (214)
Q Consensus 91 e~~a~~isk~Qe-eienkIE~adalA~KLlQR~---n~S~S~Mktts~hL~~V~~LqvevgElKgrLteVisncdaLCKR 166 (214)
+.-|.+...-+. -+-+|-||..-+|+.|=-+| |-|--|.-+.-.-+..-..-.|+-.-.--||.|+..| +|+|
T Consensus 18 lag~~~~~eE~~vrlpsKCEvCkllatEleA~l~eTGks~eVi~~gy~~ld~k~k~~v~Y~rselrl~E~tEn---iCer 94 (190)
T KOG4052|consen 18 LAGAAKCNEETTVRLPSKCEVCKLLATELEAKLEETGKSKEVIEHGYTRLDFKFKWFVLYQRSELRLAEITEN---ICER 94 (190)
T ss_pred hccccccCccccccccchhHHHHHHHHHHHHHHhhcCCcceeeeeceeeecceeeeeeeeehhHhHHHHHHHH---HHHH
Confidence 334444333333 56789999999999998887 3333333222222222222225555555688888876 7888
Q ss_pred H-----HhcCCcccc
Q 028075 167 I-----AAEGPDSLK 176 (214)
Q Consensus 167 I-----~~eGPesLr 176 (214)
+ +.+||.++|
T Consensus 95 ~ley~~hker~gs~r 109 (190)
T KOG4052|consen 95 FLEYKIHKERTGSER 109 (190)
T ss_pred HHHHhhhccCcchhH
Confidence 5 789999886
No 79
>PF04012 PspA_IM30: PspA/IM30 family; InterPro: IPR007157 This family includes PspA a protein that suppresses sigma54-dependent transcription. The PspA protein, a negative regulator of the Escherichia coli phage shock psp operon, is produced when virulence factors are exported through secretins in many Gram-negative pathogenic bacteria and its homologue in plants, VIPP1, plays a critical role in thylakoid biogenesis, essential for photosynthesis. Activation of transcription by the enhancer-dependent bacterial sigma54-containing RNA polymerase occurs through ATP hydrolysis-driven protein conformational changes enabled by activator proteins that belong to the large AAA(+) mechanochemical protein family. It has been shown that PspA directly and specifically acts upon and binds to the AAA(+) domain of the PspF transcription activator [].
Probab=28.44 E-value=3.4e+02 Score=22.37 Aligned_cols=95 Identities=25% Similarity=0.311 Sum_probs=53.4
Q ss_pred CCChHHHHHHH-----HHhHHHHHHHHHHHH-------------HHHHHHhHHHHHH-----HHHHHHHHHHhccchhhh
Q 028075 73 TVNPKVLLELF-----SMYRDWQEEKAKQIS-------------KRQEEIENKIEVA-----DALATKLLQRFGYSVSAM 129 (214)
Q Consensus 73 ~~np~v~~ELf-----S~YreWQe~~a~~is-------------k~QeeienkIE~a-----dalA~KLlQR~n~S~S~M 129 (214)
.-||..+++.+ .-|.+++...|..+. +.-++.+.+.+.| |.||...|+|-+.--.-+
T Consensus 21 ~EDP~~~l~q~ird~e~~l~~a~~~~a~~~a~~~~le~~~~~~~~~~~~~~~~A~~Al~~g~edLAr~al~~k~~~e~~~ 100 (221)
T PF04012_consen 21 AEDPEKMLEQAIRDMEEQLRKARQALARVMANQKRLERKLDEAEEEAEKWEKQAELALAAGREDLAREALQRKADLEEQA 100 (221)
T ss_pred hcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHH
Confidence 45888777643 345555554443332 2233444555555 568888887765533332
Q ss_pred hhh----hhhhccccchhhhHhhhhhHHHHHHhhhHHHHHHH
Q 028075 130 KTS----SQHLSEVHALQVEIGELKGRLTEVISNCDALCKRI 167 (214)
Q Consensus 130 ktt----s~hL~~V~~LqvevgElKgrLteVisncdaLCKRI 167 (214)
-.- ...-..|..|+-.+.+|+.+|.++=.+.+.|--|-
T Consensus 101 ~~l~~~~~~~~~~~~~l~~~l~~l~~kl~e~k~k~~~l~ar~ 142 (221)
T PF04012_consen 101 ERLEQQLDQAEAQVEKLKEQLEELEAKLEELKSKREELKARE 142 (221)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 222 22234456677777777777777777776665544
No 80
>cd01108 HTH_CueR Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators. Helix-turn-helix (HTH) transcription regulators CueR and ActP, copper efflux regulators. In Bacillus subtilis, copper induced CueR regulates the copZA operon, preventing copper toxicity. In Rhizobium leguminosarum, ActP controls copper homeostasis; it detects cytoplasmic copper stress and activates transcription in response to increasing copper concentrations. These proteins are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have two conserved cysteines that define a monovalent copper ion binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements
Probab=27.86 E-value=89 Score=24.13 Aligned_cols=18 Identities=11% Similarity=0.344 Sum_probs=11.8
Q ss_pred HHHHHHHhccchhhhhhh
Q 028075 115 ATKLLQRFGYSVSAMKTS 132 (214)
Q Consensus 115 A~KLlQR~n~S~S~Mktt 132 (214)
-++.|+.+|+|+.-||.-
T Consensus 49 ~I~~lr~~G~sL~eI~~~ 66 (127)
T cd01108 49 FIRRARDLGFSLEEIREL 66 (127)
T ss_pred HHHHHHHcCCCHHHHHHH
Confidence 456667777777776653
No 81
>PF03938 OmpH: Outer membrane protein (OmpH-like); InterPro: IPR005632 This entry includes outer membrane proteins such as OmpH (Skp) among others. OmpH (outer membrane protein H) is a major structural protein of the outer membrane. In Pasteurella multocida it acts as a channel-forming transmembrane porin []. Porins act as molecular sieves to allow the diffusion of small hydrophilic solutes through the outer membrane and also acts as a receptor for bacteriophages and bacteriocins. Porins are highly immunogenic and are conserved in bacterial families, making them attractive vaccine candidates []. The 17kDa protein (Skp, OmpH) of Escherichia coli is a homotrimeric periplasmic chaperone for newly synthesised outer-membrane proteins, the X-ray structure of which has been reported at resolutions of 2.35 A and 2.30 A [, ]. Three hairpin-shaped alpha-helical extensions reach out by approximately 60 A from a trimerisation domain, which is composed of three intersubunit beta-sheets that wind around a central axis. The alpha-helical extensions approach each other at their distal turns, resulting in a fold that resembles a 'three-pronged grasping forcep'. The overall shape of Skp is reminiscent of the cytosolic chaperone prefoldin (IPR009053 from INTERPRO), although it is based on a radically different topology. The peculiar architecture, with apparent plasticity of the prongs and distinct electrostatic and hydrophobic surface properties, supports the recently proposed biochemical mechanism of this chaperone: formation of a Skp(3)-Omp complex protects the outer membrane protein from aggregation during passage through the bacterial periplasm. The ability of Skp to prevent the aggregation of model substrates in vitro is independent of ATP. Skp can interact directly with membrane lipids and lipopolysaccharide. These interactions are needed for efficient Skp-assisted folding of membrane proteins [].; GO: 0051082 unfolded protein binding; PDB: 1SG2_C 1U2M_C.
Probab=27.13 E-value=2.4e+02 Score=21.76 Aligned_cols=47 Identities=17% Similarity=0.159 Sum_probs=33.2
Q ss_pred CCCCChHHHHHHHHHhHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Q 028075 71 SGTVNPKVLLELFSMYRDWQEEKAKQISKRQEEIENKIEVADALATK 117 (214)
Q Consensus 71 S~~~np~v~~ELfS~YreWQe~~a~~isk~QeeienkIE~adalA~K 117 (214)
=|.||...+++=+..|.+.++.--++..+.|.+++.+-.-.+++.-+
T Consensus 19 Ia~Vd~~~v~~~~~~~k~~~~~l~~~~~~~~~~l~~~~~el~~~~~~ 65 (158)
T PF03938_consen 19 IAVVDVDKVFQESPAGKDAQAKLQEKFKALQKELQAKQKELQKLQQK 65 (158)
T ss_dssp EEEE-HHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred EEEeeHHHHHHhCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35789999888888888888777777777777776666665554433
No 82
>PRK11115 transcriptional regulator PhoU; Provisional
Probab=26.99 E-value=3e+02 Score=22.37 Aligned_cols=42 Identities=12% Similarity=0.207 Sum_probs=29.5
Q ss_pred HHHHHHHhHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHH
Q 028075 79 LLELFSMYRDWQEEKAKQISKRQEEIENKIEVADALATKLLQ 120 (214)
Q Consensus 79 ~~ELfS~YreWQe~~a~~isk~QeeienkIE~adalA~KLlQ 120 (214)
+-..+.+|.....+.+++|.++.++|..--.-+....++++.
T Consensus 36 l~~~~~al~~~d~~~~~~i~~~e~~id~l~~~I~~~l~~~l~ 77 (236)
T PRK11115 36 LSDAITAMHNQDAELAKRVIEGDHKVNMMEVAIDEACVRIIA 77 (236)
T ss_pred HHHHHHHHHhCCHHHHHHHHHChHHHHHHHHHHHHHHHHHHH
Confidence 345677788888888999988888776655555555666653
No 83
>TIGR01149 mtrG N5-methyltetrahydromethanopterin:coenzyme M methyltransferase subunit G. coenzyme M methyltransferase subunit G in methanogenic archaea. This methyltranfersae is membrane-associated enzyme complex that uses methyl-transfer reaction to drive sodium-ion pump. Archaea have evolved energy-yielding pathways marked by one-carbon biochemistry featuring novel cofactors and enzymes. This transferase is involved in the transfer of 'methyl' group from N5-methyltetrahydromethanopterin to coenzyme M. In an accompanying reaction, methane is produced by two-electron reduction of the methyl moiety in methyl-coenzyme M by another enzyme methyl-coenzyme M reductase.
Probab=26.84 E-value=97 Score=23.72 Aligned_cols=29 Identities=38% Similarity=0.629 Sum_probs=20.9
Q ss_pred HHHHHHHHHHhHHHHHHHHHHHHHHHHhccch
Q 028075 95 KQISKRQEEIENKIEVADALATKLLQRFGYSV 126 (214)
Q Consensus 95 ~~isk~QeeienkIE~adalA~KLlQR~n~S~ 126 (214)
.++-+|-.+||.|+|-+- -.+.||+|-.+
T Consensus 15 ~~i~~rLd~iEeKVEf~~---~E~~Qr~Gkk~ 43 (70)
T TIGR01149 15 NEVMKRLDEIEEKVEFVN---GEVAQRIGKKV 43 (70)
T ss_pred HHHHHHHHHHHHHHHHHH---HHHHHHHhHHh
Confidence 356678889999988764 46788887543
No 84
>PF09447 Cnl2_NKP2: Cnl2/NKP2 family protein; InterPro: IPR018565 This entry includes the Cnl2 kinetochore protein [].
Probab=25.99 E-value=1.2e+02 Score=22.61 Aligned_cols=25 Identities=32% Similarity=0.594 Sum_probs=22.0
Q ss_pred HHHhHHHHHHHHHHHHHHHHHHhHH
Q 028075 83 FSMYRDWQEEKAKQISKRQEEIENK 107 (214)
Q Consensus 83 fS~YreWQe~~a~~isk~Qeeienk 107 (214)
=.+||+-|...++.+.+-.+.|+.-
T Consensus 40 r~LYr~Lq~qR~~~~d~V~~nI~~e 64 (67)
T PF09447_consen 40 RSLYRDLQAQREQVLDKVRENIDQE 64 (67)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4799999999999999999888754
No 85
>PF09731 Mitofilin: Mitochondrial inner membrane protein; InterPro: IPR019133 Mitofilin controls mitochondrial cristae morphology. Mitofilin is enriched in the narrow space between the inner boundary and the outer membranes, where it forms a homotypic interaction and assembles into a large multimeric protein complex []. The first 78 amino acids contain a typical amino-terminal-cleavable mitochondrial presequence (residues 1-43) rich in positive-charged and hydroxylated residues and a membrane anchor domain (residues 47-66). In addition, it has three centrally located coiled coil domains (residues 200-240,280-310 and 400-420) []. ; GO: 0031305 integral to mitochondrial inner membrane
Probab=25.94 E-value=5.2e+02 Score=24.49 Aligned_cols=87 Identities=17% Similarity=0.257 Sum_probs=50.4
Q ss_pred HHHHHHHHHHHHHHHHHhHHHH----------------HHHHHHHHHHHHhccchh--hhhhhhhhhccccchhhhHhhh
Q 028075 88 DWQEEKAKQISKRQEEIENKIE----------------VADALATKLLQRFGYSVS--AMKTSSQHLSEVHALQVEIGEL 149 (214)
Q Consensus 88 eWQe~~a~~isk~QeeienkIE----------------~adalA~KLlQR~n~S~S--~Mktts~hL~~V~~LqvevgEl 149 (214)
+|+.+-..++.+.++..+.+++ ++...++.|-.+|+..+. +-+--..|+..+..|+..|..|
T Consensus 311 ~~~~e~~~~~~~l~~~~~~~L~~eL~~~~~~~~~~l~~~l~~~~~e~~~~~~~~i~~~v~~Er~~~~~~l~~~~~~~~~l 390 (582)
T PF09731_consen 311 ELREEFEREREELEEKYEEELRQELKRQEEAHEEHLKNELREQAIELQREFEKEIKEKVEQERNGRLAKLAELNSRLKAL 390 (582)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5555555555555444444433 334455566666665442 3344456777777777777777
Q ss_pred hhHHH-------------HHHhhhHHHHHHHHhcCCcc
Q 028075 150 KGRLT-------------EVISNCDALCKRIAAEGPDS 174 (214)
Q Consensus 150 KgrLt-------------eVisncdaLCKRI~~eGPes 174 (214)
...+. .+..-|++|-..|....+..
T Consensus 391 e~~~~~~~~~~~~~~~~~~l~~a~~~l~~~l~~~~~~~ 428 (582)
T PF09731_consen 391 EEALDARSEAEDENRRAQQLWLAVDALKSALDSGNAGS 428 (582)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcC
Confidence 65443 33356888877777765543
No 86
>PF06401 Alpha-2-MRAP_C: Alpha-2-macroglobulin RAP, C-terminal domain ; InterPro: IPR010483 The alpha-2-macroglobulin receptor-associated protein (RAP) is a intracellular glycoprotein that binds to the 2-macroglobulin receptor and other members of the low density lipoprotein receptor family. The protein inhibits binding of all currently known ligands of these receptors []. Two different studies have provided conflicting domain boundaries.; GO: 0008201 heparin binding, 0050750 low-density lipoprotein particle receptor binding, 0005783 endoplasmic reticulum; PDB: 2FCW_A 2P03_A 2FTU_A 2P01_A.
Probab=25.70 E-value=1e+02 Score=27.47 Aligned_cols=32 Identities=34% Similarity=0.592 Sum_probs=27.0
Q ss_pred hhhhHhhhhhHHHHHHhhhHHHHHHHHhcCCcc
Q 028075 142 LQVEIGELKGRLTEVISNCDALCKRIAAEGPDS 174 (214)
Q Consensus 142 LqvevgElKgrLteVisncdaLCKRI~~eGPes 174 (214)
+..-..+||.+..++-.+||.| .|+..+||..
T Consensus 74 ~~~k~~~Lk~k~r~i~~~~drL-~r~~~~g~~~ 105 (214)
T PF06401_consen 74 LHEKHNELKEKHREINDGYDRL-RRVSHQGPNS 105 (214)
T ss_dssp CHHHHHHHHHHHHHHHHHHHHH-HHHHHTSSSS
T ss_pred HHHHHHHHHHHHHHHHHHHHHH-HHHHhcCCCc
Confidence 3444678999999999999999 5799999974
No 87
>PF05529 Bap31: B-cell receptor-associated protein 31-like ; InterPro: IPR008417 Bap31 is a polytopic integral protein of the endoplasmic reticulum membrane and a substrate of caspase-8. Bap31 is cleaved within its cytosolic domain, generating pro-apoptotic p20 Bap31 [].; GO: 0006886 intracellular protein transport, 0005783 endoplasmic reticulum, 0016021 integral to membrane
Probab=25.57 E-value=3.7e+02 Score=21.90 Aligned_cols=35 Identities=29% Similarity=0.239 Sum_probs=29.8
Q ss_pred hhccccchhhhHhhhhhHHHHHHhhhHHHHHHHHh
Q 028075 135 HLSEVHALQVEIGELKGRLTEVISNCDALCKRIAA 169 (214)
Q Consensus 135 hL~~V~~LqvevgElKgrLteVisncdaLCKRI~~ 169 (214)
.-++...++-||.++|..|...-.+.++|-|.++.
T Consensus 152 ~~~~~~~~~~ei~~lk~el~~~~~~~~~LkkQ~~~ 186 (192)
T PF05529_consen 152 LKEENKKLSEEIEKLKKELEKKEKEIEALKKQSEG 186 (192)
T ss_pred hhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44566788999999999999999999999888764
No 88
>PRK10869 recombination and repair protein; Provisional
Probab=25.51 E-value=6.3e+02 Score=24.53 Aligned_cols=95 Identities=14% Similarity=0.297 Sum_probs=0.0
Q ss_pred ChHHHHHHHHHhHHHHHH---------HHHHHHHHHHHHhHHHHHHHHH-------------------HHHHHHHhccch
Q 028075 75 NPKVLLELFSMYRDWQEE---------KAKQISKRQEEIENKIEVADAL-------------------ATKLLQRFGYSV 126 (214)
Q Consensus 75 np~v~~ELfS~YreWQe~---------~a~~isk~QeeienkIE~adal-------------------A~KLlQR~n~S~ 126 (214)
+...+.++=..|++|++. ..++..++.+.+++.|+-.+++ +-||.+..+...
T Consensus 152 ~~~~~~~~~~~y~~~~~~~~~l~~l~~~~~~~~~~~d~l~fql~Ei~~~~l~~gE~eeL~~e~~~L~n~e~i~~~~~~~~ 231 (553)
T PRK10869 152 ETSLLQEMRAAYQLWHQSCRDLAQHQQQSQERAARKQLLQYQLKELNEFAPQPGEFEQIDEEYKRLANSGQLLTTSQNAL 231 (553)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_pred hhhhh---hh---------hhhccccchhhhHhhhhhHHHHHHhhhHHHHHHHHh
Q 028075 127 SAMKT---SS---------QHLSEVHALQVEIGELKGRLTEVISNCDALCKRIAA 169 (214)
Q Consensus 127 S~Mkt---ts---------~hL~~V~~LqvevgElKgrLteVisncdaLCKRI~~ 169 (214)
..+.. .+ +.|+.+..+.-++.++-.+|.++..+.+.++..+..
T Consensus 232 ~~L~~~~~~~~~~~l~~~~~~l~~~~~~d~~~~~~~~~l~~~~~~l~~~~~~l~~ 286 (553)
T PRK10869 232 QLLADGEEVNILSQLYSAKQLLSELIGMDSKLSGVLDMLEEALIQIQEASDELRH 286 (553)
T ss_pred HHhcCCCcccHHHHHHHHHHHHHHHhhhCHhHHHHHHHHHHHHHHHHHHHHHHHH
No 89
>TIGR02051 MerR Hg(II)-responsive transcriptional regulator. This model represents the mercury (II) responsive transcriptional activator of the mer organomercurial resistance operon. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(8)-Cys-Pro, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=25.42 E-value=2.8e+02 Score=21.31 Aligned_cols=22 Identities=18% Similarity=0.137 Sum_probs=15.4
Q ss_pred HHHHHHHHhccchhhhhhhhhh
Q 028075 114 LATKLLQRFGYSVSAMKTSSQH 135 (214)
Q Consensus 114 lA~KLlQR~n~S~S~Mktts~h 135 (214)
-.++.|+.+|+|+..||.--..
T Consensus 47 ~~I~~l~~~G~sl~eI~~~l~~ 68 (124)
T TIGR02051 47 RFIKRAQELGFSLEEIGGLLGL 68 (124)
T ss_pred HHHHHHHHCCCCHHHHHHHHhc
Confidence 4566778888888888765543
No 90
>cd04779 HTH_MerR-like_sg4 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 4). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=25.16 E-value=3.4e+02 Score=21.78 Aligned_cols=26 Identities=12% Similarity=0.109 Sum_probs=18.1
Q ss_pred HHHHHHHHHHhccchhhhhhhhhhhc
Q 028075 112 DALATKLLQRFGYSVSAMKTSSQHLS 137 (214)
Q Consensus 112 dalA~KLlQR~n~S~S~Mktts~hL~ 137 (214)
...-++.|+.+|+|+.-+|.--....
T Consensus 45 ~l~~I~~lr~~G~sL~eI~~~l~~~~ 70 (134)
T cd04779 45 RLQLIEHLKGQRLSLAEIKDQLEEVQ 70 (134)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHHhhc
Confidence 34456778888999888887554443
No 91
>PRK05431 seryl-tRNA synthetase; Provisional
Probab=24.93 E-value=3.1e+02 Score=25.76 Aligned_cols=83 Identities=22% Similarity=0.356 Sum_probs=45.1
Q ss_pred HHHHHHHhHHHHHHH--HHHHHHHHHHHhHHHHHHHHHHHHHHHHhccchhhhhhhhhhhccccchhhhHhhhhhHHHHH
Q 028075 79 LLELFSMYRDWQEEK--AKQISKRQEEIENKIEVADALATKLLQRFGYSVSAMKTSSQHLSEVHALQVEIGELKGRLTEV 156 (214)
Q Consensus 79 ~~ELfS~YreWQe~~--a~~isk~QeeienkIE~adalA~KLlQR~n~S~S~Mktts~hL~~V~~LqvevgElKgrLteV 156 (214)
+-++.++|.+|.+.. .+++.+++.++..+|-. +.+. +- -...-..++..|+.+|.+++..+.++
T Consensus 27 vd~i~~ld~~~r~l~~~~~~lr~~rn~~sk~i~~-------~~~~-~~------~~~~l~~~~~~l~~~~~~~~~~~~~~ 92 (425)
T PRK05431 27 VDELLELDEERRELQTELEELQAERNALSKEIGQ-------AKRK-GE------DAEALIAEVKELKEEIKALEAELDEL 92 (425)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------Hhhc-CC------cHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 557888999998753 34444445555555422 0000 00 01123334455666666666666666
Q ss_pred HhhhHHHHHHHHhcCCccccccc
Q 028075 157 ISNCDALCKRIAAEGPDSLKASI 179 (214)
Q Consensus 157 isncdaLCKRI~~eGPesLr~sv 179 (214)
-.+-+.++-+| |-.+...|
T Consensus 93 ~~~~~~~~~~i----PN~~~~~v 111 (425)
T PRK05431 93 EAELEELLLRI----PNLPHDSV 111 (425)
T ss_pred HHHHHHHHHhC----CCCCCccC
Confidence 66666666665 55555554
No 92
>PRK14096 pgi glucose-6-phosphate isomerase; Provisional
Probab=24.91 E-value=1.8e+02 Score=28.74 Aligned_cols=44 Identities=23% Similarity=0.324 Sum_probs=32.1
Q ss_pred CCCCCCCCCCChHHHHHHHHHhHH--------------------HHHHHHHHHHHHHHHHhHHH
Q 028075 65 SSTSSASGTVNPKVLLELFSMYRD--------------------WQEEKAKQISKRQEEIENKI 108 (214)
Q Consensus 65 ~ssSs~S~~~np~v~~ELfS~Yre--------------------WQe~~a~~isk~QeeienkI 108 (214)
||.+=.-..+||.++=+||.+|.- .=+..|.+|-+.|..|+...
T Consensus 409 Ps~~I~l~~l~p~~lGaLialyE~~v~~~g~l~~IN~FDQpGVE~GK~~a~~il~~~~~~~~~~ 472 (528)
T PRK14096 409 QSITITIPEVNPRTLGALIALFERAVGLYASLVNINAYHQPGVEAGKKAAAAILDLQKKVEELL 472 (528)
T ss_pred CeEEEEeCCCCHHHHHHHHHHHHHHHHHhhhccCcCCCCCccHHHHHHHHHHHHHHHHHHHHHH
Confidence 333333347899999999999976 66777888877777766543
No 93
>cd04765 HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=24.37 E-value=78 Score=23.83 Aligned_cols=21 Identities=29% Similarity=0.444 Sum_probs=16.0
Q ss_pred HHH-HHHHhccchhhhhhhhhh
Q 028075 115 ATK-LLQRFGYSVSAMKTSSQH 135 (214)
Q Consensus 115 A~K-LlQR~n~S~S~Mktts~h 135 (214)
.++ ||+..|+++..||.--.+
T Consensus 49 ~I~~llr~~G~~l~~i~~~l~~ 70 (99)
T cd04765 49 LIKHLLYEKGYTIEGAKQALKE 70 (99)
T ss_pred HHHHHHHHCCCCHHHHHHHHHh
Confidence 455 678999999999875544
No 94
>PRK03692 putative UDP-N-acetyl-D-mannosaminuronic acid transferase; Provisional
Probab=24.35 E-value=77 Score=27.76 Aligned_cols=51 Identities=22% Similarity=0.272 Sum_probs=36.3
Q ss_pred HhHHHHHHHHHHHHHHHHhccchhhhhhhhhhhccccchhhhHhhhhhHHHHHHhhhHHHHHHHHhcCCccc
Q 028075 104 IENKIEVADALATKLLQRFGYSVSAMKTSSQHLSEVHALQVEIGELKGRLTEVISNCDALCKRIAAEGPDSL 175 (214)
Q Consensus 104 ienkIE~adalA~KLlQR~n~S~S~Mktts~hL~~V~~LqvevgElKgrLteVisncdaLCKRI~~eGPesL 175 (214)
+|-+=++++.++.+|-++||..+..+. | .|.. -..+++++++|++-|||.|
T Consensus 111 lG~~~~v~~~a~~~l~~~y~l~i~g~~----~----Gyf~-------------~~e~~~i~~~I~~s~~dil 161 (243)
T PRK03692 111 VGGKPEVLAQTEAKLRTQWNVNIVGSQ----D----GYFT-------------PEQRQALFERIHASGAKIV 161 (243)
T ss_pred ECCCHHHHHHHHHHHHHHhCCEEEEEe----C----CCCC-------------HHHHHHHHHHHHhcCCCEE
Confidence 566778999999999888876653332 1 2322 1246789999999999986
No 95
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=23.80 E-value=3.3e+02 Score=20.80 Aligned_cols=28 Identities=21% Similarity=0.179 Sum_probs=19.6
Q ss_pred chhhhHhhhhhHHHHHHhhhHHHHHHHH
Q 028075 141 ALQVEIGELKGRLTEVISNCDALCKRIA 168 (214)
Q Consensus 141 ~LqvevgElKgrLteVisncdaLCKRI~ 168 (214)
.++.|+.+|+..+.+.--..|-|=|-++
T Consensus 75 ~~~~ei~~L~~el~~L~~E~diLKKa~~ 102 (121)
T PRK09413 75 AAMKQIKELQRLLGKKTMENELLKEAVE 102 (121)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3677788888888777777776655543
No 96
>PF10157 DUF2365: Uncharacterized conserved protein (DUF2365); InterPro: IPR019314 This entry is found in a highly conserved family of proteins which have no known function.
Probab=23.48 E-value=4.4e+02 Score=22.04 Aligned_cols=80 Identities=19% Similarity=0.270 Sum_probs=45.3
Q ss_pred CCCCChHHHHHHHHHhHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHhccchh-----------hhhhh-------
Q 028075 71 SGTVNPKVLLELFSMYRDWQEEKAKQISKRQEEIENKIEVADALATKLLQRFGYSVS-----------AMKTS------- 132 (214)
Q Consensus 71 S~~~np~v~~ELfS~YreWQe~~a~~isk~QeeienkIE~adalA~KLlQR~n~S~S-----------~Mktt------- 132 (214)
-+.+||+++..|=.-= ..-|+.+.-.=+.+.+-+.-.-++-+..+|=|+.++. .|.+-
T Consensus 46 ~P~id~~~L~~LE~~a----~~ia~svd~ll~~L~~~L~~mS~~Tv~~~~~y~~sv~~~cdsvD~sik~~y~liakceEL 121 (149)
T PF10157_consen 46 IPPIDPAVLHDLERDA----QAIAESVDSLLRSLRSSLHSMSAITVEHMETYKDSVDKLCDSVDASIKSMYTLIAKCEEL 121 (149)
T ss_pred CCcccHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3458999887762211 1223334444455555555666666666666665543 34333
Q ss_pred hhhhccccchhhhHhhhhhHHH
Q 028075 133 SQHLSEVHALQVEIGELKGRLT 154 (214)
Q Consensus 133 s~hL~~V~~LqvevgElKgrLt 154 (214)
...+..|+.|.-+|+++|+-|.
T Consensus 122 n~~M~~v~~La~qIK~Ik~~lD 143 (149)
T PF10157_consen 122 NESMKPVYKLAQQIKDIKKLLD 143 (149)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 2344566777777777776554
No 97
>cd04785 HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators. Helix-turn-helix (HTH) CadR- and PbrR-like transcription regulators. CadR and PbrR regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which comprise a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=22.99 E-value=1.6e+02 Score=22.69 Aligned_cols=19 Identities=11% Similarity=0.300 Sum_probs=11.5
Q ss_pred HHHHHHHHhccchhhhhhh
Q 028075 114 LATKLLQRFGYSVSAMKTS 132 (214)
Q Consensus 114 lA~KLlQR~n~S~S~Mktt 132 (214)
-.++.|+.+|+|+.-+|.-
T Consensus 48 ~~I~~lr~~G~sL~eI~~~ 66 (126)
T cd04785 48 RFIRRARDLGFSLEEIRAL 66 (126)
T ss_pred HHHHHHHHCCCCHHHHHHH
Confidence 3455666677776666643
No 98
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=22.91 E-value=6.1e+02 Score=26.49 Aligned_cols=85 Identities=24% Similarity=0.350 Sum_probs=46.3
Q ss_pred HHHHHHHHHhccchh--------hhhhhhhhhccccchhhhHhhhhhHHHHHHhh-hHHHHHHHHhc-CCcccccccCcc
Q 028075 113 ALATKLLQRFGYSVS--------AMKTSSQHLSEVHALQVEIGELKGRLTEVISN-CDALCKRIAAE-GPDSLKASIKPL 182 (214)
Q Consensus 113 alA~KLlQR~n~S~S--------~Mktts~hL~~V~~LqvevgElKgrLteVisn-cdaLCKRI~~e-GPesLr~sv~pf 182 (214)
.|+.-|+.++|.... +-+.+-..|.+.|++=-.|-|.+ .|+..++. +|.|-+-|... | -+++++...
T Consensus 545 Ql~~~Lf~~lgl~~~kktktg~ST~~~vL~~L~~~hp~~~~ileyR-~l~Kl~sty~~~l~~~i~~~tg--RIh~~~~q~ 621 (887)
T TIGR00593 545 QLGEVLFEKLGLPVGKKTKTGYSTDADVLEKLREKHPIIALILEYR-QLTKLKSTYVDGLPELVNPDTG--RIHTTFNQT 621 (887)
T ss_pred HHHHHHHHhCCCCCCCCCCCCCCChHHHHHHhhhcCcHHHHHHHHH-HHHHHHHHHHHHHHHHhcCCCC--ceeeeeEec
Confidence 455567778877632 22223334445566533444444 35555555 67777766533 3 577777777
Q ss_pred ccccCCCcccccCCcccccC
Q 028075 183 AVTTTRSEVSCSSSSLQKDD 202 (214)
Q Consensus 183 s~a~~~~~~~~~~~~~~~~~ 202 (214)
.++| -+.+++...+|...
T Consensus 622 ~t~T--GRlSs~~PNLQNIP 639 (887)
T TIGR00593 622 GTAT--GRLSSSNPNLQNIP 639 (887)
T ss_pred ccce--eeecccCCCccccC
Confidence 5554 34555555565553
No 99
>PF11172 DUF2959: Protein of unknown function (DUF2959); InterPro: IPR021342 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=22.81 E-value=3.9e+02 Score=23.86 Aligned_cols=49 Identities=22% Similarity=0.407 Sum_probs=32.2
Q ss_pred Hhccchhhhhhhhhhhcc--------ccchhh-----hHhhhhhHHHHHHhhhHHHHHHHHh
Q 028075 121 RFGYSVSAMKTSSQHLSE--------VHALQV-----EIGELKGRLTEVISNCDALCKRIAA 169 (214)
Q Consensus 121 R~n~S~S~Mktts~hL~~--------V~~Lqv-----evgElKgrLteVisncdaLCKRI~~ 169 (214)
||.-=+.+|+.+..-+.- |-+|+- -|+-|||.+..+-.+-++|-+.++.
T Consensus 127 ~Y~~L~~aM~~Ae~km~PVL~~~~D~vL~LKHNLNA~AI~sL~~e~~~~~~di~~Li~~m~~ 188 (201)
T PF11172_consen 127 RYAQLIKAMRRAESKMQPVLAAFRDQVLYLKHNLNAQAIASLQGEFSSIESDISQLIKEMER 188 (201)
T ss_pred HHHHHHHHHHHHHHhcChHHHHHHHHHHHHhccccHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455556677777665543 334443 3677888888888888888777653
No 100
>TIGR00153 conserved hypothetical protein TIGR00153. An apparent homolog with a suggested function is Pit accessory protein from Sinorhizobium meliloti, which may be involved in phosphate (Pi) transport.
Probab=22.72 E-value=4.4e+02 Score=21.79 Aligned_cols=46 Identities=22% Similarity=0.382 Sum_probs=27.6
Q ss_pred HHHHHHHHhHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHhccch
Q 028075 78 VLLELFSMYRDWQEEKAKQISKRQEEIENKIEVADALATKLLQRFGYSV 126 (214)
Q Consensus 78 v~~ELfS~YreWQe~~a~~isk~QeeienkIE~adalA~KLlQR~n~S~ 126 (214)
.+-++|.-|..|....+.+..++=.++|++ ||.+..++.+.++-+.
T Consensus 29 ~L~~~~~~~~~~~~~~~~~~~~~I~~lE~e---aD~i~~~i~~~L~~~f 74 (216)
T TIGR00153 29 LLIKSFELLKSGNNEKDEELRKEIIEIEHE---ADEIKREIRLNLEKGA 74 (216)
T ss_pred HHHHHHHHHHhCCHHHHHHHHHHHHHHHHH---HHHHHHHHHHhCcccc
Confidence 355677777543333444444444555544 7788888888777543
No 101
>cd07603 BAR_ACAPs The Bin/Amphiphysin/Rvs (BAR) domain of ArfGAP with Coiled-coil, ANK repeat and PH domain containing proteins. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. This subfamily is composed of ACAPs (ArfGAP with Coiled-coil, ANK repeat and PH domain containing proteins), which are Arf GTPase activating proteins (GAPs) containing an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, an Arf GAP domain, and C-terminal ankyrin (ANK) repeats. Vertebrates contain at least three members, ACAP1, ACAP2, and ACAP3. ACAP1 and ACAP2 are Arf6-specific GAPs, involved in the regulation of endocytosis, phagocytosis, cell adhesion and migration, by mediating Arf6 signaling. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions.
Probab=22.10 E-value=73 Score=27.11 Aligned_cols=28 Identities=18% Similarity=0.580 Sum_probs=24.4
Q ss_pred cccchhhhHhhhhhHHHHHHhhhHHHHH
Q 028075 138 EVHALQVEIGELKGRLTEVISNCDALCK 165 (214)
Q Consensus 138 ~V~~LqvevgElKgrLteVisncdaLCK 165 (214)
.|+....+|.+|..+|..++..|.+++.
T Consensus 3 ~l~~~E~~~~~l~~~l~kl~K~~~~~~~ 30 (200)
T cd07603 3 SLEQVEADVSELETRLEKLLKLCNGMVD 30 (200)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4667788999999999999999998874
No 102
>TIGR02105 III_needle type III secretion apparatus needle protein. Type III secretion systems translocate proteins, usually virulence factors, out across both inner and outer membranes of certain Gram-negative bacteria and further across the plasma membrane and into the cytoplasm of the host cell. This protein, termed YscF in Yersinia, and EscF, PscF, EprI, etc. in other systems, forms the needle of the injection apparatus.
Probab=21.94 E-value=2.1e+02 Score=21.33 Aligned_cols=23 Identities=30% Similarity=0.595 Sum_probs=17.3
Q ss_pred ChHHHHHH------HHHhHHHHHHHHHHH
Q 028075 75 NPKVLLEL------FSMYRDWQEEKAKQI 97 (214)
Q Consensus 75 np~v~~EL------fS~YreWQe~~a~~i 97 (214)
||..|+|+ ||+||..|--..+-|
T Consensus 33 nP~~La~~Q~~~~qYs~~~n~qSs~iK~i 61 (72)
T TIGR02105 33 DPELMAELQFALNQYSAYYNIESTIVKMI 61 (72)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999998 677777776555444
No 103
>KOG2391 consensus Vacuolar sorting protein/ubiquitin receptor VPS23 [Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=21.92 E-value=7.4e+02 Score=24.08 Aligned_cols=102 Identities=17% Similarity=0.264 Sum_probs=59.2
Q ss_pred cCccccCCCCCCCcccceeeccCCCCCCCCCCChHH-HHHHHHHhHHHHHHHHHH----HHHHHHHHhHHHHHHHHHHHH
Q 028075 43 TTPILTSPPPTESSLTDILVRRSSTSSASGTVNPKV-LLELFSMYRDWQEEKAKQ----ISKRQEEIENKIEVADALATK 117 (214)
Q Consensus 43 a~PiL~spp~~EssLtDILvrk~ssSs~S~~~np~v-~~ELfS~YreWQe~~a~~----isk~QeeienkIE~adalA~K 117 (214)
-+|+=+.||+.-.+--++-...+..-...+.-|+.+ -+++.|.|+|=-+..+++ ....|++|..
T Consensus 171 ~~p~p~p~~~~gas~~~~~~~d~~~~yp~n~~~~~~irasvisa~~eklR~r~eeeme~~~aeq~slkR----------- 239 (365)
T KOG2391|consen 171 KPPLPPPPPPGGASALPYMTDDNAEPYPPNASGKLVIRASVISAVREKLRRRREEEMERLQAEQESLKR----------- 239 (365)
T ss_pred CCCCCCCCCCCccccCcccCCCCCCcCCCCcccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-----------
Confidence 345555555444454455444444434444445444 568889998765544433 2333333322
Q ss_pred HHHHhccchhhhhhhhhhh-ccccchhhhHhhhhhHHHHHHhhhHHHHHHHHh
Q 028075 118 LLQRFGYSVSAMKTSSQHL-SEVHALQVEIGELKGRLTEVISNCDALCKRIAA 169 (214)
Q Consensus 118 LlQR~n~S~S~Mktts~hL-~~V~~LqvevgElKgrLteVisncdaLCKRI~~ 169 (214)
++.-| .+-+.|..+++.|++++-.+=.|||=|-+.++.
T Consensus 240 --------------t~EeL~~G~~kL~~~~etLEqq~~~L~~niDIL~~k~~e 278 (365)
T KOG2391|consen 240 --------------TEEELNIGKQKLVAMKETLEQQLQSLQKNIDILKSKVRE 278 (365)
T ss_pred --------------hHHHHHhhHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHH
Confidence 22222 344567778888888888888999998877765
No 104
>cd07637 BAR_ACAP3 The Bin/Amphiphysin/Rvs (BAR) domain of ArfGAP with Coiled-coil, ANK repeat and PH domain containing protein 3. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. ACAP3 (ArfGAP with Coiled-coil, ANK repeat and PH domain containing protein 3), also called centaurin beta-5, is presumed to be an Arf GTPase activating protein (GAP) based on its similarity to the Arf6-specific GAPs ACAP1 and ACAP2. The specific function of ACAP3 is still unknown. ACAP3 contains an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, an Arf GAP domain, and C-terminal ankyrin (ANK) repeats. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions.
Probab=21.73 E-value=78 Score=27.12 Aligned_cols=29 Identities=10% Similarity=0.486 Sum_probs=25.0
Q ss_pred cccchhhhHhhhhhHHHHHHhhhHHHHHH
Q 028075 138 EVHALQVEIGELKGRLTEVISNCDALCKR 166 (214)
Q Consensus 138 ~V~~LqvevgElKgrLteVisncdaLCKR 166 (214)
.|+.+..+|.||..+|..++.-|.++++-
T Consensus 3 ~~~~~E~~~~~le~~l~kl~K~~~~~~d~ 31 (200)
T cd07637 3 TIDEVETDVVEIEAKLDKLVKLCSGMIEA 31 (200)
T ss_pred hHHHHHhhHHHHHHHHHHHHHHHHHHHHH
Confidence 46677889999999999999999988764
No 105
>PF02601 Exonuc_VII_L: Exonuclease VII, large subunit; InterPro: IPR020579 Exonuclease VII 3.1.11.6 from EC is composed of two nonidentical subunits; one large subunit and 4 small ones []. Exonuclease VII catalyses exonucleolytic cleavage in either 5'-3' or 3'-5' direction to yield 5'-phosphomononucleotides. The large subunit also contains the OB-fold domains (IPR004365 from INTERPRO) that bind to nucleic acids at the N terminus. This entry represents Exonuclease VII, large subunit, C-terminal. ; GO: 0008855 exodeoxyribonuclease VII activity
Probab=21.64 E-value=5.4e+02 Score=22.36 Aligned_cols=46 Identities=15% Similarity=0.246 Sum_probs=31.6
Q ss_pred CCcceeeeecCc--cCcch-----HHHhhhcccccCcccc--CCCCCCCcccceeecc
Q 028075 16 PIDDITTVSYKS--ESVDP-----ILENIKSLKITTPILT--SPPPTESSLTDILVRR 64 (214)
Q Consensus 16 ~~DeITTVse~~--e~~DP-----~LErLkSLkIa~PiL~--spp~~EssLtDILvrk 64 (214)
..|.|-=+++|- |++.+ +.+.+-..+ -||++ +++ +.-+|.|..--.
T Consensus 75 ~~Dviii~RGGGs~eDL~~FN~e~varai~~~~--~PvisaIGHe-~D~ti~D~vAd~ 129 (319)
T PF02601_consen 75 DFDVIIIIRGGGSIEDLWAFNDEEVARAIAASP--IPVISAIGHE-TDFTIADFVADL 129 (319)
T ss_pred cccEEEEecCCCChHHhcccChHHHHHHHHhCC--CCEEEecCCC-CCchHHHHHHHh
Confidence 468888888877 67644 344455544 36887 788 888999976433
No 106
>cd07665 BAR_SNX1 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 1. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. SNX1 is a component of the retromer complex, a membrane coat multimeric complex required for endosomal retrieval of lysosomal hydrolase receptors to the Golgi. The retromer consists of a cargo-recognition subcomplex and a subcomplex formed by a dimer of sorting nexins (SNX1 and/or SNX2), which ensures effcient cargo sorting by facilitating proper membrane localization
Probab=21.46 E-value=5.7e+02 Score=22.59 Aligned_cols=33 Identities=18% Similarity=0.327 Sum_probs=26.5
Q ss_pred cccchhhhHhhhhhHHHHHHhhhHHHHHHHHhc
Q 028075 138 EVHALQVEIGELKGRLTEVISNCDALCKRIAAE 170 (214)
Q Consensus 138 ~V~~LqvevgElKgrLteVisncdaLCKRI~~e 170 (214)
-++.++-||.|++++..+.=..++.++++|..|
T Consensus 160 K~~~a~~Ev~e~e~k~~~a~~~fe~is~~ik~E 192 (234)
T cd07665 160 KLQQAKDEIAEWESRVTQYERDFERISATVRKE 192 (234)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445567889999999988888888888888765
No 107
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=21.33 E-value=1.7e+02 Score=23.20 Aligned_cols=16 Identities=6% Similarity=0.287 Sum_probs=8.9
Q ss_pred HHHHHHhccchhhhhh
Q 028075 116 TKLLQRFGYSVSAMKT 131 (214)
Q Consensus 116 ~KLlQR~n~S~S~Mkt 131 (214)
++.|+.+|+|+.-||.
T Consensus 50 I~~lr~~G~sl~eI~~ 65 (135)
T PRK10227 50 LRQARQVGFNLEESGE 65 (135)
T ss_pred HHHHHHCCCCHHHHHH
Confidence 4555555666555554
No 108
>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=21.25 E-value=3.5e+02 Score=20.22 Aligned_cols=20 Identities=25% Similarity=0.341 Sum_probs=14.1
Q ss_pred HHHHHHHhccchhhhhhhhh
Q 028075 115 ATKLLQRFGYSVSAMKTSSQ 134 (214)
Q Consensus 115 A~KLlQR~n~S~S~Mktts~ 134 (214)
.++.|+.+|+|+..||.--.
T Consensus 49 ~I~~lr~~G~sL~eI~~~l~ 68 (113)
T cd01109 49 FIKCLRNTGMSIKDIKEYAE 68 (113)
T ss_pred HHHHHHHcCCCHHHHHHHHH
Confidence 46677788888887776443
No 109
>cd07653 F-BAR_CIP4-like The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Cdc42-Interacting Protein 4 and similar proteins. F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. This subfamily is composed of Cdc42-Interacting Protein 4 (CIP4), Formin Binding Protein 17 (FBP17), FormiN Binding Protein 1-Like (FNBP1L), and similar proteins. CIP4 and FNBP1L are Cdc42 effectors that bind Wiskott-Aldrich syndrome protein (WASP) and function in endocytosis. CIP4 and FBP17 bind to the Fas ligand and may be implicated in the inflammatory response. CIP4 may also play a role in phagocytosis. Members of this subfamily typically contain an N-terminal F-BAR domain and a C-terminal SH3 domain. In addition, some members such as FNBP1L contain a central Cdc42-binding HR1 domain. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged l
Probab=21.14 E-value=4.9e+02 Score=21.67 Aligned_cols=79 Identities=16% Similarity=0.228 Sum_probs=48.8
Q ss_pred HHhHHHHHHH--HHHHHHHHHHHhHHHHHHHHHHHHHHHHhccchhhh-hhhhhhhccccchhhhHhhhhhHHHHHHhhh
Q 028075 84 SMYRDWQEEK--AKQISKRQEEIENKIEVADALATKLLQRFGYSVSAM-KTSSQHLSEVHALQVEIGELKGRLTEVISNC 160 (214)
Q Consensus 84 S~YreWQe~~--a~~isk~QeeienkIE~adalA~KLlQR~n~S~S~M-ktts~hL~~V~~LqvevgElKgrLteVisnc 160 (214)
+++.-|..-. +..++..-+.+.+.| ...+...|.-=..-+ +..-.+.++...+|-++..+-..|...-.+|
T Consensus 62 s~~~aw~~i~~e~~~~a~~H~~~a~~l------~~~v~~~l~~~~~~~~~~rK~~~~~~~kl~~~~~~~~~~l~kskk~Y 135 (251)
T cd07653 62 SSVKAFRSILNEVNDIAGQHELIAENL------NSNVCKELKTLISELRQERKKHLSEGSKLQQKLESSIKQLEKSKKAY 135 (251)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5667776543 333444444443333 333333332222222 3334567788889999999999999999999
Q ss_pred HHHHHHHH
Q 028075 161 DALCKRIA 168 (214)
Q Consensus 161 daLCKRI~ 168 (214)
+.+||-..
T Consensus 136 ~~~~ke~~ 143 (251)
T cd07653 136 EKAFKEAE 143 (251)
T ss_pred HHHHHHHH
Confidence 99997644
No 110
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=21.07 E-value=1.9e+02 Score=25.11 Aligned_cols=56 Identities=27% Similarity=0.278 Sum_probs=34.6
Q ss_pred HHHHHHHHHHHHh---ccchhhhhhhhhhhccccchhhhHhhhhhHHHHHHhhhHHHHHHHHhcCC
Q 028075 110 VADALATKLLQRF---GYSVSAMKTSSQHLSEVHALQVEIGELKGRLTEVISNCDALCKRIAAEGP 172 (214)
Q Consensus 110 ~adalA~KLlQR~---n~S~S~Mktts~hL~~V~~LqvevgElKgrLteVisncdaLCKRI~~eGP 172 (214)
-|-.||-+||++| |-=..++..+-+-|..|.+ ||+-| ..-|.-+-.|++|+..+..
T Consensus 33 ~~~~lA~~ll~~f~~~g~l~~l~~a~~~eL~~i~G----iG~ak---a~~l~a~~El~rR~~~~~~ 91 (218)
T TIGR00608 33 DVLSLSKRLLDVFGRQDSLGHLLSAPPEELSSVPG----IGEAK---AIQLKAAVELAKRYAKSRM 91 (218)
T ss_pred CHHHHHHHHHHHhcccCCHHHHHhCCHHHHHhCcC----CcHHH---HHHHHHHHHHHHHHHhhhh
Confidence 4567999999999 5333445555555665554 34444 2334556778888876553
No 111
>PRK06285 chorismate mutase; Provisional
Probab=20.94 E-value=3.3e+02 Score=20.32 Aligned_cols=34 Identities=24% Similarity=0.340 Sum_probs=25.0
Q ss_pred HHHHHHHhHHHHHHHHHHHHHH-HHhccchhhhhh
Q 028075 98 SKRQEEIENKIEVADALATKLL-QRFGYSVSAMKT 131 (214)
Q Consensus 98 sk~QeeienkIE~adalA~KLl-QR~n~S~S~Mkt 131 (214)
.+.-+++..+|+..|.--++|| +|+.+..-+.+.
T Consensus 6 ~~~L~elR~~ID~ID~~iv~Ll~~R~~l~~~I~~~ 40 (96)
T PRK06285 6 EKRLNEIRKRIDEIDEQIIDLIAERTSLAKEIAEL 40 (96)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4456789999999998888877 577776555433
No 112
>PF08900 DUF1845: Domain of unknown function (DUF1845); InterPro: IPR014996 Members of this protein family, such as PFL4669, are found in integrating conjugative elements (ICE) of the PFGI-1 class as in Pseudomonas fluorescens.
Probab=20.77 E-value=2.3e+02 Score=24.40 Aligned_cols=32 Identities=19% Similarity=0.304 Sum_probs=21.5
Q ss_pred ccccchhhhHh---hhhhHHHHHHhhhHHHHHHHH
Q 028075 137 SEVHALQVEIG---ELKGRLTEVISNCDALCKRIA 168 (214)
Q Consensus 137 ~~V~~Lqvevg---ElKgrLteVisncdaLCKRI~ 168 (214)
..++|+.+.|. -+=-++-..|-.||.|..++-
T Consensus 102 ~s~~P~~~~l~~~splGy~~v~LL~~yD~L~~~v~ 136 (217)
T PF08900_consen 102 QSVQPVDVPLFFRSPLGYRCVYLLVDYDQLARKVL 136 (217)
T ss_pred ccCCCccceeEecCHHHHHHHHHHHHHHHHHHHHH
Confidence 34556666664 234567788889998887763
No 113
>PHA02557 22 prohead core protein; Provisional
Probab=20.50 E-value=5.2e+02 Score=24.10 Aligned_cols=74 Identities=19% Similarity=0.319 Sum_probs=53.7
Q ss_pred hHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHH---HHHhccchhhhhhhhhhhccccchhhhHhhhhhHHHHHHhhhHH
Q 028075 86 YRDWQEEKAKQISKRQEEIENKIEVADALATKL---LQRFGYSVSAMKTSSQHLSEVHALQVEIGELKGRLTEVISNCDA 162 (214)
Q Consensus 86 YreWQe~~a~~isk~QeeienkIE~adalA~KL---lQR~n~S~S~Mktts~hL~~V~~LqvevgElKgrLteVisncda 162 (214)
-.+|-.++...|.. +-|-|.++.+-.-| |---|..+-- ...+.|-.|+-++.|++.++++.+..-.+
T Consensus 97 ~~eW~~ENk~Av~~-----~IKaem~Es~l~GLK~lF~Ehnv~vpe-----e~vdvV~em~~~L~E~e~~~~~l~~en~~ 166 (271)
T PHA02557 97 AKEWLAENKLAVDR-----GIKAELFESFLGGLKELFVEHNVVVPE-----EKVDVVAEMEEELDEMEEELNELFEENVA 166 (271)
T ss_pred HHHHHHHhHHHHHH-----HHHHHHHHHHHHHHHHHHHHhCcCCcH-----HHhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35788887776654 55667777775444 4444554432 33567888999999999999999999999
Q ss_pred HHHHHHh
Q 028075 163 LCKRIAA 169 (214)
Q Consensus 163 LCKRI~~ 169 (214)
|-++|+.
T Consensus 167 l~e~i~~ 173 (271)
T PHA02557 167 LEEYINE 173 (271)
T ss_pred HHHHHHH
Confidence 9998864
No 114
>PF08614 ATG16: Autophagy protein 16 (ATG16); InterPro: IPR013923 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 []. This entry represents auotphagy protein 16 (Apg16), which is required for the function of the Apg12p-Apg5p conjugate.; PDB: 3A7O_D 3A7P_B.
Probab=20.42 E-value=75 Score=26.25 Aligned_cols=31 Identities=26% Similarity=0.423 Sum_probs=21.4
Q ss_pred ccccchhhhHhhhhhHHHHHHhhhHHHHHHH
Q 028075 137 SEVHALQVEIGELKGRLTEVISNCDALCKRI 167 (214)
Q Consensus 137 ~~V~~LqvevgElKgrLteVisncdaLCKRI 167 (214)
++...||.+..-+.+++..+=...+.|-+|.
T Consensus 151 DE~~~L~l~~~~~e~k~~~l~~En~~Lv~Rw 181 (194)
T PF08614_consen 151 DELQALQLQLNMLEEKLRKLEEENRELVERW 181 (194)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3455677777777777777777777777665
No 115
>TIGR02553 SipD_IpaD_SspD type III effector protein IpaD/SipD/SspD. These proteins are found within type III secretion operons and have been shown to be secreted by that system.
Probab=20.20 E-value=4.6e+02 Score=24.78 Aligned_cols=73 Identities=19% Similarity=0.196 Sum_probs=53.2
Q ss_pred hHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHhccchhhhhhhhhhhc---cccchhhhHhhhhhHHHHHHhhhH
Q 028075 86 YRDWQEEKAKQISKRQEEIENKIEVADALATKLLQRFGYSVSAMKTSSQHLS---EVHALQVEIGELKGRLTEVISNCD 161 (214)
Q Consensus 86 YreWQe~~a~~isk~QeeienkIE~adalA~KLlQR~n~S~S~Mktts~hL~---~V~~LqvevgElKgrLteVisncd 161 (214)
|+|---..++-|+...++.-...+-+=.-.++..|-||--+|.| +.|++ +=..++..+..||..|.+++.+|.
T Consensus 103 ~aelw~~Is~~I~~Ik~dYldvYa~lvk~YTd~yQ~fn~~lSkl---s~~IsaG~DGn~VkFd~~~lk~~l~~~~~Ky~ 178 (308)
T TIGR02553 103 DDPIWDMLSDVIGKIGDSYLGVYENVVEGYTDFYQAFSDILSKM---QDWISPGKDGNNVKLDVGKLKALLQQLIDHLP 178 (308)
T ss_pred HHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHH---hhhcccCCCCCeeeeCHHHHHHHHHHHHHHhc
Confidence 44433456777887777766666666667889999999766666 55554 445778888889999999988876
No 116
>PF04508 Pox_A_type_inc: Viral A-type inclusion protein repeat ; InterPro: IPR007596 The repeat is found in the A-type inclusion protein of the Poxvirus family [].; GO: 0016032 viral reproduction
Probab=20.07 E-value=69 Score=19.84 Aligned_cols=21 Identities=29% Similarity=0.458 Sum_probs=16.2
Q ss_pred cccchhhhHhhhhhHHHHHHh
Q 028075 138 EVHALQVEIGELKGRLTEVIS 158 (214)
Q Consensus 138 ~V~~LqvevgElKgrLteVis 158 (214)
+|..|+-.|.+|+..|++-..
T Consensus 2 E~~rlr~rI~dLer~L~~C~~ 22 (23)
T PF04508_consen 2 EMNRLRNRISDLERQLSECRR 22 (23)
T ss_pred hHHHHHHHHHHHHHHHHHHhc
Confidence 566788889999999887443
Done!