Query 027481
Match_columns 223
No_of_seqs 121 out of 311
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 10:33:26 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027481.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027481hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3067 Translin family protei 100.0 1.4E-33 3E-38 239.4 14.2 142 79-222 5-150 (226)
2 PF01997 Translin: Translin fa 100.0 5E-34 1.1E-38 244.2 9.4 124 93-222 1-129 (200)
3 PRK14562 haloacid dehalogenase 100.0 6E-33 1.3E-37 239.2 13.7 124 78-222 2-125 (204)
4 KOG3066 Translin-associated pr 100.0 1.6E-32 3.4E-37 237.6 9.2 150 68-222 25-180 (271)
5 COG2178 Predicted RNA-binding 99.9 2.7E-24 5.9E-29 183.9 11.3 123 79-222 2-124 (204)
6 KOG4098 Molecular chaperone Pr 83.0 9.5 0.00021 31.5 8.1 45 74-119 16-70 (140)
7 KOG3850 Predicted membrane pro 73.9 45 0.00097 32.3 10.7 36 85-120 262-297 (455)
8 COG4026 Uncharacterized protei 73.9 16 0.00034 33.0 7.4 39 128-166 163-201 (290)
9 PF10157 DUF2365: Uncharacteri 70.8 47 0.001 27.7 9.2 72 74-152 64-143 (149)
10 PF10241 KxDL: Uncharacterized 70.0 44 0.00095 25.1 8.1 61 98-158 26-88 (88)
11 PF14728 PHTB1_C: PTHB1 C-term 65.5 63 0.0014 30.8 9.9 70 82-151 199-270 (377)
12 PF10267 Tmemb_cc2: Predicted 59.8 1.3E+02 0.0028 29.0 11.0 30 140-176 281-310 (395)
13 PF07851 TMPIT: TMPIT-like pro 59.5 1E+02 0.0023 29.0 10.1 53 102-154 37-94 (330)
14 PF10668 Phage_terminase: Phag 59.2 12 0.00026 26.7 3.0 25 177-201 12-36 (60)
15 KOG0994 Extracellular matrix g 56.7 1.1E+02 0.0024 33.9 10.6 78 73-152 1408-1485(1758)
16 COG1283 NptA Na+/phosphate sym 53.2 1.5E+02 0.0033 29.7 10.6 50 74-123 343-392 (533)
17 TIGR00996 Mtu_fam_mce virulenc 53.2 42 0.0009 29.8 6.2 30 77-106 168-197 (291)
18 PF10428 SOG2: RAM signalling 47.0 2.8E+02 0.0061 26.9 13.4 18 36-53 252-269 (445)
19 PRK15365 type III secretion sy 44.2 1.6E+02 0.0034 23.3 8.0 75 78-152 14-90 (107)
20 PF05225 HTH_psq: helix-turn-h 44.0 31 0.00066 22.7 2.9 38 169-217 5-42 (45)
21 PHA00003 B internal scaffoldin 42.6 9.5 0.00021 30.5 0.3 90 51-164 23-112 (120)
22 PF04380 BMFP: Membrane fusoge 40.8 1.5E+02 0.0032 21.9 7.7 67 75-147 5-76 (79)
23 PF10168 Nup88: Nuclear pore c 39.4 1.6E+02 0.0036 30.4 8.7 13 110-122 613-625 (717)
24 PF10392 COG5: Golgi transport 38.2 2E+02 0.0043 22.8 7.4 28 125-152 69-96 (132)
25 KOG1319 bHLHZip transcription 37.8 2.5E+02 0.0054 24.8 8.3 70 86-155 64-156 (229)
26 cd07590 BAR_Bin3 The Bin/Amphi 37.5 2.9E+02 0.0063 24.4 10.3 67 128-200 145-215 (225)
27 KOG3910 Helix loop helix trans 36.8 68 0.0015 32.1 5.2 50 93-144 530-582 (632)
28 PF06160 EzrA: Septation ring 36.6 4.4E+02 0.0095 26.2 11.2 81 75-155 284-371 (560)
29 PRK04778 septation ring format 36.3 4.4E+02 0.0096 26.1 11.5 101 75-183 378-489 (569)
30 PF00015 MCPsignal: Methyl-acc 36.1 1.4E+02 0.003 24.4 6.4 27 96-122 81-107 (213)
31 PF10158 LOH1CR12: Tumour supp 36.0 55 0.0012 26.6 3.9 31 169-199 89-119 (131)
32 PRK13502 transcriptional activ 35.8 2.9E+02 0.0063 23.9 9.7 67 145-212 196-275 (282)
33 PF10018 Med4: Vitamin-D-recep 35.4 74 0.0016 26.9 4.7 43 80-122 12-54 (188)
34 PLN00047 photosystem II biogen 35.0 1.7E+02 0.0037 27.0 7.2 63 138-211 169-234 (283)
35 KOG3820 Aromatic amino acid hy 34.9 75 0.0016 31.0 5.1 72 134-216 187-265 (461)
36 PF00804 Syntaxin: Syntaxin; 34.5 1.7E+02 0.0038 20.9 6.9 65 87-151 4-72 (103)
37 cd07591 BAR_Rvs161p The Bin/Am 33.2 3.3E+02 0.0072 23.8 11.5 75 128-215 144-223 (224)
38 cd07662 BAR_SNX6 The Bin/Amphi 32.7 3.6E+02 0.0077 24.0 10.5 73 77-152 20-100 (218)
39 PRK11100 sensory histidine kin 32.5 2.3E+02 0.0049 25.8 7.8 45 78-122 239-283 (475)
40 PF14735 HAUS4: HAUS augmin-li 32.3 2.5E+02 0.0054 25.1 7.7 19 134-152 208-226 (238)
41 KOG4514 Uncharacterized conser 31.8 2.3E+02 0.005 24.9 7.1 11 96-106 167-177 (222)
42 PF06160 EzrA: Septation ring 31.6 2.6E+02 0.0056 27.8 8.5 39 132-170 411-454 (560)
43 PF12205 GIT1_C: G protein-cou 31.5 2.8E+02 0.0061 22.4 8.0 69 97-178 12-80 (123)
44 PF12825 DUF3818: Domain of un 31.0 3.8E+02 0.0082 25.2 9.1 94 75-169 201-319 (341)
45 KOG1666 V-SNARE [Intracellular 30.6 1.7E+02 0.0036 26.2 6.2 63 110-175 16-80 (220)
46 smart00150 SPEC Spectrin repea 30.2 1.9E+02 0.0041 20.0 8.1 59 78-152 36-94 (101)
47 PF13427 DUF4111: Domain of un 29.9 2.1E+02 0.0045 22.1 6.1 49 135-196 12-60 (106)
48 PF00165 HTH_AraC: Bacterial r 29.9 32 0.0007 21.6 1.3 25 188-212 9-41 (42)
49 PF10398 DUF2443: Protein of u 29.7 2.4E+02 0.0053 21.1 7.6 53 97-149 3-71 (79)
50 PF15011 CK2S: Casein Kinase 2 28.5 1.5E+02 0.0033 24.9 5.5 36 76-111 67-102 (168)
51 PF05633 DUF793: Protein of un 28.3 3.5E+02 0.0075 26.1 8.4 73 79-152 288-365 (389)
52 PF01369 Sec7: Sec7 domain; I 27.5 62 0.0014 27.3 3.0 44 176-220 39-82 (190)
53 PF04355 SmpA_OmlA: SmpA / Oml 27.2 25 0.00055 24.7 0.4 30 183-214 13-44 (71)
54 PRK10404 hypothetical protein; 27.1 3E+02 0.0065 21.3 6.8 21 92-112 7-27 (101)
55 PF09548 Spore_III_AB: Stage I 27.1 1.7E+02 0.0038 24.2 5.5 48 124-173 49-97 (170)
56 PF13713 BRX_N: Transcription 27.0 85 0.0018 20.5 2.8 24 129-152 6-29 (39)
57 KOG0201 Serine/threonine prote 26.7 51 0.0011 32.3 2.5 80 129-217 47-126 (467)
58 PF00435 Spectrin: Spectrin re 26.6 2.2E+02 0.0049 19.7 8.6 62 85-152 36-97 (105)
59 PF10234 Cluap1: Clusterin-ass 26.5 2.5E+02 0.0055 25.6 6.8 55 130-184 199-253 (267)
60 PRK04778 septation ring format 26.4 3.6E+02 0.0078 26.8 8.5 61 127-194 410-475 (569)
61 PF04539 Sigma70_r3: Sigma-70 26.0 51 0.0011 23.2 1.9 18 183-200 16-33 (78)
62 PF10475 DUF2450: Protein of u 25.7 3.9E+02 0.0085 24.0 8.0 25 82-106 59-83 (291)
63 PF05667 DUF812: Protein of un 25.4 1.9E+02 0.0042 29.2 6.4 19 158-176 552-570 (594)
64 PRK11637 AmiB activator; Provi 25.1 4.9E+02 0.011 24.6 8.9 17 77-93 44-60 (428)
65 PF08700 Vps51: Vps51/Vps67; 24.9 2.6E+02 0.0057 19.9 7.5 74 77-151 7-81 (87)
66 PF10498 IFT57: Intra-flagella 24.4 2.5E+02 0.0055 26.6 6.7 22 90-111 280-301 (359)
67 PF02403 Seryl_tRNA_N: Seryl-t 24.3 3E+02 0.0065 20.7 6.0 30 77-106 30-59 (108)
68 cd07604 BAR_ASAPs The Bin/Amph 24.2 3.8E+02 0.0081 23.5 7.3 66 77-151 60-127 (215)
69 PF12728 HTH_17: Helix-turn-he 23.8 60 0.0013 21.0 1.8 14 187-200 1-14 (51)
70 TIGR02492 flgK_ends flagellar 23.5 5.2E+02 0.011 23.5 8.5 71 73-143 104-178 (322)
71 KOG4796 RNA polymerase II elon 22.9 4.7E+02 0.01 26.6 8.3 33 82-114 507-539 (604)
72 PF07182 DUF1402: Protein of u 22.8 2E+02 0.0043 26.6 5.4 59 41-106 11-69 (303)
73 PRK10807 paraquat-inducible pr 22.8 7.7E+02 0.017 24.6 10.2 46 138-184 476-525 (547)
74 cd00176 SPEC Spectrin repeats, 22.8 3.8E+02 0.0083 21.1 8.0 63 84-151 140-202 (213)
75 PF12732 YtxH: YtxH-like prote 22.4 2.9E+02 0.0063 19.6 6.8 14 93-106 25-38 (74)
76 cd03345 eu_TyrOH Eukaryotic ty 22.4 4.6E+02 0.0099 24.4 7.8 70 134-217 62-141 (298)
77 PF04136 Sec34: Sec34-like fam 21.9 4.6E+02 0.0099 21.6 8.2 19 162-180 94-112 (157)
78 PF01726 LexA_DNA_bind: LexA D 21.7 1.7E+02 0.0036 20.7 3.9 43 170-215 8-50 (65)
79 TIGR02833 spore_III_AB stage I 21.7 2.9E+02 0.0062 23.1 5.9 61 111-173 31-97 (170)
80 PRK09940 transcriptional regul 21.6 4.8E+02 0.01 23.4 7.6 31 181-213 193-232 (253)
81 smart00753 PAM PCI/PINT associ 21.5 1.6E+02 0.0035 21.0 3.8 44 168-215 5-48 (88)
82 smart00088 PINT motif in prote 21.5 1.6E+02 0.0035 21.0 3.8 44 168-215 5-48 (88)
83 PF04799 Fzo_mitofusin: fzo-li 21.4 2.5E+02 0.0053 24.1 5.4 34 73-106 102-136 (171)
84 cd00171 Sec7 Sec7 domain; Doma 21.3 1.7E+02 0.0036 24.7 4.4 45 175-220 34-78 (185)
85 PF04136 Sec34: Sec34-like fam 21.3 4.7E+02 0.01 21.6 7.8 22 85-106 5-26 (157)
86 PF10146 zf-C4H2: Zinc finger- 21.2 5.6E+02 0.012 22.7 7.9 69 83-151 4-90 (230)
87 KOG4025 Putative apoptosis rel 21.1 3.1E+02 0.0067 23.8 5.9 17 104-120 96-112 (207)
88 PF04108 APG17: Autophagy prot 21.0 4.1E+02 0.009 25.3 7.5 13 161-173 344-356 (412)
89 PF08668 HDOD: HDOD domain; I 20.9 4.6E+02 0.01 21.3 9.0 119 80-222 6-133 (196)
90 PF10504 DUF2452: Protein of u 20.9 1.5E+02 0.0033 25.1 4.0 38 127-164 62-102 (159)
91 PRK11637 AmiB activator; Provi 20.8 6.5E+02 0.014 23.8 8.8 11 80-90 54-64 (428)
92 PF09756 DDRGK: DDRGK domain; 20.6 22 0.00047 30.8 -1.1 28 174-201 100-127 (188)
93 KOG0977 Nuclear envelope prote 20.5 8.1E+02 0.018 24.8 9.5 51 71-121 26-76 (546)
94 PRK15361 pathogenicity island 20.4 1.3E+02 0.0028 26.4 3.5 49 38-99 11-66 (195)
95 PF03962 Mnd1: Mnd1 family; I 20.4 5.4E+02 0.012 21.9 11.2 25 176-200 159-183 (188)
96 PRK08307 stage III sporulation 20.1 2.9E+02 0.0063 23.1 5.6 84 111-200 32-121 (171)
97 PRK11548 outer membrane biogen 20.1 51 0.0011 25.7 1.0 31 181-213 45-77 (113)
No 1
>KOG3067 consensus Translin family protein [General function prediction only]
Probab=100.00 E-value=1.4e-33 Score=239.44 Aligned_cols=142 Identities=39% Similarity=0.619 Sum_probs=137.2
Q ss_pred HHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHhhccC-CCchhHHhcHHHHHHHHHHHHHHHHHHhccCCCc
Q 027481 79 EKQFEDFRVKLDEAGSLRERIRAVVNEIESITRLMHASLLHVHQS-RPLSEVLEKPKAQVDGLKELYGRLAEVLCECPGE 157 (223)
Q Consensus 79 ~~~F~~fr~eLDe~~d~RErI~kisRdIe~~tr~sk~vI~~lHr~-~~~~~~l~~A~~~l~~i~~~~~~La~~l~~~p~~ 157 (223)
.++|.++++.+|++|++||+|++++++||.++|.++..|+.+|+. +++++.|..|++.+..+++++..|++..+ +++
T Consensus 5 ~sif~q~q~~id~e~~iRE~iravV~~ie~~~r~iq~~L~~vhq~~~~i~k~~~~are~~~~~kq~~~~LaE~~~--~~q 82 (226)
T KOG3067|consen 5 KSIFIQLQDFIDKEQSIREKIRAVVDEIEEKLREIQLLLQNVHQNENLIPKECGLAREDLENIKQKYRMLAELPP--AGQ 82 (226)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccchHHHHHHHHHHHHHHHHHHHHhhcCC--ccc
Confidence 378999999999999999999999999999999999999999998 68999999999999999999999999999 899
Q ss_pred cchhccccchhHHHHHHHHHHHHHHhcCCccCHHHHHHHhCCCC---CccCcChhHHhhhhhhccccC
Q 027481 158 YYRFHNDWRSETQTVVSLLAFMHWLETGKLLMHTEAEEKLGMNQ---AEFALDIEDYLIGEHSDECHI 222 (223)
Q Consensus 158 yYRY~~~ws~~lQE~VEalsf~~yLe~g~Llt~eEv~~~Lgv~~---~~f~L~~eDYLlGL~DLtGEi 222 (223)
||||+++|++.+|..|+..+|++||++|.|+|+++|+++||++. .+|||++||||.|++.|+.|+
T Consensus 83 yyry~~~w~~~~Q~vv~l~alv~~Let~~Llt~e~v~eilgl~p~~s~~FhLdvedyl~gvl~L~seL 150 (226)
T KOG3067|consen 83 YYRYNGHWRRSTQRVVSLPALVAWLETGTLLTREEVTEILGLEPDRSEGFHLDVEDYLSGVLFLASEL 150 (226)
T ss_pred eEEecchHHHHHHHHHHHHHHHHHHhhcccccHHHHHHHhcCCccccccceeeHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999987 689999999999999999875
No 2
>PF01997 Translin: Translin family; InterPro: IPR002848 Translins are DNA-binding proteins that specifically recognise consensus sequences at the breakpoint junctions in chromosomal translocations, mostly involving immunoglobulin (Ig)/T-cell receptor gene segments. They seem to recognise single-stranded DNA ends generated by staggered breaks occuring at recombination hot spots []. Translin folds into an alpha-alpha superhelix, consisting of two curved layers of alpha/alpha topology [, ].; GO: 0043565 sequence-specific DNA binding; PDB: 3QB5_K 3PJA_L 1J1J_D 3RIU_C 3AXJ_B 4DG7_C 2QVA_C 2QRX_A 1KEY_C.
Probab=100.00 E-value=5e-34 Score=244.22 Aligned_cols=124 Identities=32% Similarity=0.534 Sum_probs=112.7
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHhhccCC--CchhHHhcHHHHHHHHHHHHHHHHHHhccCCCccchhccccchhHH
Q 027481 93 GSLRERIRAVVNEIESITRLMHASLLHVHQSR--PLSEVLEKPKAQVDGLKELYGRLAEVLCECPGEYYRFHNDWRSETQ 170 (223)
Q Consensus 93 ~d~RErI~kisRdIe~~tr~sk~vI~~lHr~~--~~~~~l~~A~~~l~~i~~~~~~La~~l~~~p~~yYRY~~~ws~~lQ 170 (223)
||+||+|+++|||| ++.||++||.+||.. +..+++++|++.++++++.+++|+ +++ +.+||||++.|++++|
T Consensus 1 ~d~RE~iik~sRdi---~~~Sk~~I~~lhr~~~~~~~~~l~~a~~~l~~l~~~~~~l~-~~~--~~~~~~y~~~~s~~lQ 74 (200)
T PF01997_consen 1 HDRRERIIKLSRDI---TRLSKKIIFALHRIDQEKAEKILEEAEEKLKELKKLLKQLA-ELP--GHPFYRYHGAYSPGLQ 74 (200)
T ss_dssp HHHHHHHHHHHHHH---HHHHHHHHHHCCTCTTHHHHHHHHHHHHHHHHHHCHSHHHH-HCT--TCGHHHHGGGTHHHHH
T ss_pred CcHHHHHHHHHHHH---HHHHHHHHHHHHhccccchHHHHHHHHHHHHHHHHHHhhhc-ccC--CCcHHHHHHHHHHHHH
Confidence 79999999999999 999999999999983 355789999999999999999999 888 5569999999999999
Q ss_pred HHHHHHHHHHHHhcCCccCHHHHHHHhCCCC---CccCcChhHHhhhhhhccccC
Q 027481 171 TVVSLLAFMHWLETGKLLMHTEAEEKLGMNQ---AEFALDIEDYLIGEHSDECHI 222 (223)
Q Consensus 171 E~VEalsf~~yLe~g~Llt~eEv~~~Lgv~~---~~f~L~~eDYLlGL~DLtGEi 222 (223)
|||||++|++||++|+|+|++|+++.||+.. ..|||+++|||+||+|||||+
T Consensus 75 E~vEa~~f~~~l~~~~L~t~~ev~~~l~~~~~~~~~~~v~~~dYL~Gl~DltGEL 129 (200)
T PF01997_consen 75 EYVEAISFYHYLETGRLLTPEEVGEILGFSEDDEDRFHVTPEDYLLGLADLTGEL 129 (200)
T ss_dssp HHHHHHHHHHHHHHSSS--HHHHHHHCTCBSSTSCSSB--HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCCCCCHHHHHHHHhhccccccceecCHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999875 689999999999999999996
No 3
>PRK14562 haloacid dehalogenase superfamily protein; Provisional
Probab=100.00 E-value=6e-33 Score=239.19 Aligned_cols=124 Identities=22% Similarity=0.295 Sum_probs=116.7
Q ss_pred HHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCchhHHhcHHHHHHHHHHHHHHHHHHhccCCCc
Q 027481 78 MEKQFEDFRVKLDEAGSLRERIRAVVNEIESITRLMHASLLHVHQSRPLSEVLEKPKAQVDGLKELYGRLAEVLCECPGE 157 (223)
Q Consensus 78 v~~~F~~fr~eLDe~~d~RErI~kisRdIe~~tr~sk~vI~~lHr~~~~~~~l~~A~~~l~~i~~~~~~La~~l~~~p~~ 157 (223)
+.++|++++++||++||+||+|+++|||| ++.|+.+|+.+|+.. +++|++.++++++.+++|+++++++|
T Consensus 2 ~~~~~~~~~~~Ld~~~~~RE~iik~sRdI---~~~Sk~~I~~lHr~~-----~~~a~~~l~~a~~~~~~l~~~~~~~~-- 71 (204)
T PRK14562 2 IEEIIDSIREELEEKDEAREEALKLSREI---VRLSGDAIRAIHRGD-----FEEAEKLLKEAEELVKELKELLKDHP-- 71 (204)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHhhcc-----HHHHHHHHHHHHHHHHHHHHHhccCc--
Confidence 56789999999999999999999999999 999999999999953 78899999999999999999999555
Q ss_pred cchhccccchhHHHHHHHHHHHHHHhcCCccCHHHHHHHhCCCCCccCcChhHHhhhhhhccccC
Q 027481 158 YYRFHNDWRSETQTVVSLLAFMHWLETGKLLMHTEAEEKLGMNQAEFALDIEDYLIGEHSDECHI 222 (223)
Q Consensus 158 yYRY~~~ws~~lQE~VEalsf~~yLe~g~Llt~eEv~~~Lgv~~~~f~L~~eDYLlGL~DLtGEi 222 (223)
+|+|+++|++++||||||++|++||++|+|+|++| |+|+++|||+||+|+|||+
T Consensus 72 ~~~y~~~~~~~lQEyvEA~~f~~~l~~~~l~s~ee-----------l~v~~~dYLlGl~Dl~GEL 125 (204)
T PRK14562 72 ELYYAGYVGTALQEYVEALLVYSLLFENKIPSPEE-----------LGVPEAAYLLGLADAIGEL 125 (204)
T ss_pred hhhhhhhcchHHHHHHHHHHHHHHHcCCCCCCHHH-----------cCCCHHHHHhHHHHHHhHH
Confidence 89999999999999999999999999999999999 4578999999999999996
No 4
>KOG3066 consensus Translin-associated protein X [General function prediction only]
Probab=99.97 E-value=1.6e-32 Score=237.57 Aligned_cols=150 Identities=19% Similarity=0.267 Sum_probs=134.3
Q ss_pred CCCCCCCcchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHhhccC---CCchhHHhcHHHHHHHHHH-H
Q 027481 68 TGGETDAPASMEKQFEDFRVKLDEAGSLRERIRAVVNEIESITRLMHASLLHVHQS---RPLSEVLEKPKAQVDGLKE-L 143 (223)
Q Consensus 68 ~~~~~~~~~~v~~~F~~fr~eLDe~~d~RErI~kisRdIe~~tr~sk~vI~~lHr~---~~~~~~l~~A~~~l~~i~~-~ 143 (223)
.+.|++..++|++.|.+|+++|+++||+||||+|+|||| |.+||++||++||+ .+..+++.++...++.++. .
T Consensus 25 kartmsteSsm~~aF~sf~~~L~~~~dKrEriVklSRdI---Ti~SKr~IFllHr~ss~~~~e~~l~~~~~~le~vr~k~ 101 (271)
T KOG3066|consen 25 KARTMSTESSMEEAFLSFKNFLQEDQDKRERIVKLSRDI---TIQSKRMIFLLHRTSSSGFPEPKLFDRTSILEKVRHKE 101 (271)
T ss_pred cccccCccchHHHHHHHHHHHHHHhHHHHHHHHhhhhhh---eeccceeeeeeeecccCCCcchhhhhhhhHHHHHHHHH
Confidence 477889999999999999999999999999999999999 99999999999998 2345678888889987666 4
Q ss_pred HHHHHHHhccCCCccchhccccchhHHHHHHHHHHHHHHhcCCccCHHHHHHHh-CCCC-CccCcChhHHhhhhhhcccc
Q 027481 144 YGRLAEVLCECPGEYYRFHNDWRSETQTVVSLLAFMHWLETGKLLMHTEAEEKL-GMNQ-AEFALDIEDYLIGEHSDECH 221 (223)
Q Consensus 144 ~~~La~~l~~~p~~yYRY~~~ws~~lQE~VEalsf~~yLe~g~Llt~eEv~~~L-gv~~-~~f~L~~eDYLlGL~DLtGE 221 (223)
+..|+.++. +.++|+|+++++.|+||||||++|.+|+.+|+|.+.+|+..-| .+.. -...|++-||++|++|||||
T Consensus 102 f~~l~~EL~--G~d~~kf~rA~t~GlQEYVEAvtF~~f~lsgtLc~~dein~~lvpl~~~~rl~in~iDYvLGvaDlTGE 179 (271)
T KOG3066|consen 102 FESLKRELA--GLDADKFSRACTHGLQEYVEAVTFKFFLLSGTLCQTDEINSCLVPLDSSFRLSINFIDYVLGVADLTGE 179 (271)
T ss_pred HHHHHHHhc--CCcHHHHHHhhcccHHHHHHHHHHHHHHHhccccchhhhhheecccCCccceeeeHHHHHHHHhhhHHH
Confidence 799999999 7779999999999999999999999999999999999998765 2222 35688999999999999999
Q ss_pred C
Q 027481 222 I 222 (223)
Q Consensus 222 i 222 (223)
|
T Consensus 180 l 180 (271)
T KOG3066|consen 180 L 180 (271)
T ss_pred H
Confidence 7
No 5
>COG2178 Predicted RNA-binding protein of the translin family [Translation, ribosomal structure and biogenesis]
Probab=99.91 E-value=2.7e-24 Score=183.94 Aligned_cols=123 Identities=22% Similarity=0.329 Sum_probs=116.4
Q ss_pred HHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCchhHHhcHHHHHHHHHHHHHHHHHHhccCCCcc
Q 027481 79 EKQFEDFRVKLDEAGSLRERIRAVVNEIESITRLMHASLLHVHQSRPLSEVLEKPKAQVDGLKELYGRLAEVLCECPGEY 158 (223)
Q Consensus 79 ~~~F~~fr~eLDe~~d~RErI~kisRdIe~~tr~sk~vI~~lHr~~~~~~~l~~A~~~l~~i~~~~~~La~~l~~~p~~y 158 (223)
.+.+.++++.|+++++.||++++++|+| +|.|+.+|+.+|+++ .++|+..++++.+.+++|+..+.++|+.|
T Consensus 2 ~e~i~si~~~L~e~d~~REE~l~lsRei---~r~s~~aI~~~H~~~-----~eeA~~~l~~a~~~v~~Lk~~l~~~pel~ 73 (204)
T COG2178 2 REEINSIREVLQEKDKAREEALKLSREI---VRLSGEAIFLLHRGD-----FEEAEKKLKKASEAVEKLKRLLAGFPELY 73 (204)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHhcc-----HHHHHHHHHHHHHHHHHHHHHHhhhHHHH
Confidence 4679999999999999999999999999 999999999999976 89999999999999999999999999766
Q ss_pred chhccccchhHHHHHHHHHHHHHHhcCCccCHHHHHHHhCCCCCccCcChhHHhhhhhhccccC
Q 027481 159 YRFHNDWRSETQTVVSLLAFMHWLETGKLLMHTEAEEKLGMNQAEFALDIEDYLIGEHSDECHI 222 (223)
Q Consensus 159 YRY~~~ws~~lQE~VEalsf~~yLe~g~Llt~eEv~~~Lgv~~~~f~L~~eDYLlGL~DLtGEi 222 (223)
|.+....++||||||.+|+.|+.+|.+++.+| |||+ +.|||+||+|++||+
T Consensus 74 --~ag~~~~a~QEyvEA~~l~~~l~~~~~ps~~E----L~V~-------~~~YilGl~D~vGEL 124 (204)
T COG2178 74 --FAGFVTTALQEYVEATLLYSILKDGRLPSPEE----LGVP-------PIAYILGLADAVGEL 124 (204)
T ss_pred --HHHhhcchHHHHHHHHHHHHHHhcCCCCCHHH----cCCC-------HHHHHHHHHHHHHHH
Confidence 77999999999999999999999999999999 8855 999999999999997
No 6
>KOG4098 consensus Molecular chaperone Prefoldin, subunit 2 [Posttranslational modification, protein turnover, chaperones]
Probab=82.96 E-value=9.5 Score=31.51 Aligned_cols=45 Identities=16% Similarity=0.297 Sum_probs=31.0
Q ss_pred CcchHHHHHHHHHHHHhh--------hhhHHH--HHHHHHHHHHHHHHHHHHHHHh
Q 027481 74 APASMEKQFEDFRVKLDE--------AGSLRE--RIRAVVNEIESITRLMHASLLH 119 (223)
Q Consensus 74 ~~~~v~~~F~~fr~eLDe--------~~d~RE--rI~kisRdIe~~tr~sk~vI~~ 119 (223)
....+..+|..+|+++.+ +.|+|| .+++.-.++|. +|.+-++|--
T Consensus 16 ~q~~v~a~yn~~r~el~~ia~ki~~LE~d~~EH~lVi~tlk~~dp-~RKCfRmIgG 70 (140)
T KOG4098|consen 16 SQQAVVAKYNALRSELQQIASKITDLEMDLREHKLVIETLKDLDP-TRKCFRMIGG 70 (140)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhcCh-hhHHHHHhcc
Confidence 335578889999988743 345555 67777888766 6777766653
No 7
>KOG3850 consensus Predicted membrane protein [Function unknown]
Probab=73.91 E-value=45 Score=32.28 Aligned_cols=36 Identities=11% Similarity=0.210 Sum_probs=19.1
Q ss_pred HHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 027481 85 FRVKLDEAGSLRERIRAVVNEIESITRLMHASLLHV 120 (223)
Q Consensus 85 fr~eLDe~~d~RErI~kisRdIe~~tr~sk~vI~~l 120 (223)
|.+-+++.++++|-...+-+++|..--.+++=+..+
T Consensus 262 l~aileeL~eIk~~q~~Leesye~Lke~~krdy~fi 297 (455)
T KOG3850|consen 262 LDAILEELREIKETQALLEESYERLKEQIKRDYKFI 297 (455)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455555556666666666666654444444444333
No 8
>COG4026 Uncharacterized protein containing TOPRIM domain, potential nuclease [General function prediction only]
Probab=73.91 E-value=16 Score=32.99 Aligned_cols=39 Identities=28% Similarity=0.521 Sum_probs=30.3
Q ss_pred hHHhcHHHHHHHHHHHHHHHHHHhccCCCccchhccccc
Q 027481 128 EVLEKPKAQVDGLKELYGRLAEVLCECPGEYYRFHNDWR 166 (223)
Q Consensus 128 ~~l~~A~~~l~~i~~~~~~La~~l~~~p~~yYRY~~~ws 166 (223)
.-+++..+.++.+....+.|.+.+..-++.||+..+.|.
T Consensus 163 ~e~ee~~erlk~le~E~s~LeE~~~~l~~ev~~L~~r~~ 201 (290)
T COG4026 163 AEYEEVQERLKRLEVENSRLEEMLKKLPGEVYDLKKRWD 201 (290)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhchhHHHHHHHHHH
Confidence 346677777888888788888888777788888888886
No 9
>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=70.83 E-value=47 Score=27.69 Aligned_cols=72 Identities=11% Similarity=0.227 Sum_probs=46.5
Q ss_pred CcchHHHHHHHHHHHHhhhhh--------HHHHHHHHHHHHHHHHHHHHHHHHhhccCCCchhHHhcHHHHHHHHHHHHH
Q 027481 74 APASMEKQFEDFRVKLDEAGS--------LRERIRAVVNEIESITRLMHASLLHVHQSRPLSEVLEKPKAQVDGLKELYG 145 (223)
Q Consensus 74 ~~~~v~~~F~~fr~eLDe~~d--------~RErI~kisRdIe~~tr~sk~vI~~lHr~~~~~~~l~~A~~~l~~i~~~~~ 145 (223)
....+..++.+++..|+.--+ -|+-+-+++..+|..++.+..+|.++- .+++.-+.+..+.++++
T Consensus 64 ia~svd~ll~~L~~~L~~mS~~Tv~~~~~y~~sv~~~cdsvD~sik~~y~liakce-------ELn~~M~~v~~La~qIK 136 (149)
T PF10157_consen 64 IAESVDSLLRSLRSSLHSMSAITVEHMETYKDSVDKLCDSVDASIKSMYTLIAKCE-------ELNESMKPVYKLAQQIK 136 (149)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHH
Confidence 445677778888887765543 477777888888777777777777652 24444444555556666
Q ss_pred HHHHHhc
Q 027481 146 RLAEVLC 152 (223)
Q Consensus 146 ~La~~l~ 152 (223)
.|+..++
T Consensus 137 ~Ik~~lD 143 (149)
T PF10157_consen 137 DIKKLLD 143 (149)
T ss_pred HHHHHHH
Confidence 6665554
No 10
>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=70.03 E-value=44 Score=25.11 Aligned_cols=61 Identities=20% Similarity=0.305 Sum_probs=35.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhccC-CCchhHHhcHHHHHHHHHHHHHHHHHHhcc-CCCcc
Q 027481 98 RIRAVVNEIESITRLMHASLLHVHQS-RPLSEVLEKPKAQVDGLKELYGRLAEVLCE-CPGEY 158 (223)
Q Consensus 98 rI~kisRdIe~~tr~sk~vI~~lHr~-~~~~~~l~~A~~~l~~i~~~~~~La~~l~~-~p~~y 158 (223)
++-+..+.|......+..-+..++.- .+..+.+.+.+..|+-|.+.+..|+..+.. ||++|
T Consensus 26 ~ln~tn~~L~~~n~~s~~rl~~~~~~f~~~~~~l~~mK~DLd~i~krir~lk~kl~~~yP~~y 88 (88)
T PF10241_consen 26 RLNKTNEELLNLNDLSQQRLAEARERFARHTKLLKEMKKDLDYIFKRIRSLKAKLAKQYPEEY 88 (88)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcC
Confidence 34444444433344444444444322 334455677788888888888888888753 66654
No 11
>PF14728 PHTB1_C: PTHB1 C-terminus
Probab=65.47 E-value=63 Score=30.76 Aligned_cols=70 Identities=13% Similarity=0.203 Sum_probs=42.9
Q ss_pred HHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHhhccC--CCchhHHhcHHHHHHHHHHHHHHHHHHh
Q 027481 82 FEDFRVKLDEAGSLRERIRAVVNEIESITRLMHASLLHVHQS--RPLSEVLEKPKAQVDGLKELYGRLAEVL 151 (223)
Q Consensus 82 F~~fr~eLDe~~d~RErI~kisRdIe~~tr~sk~vI~~lHr~--~~~~~~l~~A~~~l~~i~~~~~~La~~l 151 (223)
++.|.+.+|++++.|.++.+....|+...++-..+=-++-.. +..+..++.-...++.-..++..+.+.+
T Consensus 199 l~~~~~~id~H~~lr~~~~~~~~~L~~~a~QfRaIQrrlL~r~kd~~p~~l~~L~~LLe~ty~~l~~~~d~~ 270 (377)
T PF14728_consen 199 LQEYFEIIDQHFELRQELKELEEELDERAQQFRAIQRRLLTRFKDKNPAPLDNLDTLLEGTYRQLIALADEI 270 (377)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcchhHHHHHHHHHHHHHHHHHHHH
Confidence 677888899999999999999999988777766543344311 2223334444444444444443343333
No 12
>PF10267 Tmemb_cc2: Predicted transmembrane and coiled-coil 2 protein; InterPro: IPR019394 This family of transmembrane coiled-coil containing proteins is conserved from worms to humans. Its function is unknown.
Probab=59.83 E-value=1.3e+02 Score=28.98 Aligned_cols=30 Identities=17% Similarity=0.232 Sum_probs=15.8
Q ss_pred HHHHHHHHHHHhccCCCccchhccccchhHHHHHHHH
Q 027481 140 LKELYGRLAEVLCECPGEYYRFHNDWRSETQTVVSLL 176 (223)
Q Consensus 140 i~~~~~~La~~l~~~p~~yYRY~~~ws~~lQE~VEal 176 (223)
+++.++.+.+.+. |.+ ......+||.+|.+
T Consensus 281 LKqeLa~~EEK~~------Yqs-~eRaRdi~E~~Es~ 310 (395)
T PF10267_consen 281 LKQELASMEEKMA------YQS-YERARDIWEVMESC 310 (395)
T ss_pred HHHHHHhHHHHHH------HHH-HHHHhHHHHHHHHH
Confidence 3444455555555 333 23345777777764
No 13
>PF07851 TMPIT: TMPIT-like protein; InterPro: IPR012926 A number of members of this family are annotated as being transmembrane proteins induced by tumour necrosis factor alpha, but no literature was found to support this. ; GO: 0016021 integral to membrane
Probab=59.55 E-value=1e+02 Score=28.97 Aligned_cols=53 Identities=9% Similarity=0.064 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHHHHHHHhhccC-----CCchhHHhcHHHHHHHHHHHHHHHHHHhccC
Q 027481 102 VVNEIESITRLMHASLLHVHQS-----RPLSEVLEKPKAQVDGLKELYGRLAEVLCEC 154 (223)
Q Consensus 102 isRdIe~~tr~sk~vI~~lHr~-----~~~~~~l~~A~~~l~~i~~~~~~La~~l~~~ 154 (223)
.+..|+...+..+.+...+.+. .+..+.+++.++.+++.+..+..+.+.+|+.
T Consensus 37 C~ssI~~QkkrLk~L~~sLk~~~~~~~~e~~~~i~~L~~~Ik~r~~~l~DmEa~LPkk 94 (330)
T PF07851_consen 37 CSSSISHQKKRLKELKKSLKRCKKSLSAEERELIEKLEEDIKERRCQLFDMEAFLPKK 94 (330)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhccCCChhHHHHHHHHHHHHHHHHhhHHHHHhhCCCC
Confidence 3444444444445444444443 1234556777777778777888888888743
No 14
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=59.18 E-value=12 Score=26.67 Aligned_cols=25 Identities=28% Similarity=0.436 Sum_probs=22.8
Q ss_pred HHHHHHhcCCccCHHHHHHHhCCCC
Q 027481 177 AFMHWLETGKLLMHTEAEEKLGMNQ 201 (223)
Q Consensus 177 sf~~yLe~g~Llt~eEv~~~Lgv~~ 201 (223)
+|-.|++++.=++..|||+.||++.
T Consensus 12 A~e~y~~~~g~i~lkdIA~~Lgvs~ 36 (60)
T PF10668_consen 12 AFEIYKESNGKIKLKDIAEKLGVSE 36 (60)
T ss_pred HHHHHHHhCCCccHHHHHHHHCCCH
Confidence 6888999999999999999999864
No 15
>KOG0994 consensus Extracellular matrix glycoprotein Laminin subunit beta [Extracellular structures]
Probab=56.73 E-value=1.1e+02 Score=33.86 Aligned_cols=78 Identities=12% Similarity=0.042 Sum_probs=42.5
Q ss_pred CCcchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCchhHHhcHHHHHHHHHHHHHHHHHHhc
Q 027481 73 DAPASMEKQFEDFRVKLDEAGSLRERIRAVVNEIESITRLMHASLLHVHQSRPLSEVLEKPKAQVDGLKELYGRLAEVLC 152 (223)
Q Consensus 73 ~~~~~v~~~F~~fr~eLDe~~d~RErI~kisRdIe~~tr~sk~vI~~lHr~~~~~~~l~~A~~~l~~i~~~~~~La~~l~ 152 (223)
+....-..+=....++|+...+.-|++++.+|+....+.+++.--+++- .+...-..++++-.++++.++.++..-+.
T Consensus 1408 t~A~~A~~~A~~~~~~l~~~~ae~eq~~~~v~ea~~~aseA~~~Aq~~~--~~a~as~~q~~~s~~el~~Li~~v~~Flt 1485 (1758)
T KOG0994|consen 1408 TRAGGALLMAGDADTQLRSKLAEAEQTLSMVREAKLSASEAQQSAQRAL--EQANASRSQMEESNRELRNLIQQVRDFLT 1485 (1758)
T ss_pred cccchHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 3334444455667778888888888999999988544444443333321 11122233444444445555555555443
No 16
>COG1283 NptA Na+/phosphate symporter [Inorganic ion transport and metabolism]
Probab=53.24 E-value=1.5e+02 Score=29.67 Aligned_cols=50 Identities=12% Similarity=0.208 Sum_probs=43.2
Q ss_pred CcchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHhhccC
Q 027481 74 APASMEKQFEDFRVKLDEAGSLRERIRAVVNEIESITRLMHASLLHVHQS 123 (223)
Q Consensus 74 ~~~~v~~~F~~fr~eLDe~~d~RErI~kisRdIe~~tr~sk~vI~~lHr~ 123 (223)
-.+.++.||..+.+.+..+..+=++|++.=+.+|+.-+++|.-+.++++.
T Consensus 343 ~~d~ie~ml~~~~~~~~~~~~~~~~i~~~e~~vd~~~~~Ik~YL~~ls~~ 392 (533)
T COG1283 343 LGDSIEQMLERLYEYIEGDAKKVKEIRKLEDAVDRLYEEIKLYLARLSKE 392 (533)
T ss_pred HHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence 34668888999999997777777889999999999999999999999986
No 17
>TIGR00996 Mtu_fam_mce virulence factor Mce family protein. Members of this paralogous family are found as six tandem homologous proteins in the same orientation per cassette, in four separate cassettes in Mycobacterium tuberculosis. The six members of each cassette represent six subfamilies. One subfamily includes the protein mce (mycobacterial cell entry), a virulence protein required for invasion of non-phagocytic cells.
Probab=53.21 E-value=42 Score=29.75 Aligned_cols=30 Identities=7% Similarity=0.185 Sum_probs=14.1
Q ss_pred hHHHHHHHHHHHHhhhhhHHHHHHHHHHHH
Q 027481 77 SMEKQFEDFRVKLDEAGSLRERIRAVVNEI 106 (223)
Q Consensus 77 ~v~~~F~~fr~eLDe~~d~RErI~kisRdI 106 (223)
.+.++..+...-.+.-++..+.|..+.+.+
T Consensus 168 ~l~~~l~~l~~l~~~l~~~~~~i~~ll~~l 197 (291)
T TIGR00996 168 QLRNLLDGLAQLTAALNARDGDIGALIDNL 197 (291)
T ss_pred HHHHHHHHHHHHHHHHHhcchhHHHHHHHH
Confidence 444444555444444444444444444443
No 18
>PF10428 SOG2: RAM signalling pathway protein; InterPro: IPR019487 The RAM signalling pathway regulates Ace2p transcription factor activity and cellular morphogenesis in Saccharomyces cerevisiae (Baker's yeast), and is thought to be conserved amongst eukaryotes []. This entry is found in one of the components of this pathway, the leucine-rich repeat-containing protein SOG2.
Probab=46.99 E-value=2.8e+02 Score=26.92 Aligned_cols=18 Identities=50% Similarity=0.717 Sum_probs=11.1
Q ss_pred CCCCCCCCCCCCCCcccc
Q 027481 36 SSPPSSLVSPSKPETFRF 53 (223)
Q Consensus 36 ~~~~~~~~~~~~~~~~~~ 53 (223)
++++.+...|+.+++|+-
T Consensus 252 ~~~~~~~~tprsg~s~~~ 269 (445)
T PF10428_consen 252 SSPPSSAATPRSGESFPS 269 (445)
T ss_pred CCCCccCCCCCCCccCCC
Confidence 445556677777766543
No 19
>PRK15365 type III secretion system chaperone SseA; Provisional
Probab=44.19 E-value=1.6e+02 Score=23.28 Aligned_cols=75 Identities=12% Similarity=0.205 Sum_probs=48.6
Q ss_pred HHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHhhccC--CCchhHHhcHHHHHHHHHHHHHHHHHHhc
Q 027481 78 MEKQFEDFRVKLDEAGSLRERIRAVVNEIESITRLMHASLLHVHQS--RPLSEVLEKPKAQVDGLKELYGRLAEVLC 152 (223)
Q Consensus 78 v~~~F~~fr~eLDe~~d~RErI~kisRdIe~~tr~sk~vI~~lHr~--~~~~~~l~~A~~~l~~i~~~~~~La~~l~ 152 (223)
+..-+..+...|++-++.|..|-..-.+=-+....+...+..+|.. .-+..+-.++...++.|...+++|-.-+.
T Consensus 14 L~~rYs~L~s~lkKfkq~q~~I~q~L~eRA~~d~kaRE~l~rLd~aFP~G~~~~~qE~~k~m~~i~~~FKQLEt~LK 90 (107)
T PRK15365 14 LEQSYMQLNHCLKKFHQIRAKVSQQLAERAESPKKSRETESILHNLFPQGVAGVNQEAEKDLKKIVSLFKQLEVRLK 90 (107)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCcchhhHHhHHHHHHHHHHHHHHHHHHHHHH
Confidence 4444667777888888888888444433333345566677777765 33434455677777777777887777665
No 20
>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster []. In pipsqueak this domain binds to GAGA sequence []. The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex [].; GO: 0003677 DNA binding; PDB: 2COB_A.
Probab=44.03 E-value=31 Score=22.74 Aligned_cols=38 Identities=24% Similarity=0.340 Sum_probs=24.5
Q ss_pred HHHHHHHHHHHHHHhcCCccCHHHHHHHhCCCCCccCcChhHHhhhhhh
Q 027481 169 TQTVVSLLAFMHWLETGKLLMHTEAEEKLGMNQAEFALDIEDYLIGEHS 217 (223)
Q Consensus 169 lQE~VEalsf~~yLe~g~Llt~eEv~~~Lgv~~~~f~L~~eDYLlGL~D 217 (223)
+|+.|+++- +|. ++..++++..||| .=|+.||+-|-..
T Consensus 5 l~~Ai~~v~------~g~-~S~r~AA~~ygVp----~sTL~~r~~g~~~ 42 (45)
T PF05225_consen 5 LQKAIEAVK------NGK-MSIRKAAKKYGVP----RSTLRRRLRGKPS 42 (45)
T ss_dssp HHHHHHHHH------TTS-S-HHHHHHHHT------HHHHHHHHHHTTT
T ss_pred HHHHHHHHH------hCC-CCHHHHHHHHCcC----HHHHHHHHcCCCC
Confidence 455554443 777 9999999999998 3456788777543
No 21
>PHA00003 B internal scaffolding protein
Probab=42.57 E-value=9.5 Score=30.52 Aligned_cols=90 Identities=11% Similarity=0.165 Sum_probs=46.0
Q ss_pred cccccccCCCcccccCCCCCCCCCcchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCchhHH
Q 027481 51 FRFRRRSSPLRVRYSSMTGGETDAPASMEKQFEDFRVKLDEAGSLRERIRAVVNEIESITRLMHASLLHVHQSRPLSEVL 130 (223)
Q Consensus 51 ~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~F~~fr~eLDe~~d~RErI~kisRdIe~~tr~sk~vI~~lHr~~~~~~~l 130 (223)
.-+|++..+.-.+.+-++.+| .+-.--|+..+..++.+...|. +| +..+.++.=|-+ +
T Consensus 23 pq~Rne~~~n~s~~~g~~~~t----~p~gLRrdpvq~d~EaERqkr~-------~i-----Eagk~~c~RrFG------g 80 (120)
T PHA00003 23 SQLRNEAAVNGSSVQGVANGT----DPSGLRRDPVQQDLEAERQKRA-------DI-----EAGKAICARRFG------G 80 (120)
T ss_pred hhhccCCCCCCCcccCCCCCC----CccccccCcccchHHHHHHHHH-------HH-----HHHHHHHHHHcC------C
Confidence 345655554433333333222 2222236777777776665554 33 466677777754 1
Q ss_pred hcHHHHHHHHHHHHHHHHHHhccCCCccchhccc
Q 027481 131 EKPKAQVDGLKELYGRLAEVLCECPGEYYRFHND 164 (223)
Q Consensus 131 ~~A~~~l~~i~~~~~~La~~l~~~p~~yYRY~~~ 164 (223)
.-+.++-.++...+..-..-++ |.+||||+|.
T Consensus 81 Atcddksa~iya~FD~~d~rVQ--paEFYRFnD~ 112 (120)
T PHA00003 81 ATCDDKSAKIYAQFDPNDRRVQ--PAEFYRFNDG 112 (120)
T ss_pred CCcchHHHHHhcccCcccceec--hhHheecccc
Confidence 1122222334444443344455 6779999985
No 22
>PF04380 BMFP: Membrane fusogenic activity; InterPro: IPR007475 BMFP consists of two structural domains, a coiled-coil C-terminal domain via which the protein self-associates as a trimer, and an N-terminal domain disordered at neutral pH but adopting an amphipathic alpha-helical structure in the presence of phospholipid vesicles, high ionic strength, acidic pH or SDS. BMFP interacts with phospholipid vesicles though the predicted amphipathic alpha-helix induced in the N-terminal half of the protein and promotes aggregation and fusion of vesicles in vitro.
Probab=40.80 E-value=1.5e+02 Score=21.87 Aligned_cols=67 Identities=15% Similarity=0.229 Sum_probs=41.7
Q ss_pred cchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHhhccC--CC---chhHHhcHHHHHHHHHHHHHHH
Q 027481 75 PASMEKQFEDFRVKLDEAGSLRERIRAVVNEIESITRLMHASLLHVHQS--RP---LSEVLEKPKAQVDGLKELYGRL 147 (223)
Q Consensus 75 ~~~v~~~F~~fr~eLDe~~d~RErI~kisRdIe~~tr~sk~vI~~lHr~--~~---~~~~l~~A~~~l~~i~~~~~~L 147 (223)
+..+.++...+.+-+...+..++.+.+.+|.+ ....+..+.=+ ++ ..+++.+++++++.+...++.|
T Consensus 5 ~~~~d~~~~~~~~~~~~~~~~~~e~e~~~r~~------l~~~l~kldlVtREEFd~q~~~L~~~r~kl~~LEarl~~L 76 (79)
T PF04380_consen 5 NKIFDDLAKQISEALPAAQGPREEIEKNIRAR------LQSALSKLDLVTREEFDAQKAVLARTREKLEALEARLAAL 76 (79)
T ss_pred hhHHHHHHHHHHHHHHhhhhhHHHHHHHHHHH------HHHHHHHCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35566666666666666678888888888876 55566655433 11 2245566666666666666554
No 23
>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=39.45 E-value=1.6e+02 Score=30.37 Aligned_cols=13 Identities=8% Similarity=0.105 Sum_probs=7.9
Q ss_pred HHHHHHHHHhhcc
Q 027481 110 TRLMHASLLHVHQ 122 (223)
Q Consensus 110 tr~sk~vI~~lHr 122 (223)
.+.++.+++.++.
T Consensus 613 ~~R~~~vl~~l~~ 625 (717)
T PF10168_consen 613 MKRVDRVLQLLNS 625 (717)
T ss_pred HHHHHHHHHHHhc
Confidence 4556666666654
No 24
>PF10392 COG5: Golgi transport complex subunit 5; InterPro: IPR019465 The conserved oligomeric Golgi (COG) complex is a peripheral membrane complex involved in intra-Golgi protein trafficking. Subunit 5 is located in the smaller, B lobe, together with subunits 6-8, and has been shown to bind subunits 1 and 7 [].
Probab=38.16 E-value=2e+02 Score=22.84 Aligned_cols=28 Identities=29% Similarity=0.465 Sum_probs=20.2
Q ss_pred CchhHHhcHHHHHHHHHHHHHHHHHHhc
Q 027481 125 PLSEVLEKPKAQVDGLKELYGRLAEVLC 152 (223)
Q Consensus 125 ~~~~~l~~A~~~l~~i~~~~~~La~~l~ 152 (223)
+...+++..+..++.+..-+.+|..++-
T Consensus 69 ~~~~~l~~v~~~v~~L~~s~~RL~~eV~ 96 (132)
T PF10392_consen 69 ELESVLQAVRSSVESLQSSYERLRSEVI 96 (132)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3445666777777788888888887775
No 25
>KOG1319 consensus bHLHZip transcription factor BIGMAX [Transcription]
Probab=37.80 E-value=2.5e+02 Score=24.80 Aligned_cols=70 Identities=17% Similarity=0.306 Sum_probs=38.5
Q ss_pred HHHHhhhhhHHHHHHHHHHHHHHH----------H-HHHHHH--------HHhhccC-CCchhH---HhcHHHHHHHHHH
Q 027481 86 RVKLDEAGSLRERIRAVVNEIESI----------T-RLMHAS--------LLHVHQS-RPLSEV---LEKPKAQVDGLKE 142 (223)
Q Consensus 86 r~eLDe~~d~RErI~kisRdIe~~----------t-r~sk~v--------I~~lHr~-~~~~~~---l~~A~~~l~~i~~ 142 (223)
++.+..++.+||.|.+==.|+-.. . +.++.+ |+.+|.- .+.++. +.+-...|+.|+.
T Consensus 64 ~aHtqaEqkRRdAIk~GYddLq~LvP~cq~~ds~g~KlskA~ILqksidyi~~L~~~k~kqe~e~s~L~k~vtAL~iIk~ 143 (229)
T KOG1319|consen 64 RAHTQAEQKRRDAIKRGYDDLQTLVPTCQQQDSIGQKLSKAIILQKTIDYIQFLHKEKKKQEEEVSTLRKDVTALKIIKV 143 (229)
T ss_pred HHHHHHHHHHHHHHHhchHHHHHhccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 347888999999998755444211 1 233332 3445543 111111 2233334566777
Q ss_pred HHHHHHHHhccCC
Q 027481 143 LYGRLAEVLCECP 155 (223)
Q Consensus 143 ~~~~La~~l~~~p 155 (223)
.|.++..-.+..|
T Consensus 144 ~YEqM~~~~qdnp 156 (229)
T KOG1319|consen 144 NYEQMVKAHQDNP 156 (229)
T ss_pred HHHHHHHhcccCC
Confidence 7888877777544
No 26
>cd07590 BAR_Bin3 The Bin/Amphiphysin/Rvs (BAR) domain of Bridging integrator 3. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Bridging integrator 3 (Bin3) is widely expressed in many tissues except in the brain. It plays roles in regulating filamentous actin localization and in cell division. In humans, the Bin3 gene is located in chromosome 8p21.3, a region that is implicated in cancer suppression. Homozygous inactivation of the Bin3 gene in mice led to the development of cataracts and an increased likelihood of lymphomas during aging, suggesting a role for Bin3 in lens development and cancer suppression. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions.
Probab=37.50 E-value=2.9e+02 Score=24.39 Aligned_cols=67 Identities=13% Similarity=0.160 Sum_probs=46.0
Q ss_pred hHHhcHHHHHHHHHHHH----HHHHHHhccCCCccchhccccchhHHHHHHHHHHHHHHhcCCccCHHHHHHHhCCC
Q 027481 128 EVLEKPKAQVDGLKELY----GRLAEVLCECPGEYYRFHNDWRSETQTVVSLLAFMHWLETGKLLMHTEAEEKLGMN 200 (223)
Q Consensus 128 ~~l~~A~~~l~~i~~~~----~~La~~l~~~p~~yYRY~~~ws~~lQE~VEalsf~~yLe~g~Llt~eEv~~~Lgv~ 200 (223)
.-+.+|++.+...++.| ..|.+++| .-|..-...+.+.+|.++-+-. .+|-+..+. +.+++..|.-+
T Consensus 145 ~KL~kae~el~~Ak~~ye~~N~~L~~ELP---~l~~~r~~f~~p~Fqsl~~~Ql-~f~~e~~k~--~~~l~~~~d~~ 215 (225)
T cd07590 145 AKLEQAEKALAAARADFEKQNIKLLEELP---KFYNGRTDYFQPCFEALIKSQV-LYYSQSTKI--FTQLAPNLDNP 215 (225)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhH---HHHHHccHHHHHHHHHHHHHHH-HHHHHHHHH--HHHHHHhhccc
Confidence 45778888888888877 44555555 2233345667789999888855 677776666 77888877644
No 27
>KOG3910 consensus Helix loop helix transcription factor [Transcription]
Probab=36.81 E-value=68 Score=32.09 Aligned_cols=50 Identities=20% Similarity=0.292 Sum_probs=32.6
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHhhccC-CCch--hHHhcHHHHHHHHHHHH
Q 027481 93 GSLRERIRAVVNEIESITRLMHASLLHVHQS-RPLS--EVLEKPKAQVDGLKELY 144 (223)
Q Consensus 93 ~d~RErI~kisRdIe~~tr~sk~vI~~lHr~-~~~~--~~l~~A~~~l~~i~~~~ 144 (223)
+.-||||| +|||..+-++..++.+.=-.. ++.. -++.+|.+.|-.+.+++
T Consensus 530 NNARERlR--VRDINeAfKELGRMCqlHlkSeKpQTKLgILhqAVsVIlsLEQQV 582 (632)
T KOG3910|consen 530 NNARERLR--VRDINEAFKELGRMCQLHLKSEKPQTKLGILHQAVSVILSLEQQV 582 (632)
T ss_pred hhhhhhee--hhhHHHHHHHHHHHHHHhhcccCcchhhhHHHHHHHHHHHHHHHH
Confidence 45688887 799988888888877653233 1111 35677877776555554
No 28
>PF06160 EzrA: Septation ring formation regulator, EzrA ; InterPro: IPR010379 During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerises into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation [].; GO: 0000921 septin ring assembly, 0005940 septin ring, 0016021 integral to membrane
Probab=36.56 E-value=4.4e+02 Score=26.19 Aligned_cols=81 Identities=10% Similarity=0.178 Sum_probs=59.2
Q ss_pred cchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHhhccC------CC-chhHHhcHHHHHHHHHHHHHHH
Q 027481 75 PASMEKQFEDFRVKLDEAGSLRERIRAVVNEIESITRLMHASLLHVHQS------RP-LSEVLEKPKAQVDGLKELYGRL 147 (223)
Q Consensus 75 ~~~v~~~F~~fr~eLDe~~d~RErI~kisRdIe~~tr~sk~vI~~lHr~------~~-~~~~l~~A~~~l~~i~~~~~~L 147 (223)
...+..+++.+..+.++.+.+.+....+...|+......+.+..-+.+. ++ -.+...+..+.++.+.+.+..+
T Consensus 284 ~~~Id~lYd~le~E~~Ak~~V~~~~~~l~~~l~~~~~~~~~l~~e~~~v~~sY~L~~~e~~~~~~l~~~l~~l~~~~~~~ 363 (560)
T PF06160_consen 284 EERIDQLYDILEKEVEAKKYVEKNLKELYEYLEHAKEQNKELKEELERVSQSYTLNHNELEIVRELEKQLKELEKRYEDL 363 (560)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHHHHHHHHHHH
Confidence 3467778999999999999998888888888877777777666655544 21 2233556677788888888888
Q ss_pred HHHhccCC
Q 027481 148 AEVLCECP 155 (223)
Q Consensus 148 a~~l~~~p 155 (223)
...+.+..
T Consensus 364 ~~~i~~~~ 371 (560)
T PF06160_consen 364 EERIEEQQ 371 (560)
T ss_pred HHHHHcCC
Confidence 88887433
No 29
>PRK04778 septation ring formation regulator EzrA; Provisional
Probab=36.26 E-value=4.4e+02 Score=26.12 Aligned_cols=101 Identities=15% Similarity=0.130 Sum_probs=51.8
Q ss_pred cchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHh-------hccC---CCchhHHhcHHHHHHHHHHHH
Q 027481 75 PASMEKQFEDFRVKLDEAGSLRERIRAVVNEIESITRLMHASLLH-------VHQS---RPLSEVLEKPKAQVDGLKELY 144 (223)
Q Consensus 75 ~~~v~~~F~~fr~eLDe~~d~RErI~kisRdIe~~tr~sk~vI~~-------lHr~---~~~~~~l~~A~~~l~~i~~~~ 144 (223)
-+.+.+.++.+.+++++-..-++.|.+...++...-..++.-|.. +.+. ..+|.+-+.-...+..+...+
T Consensus 378 ysel~e~leel~e~leeie~eq~ei~e~l~~Lrk~E~eAr~kL~~~~~~L~~ikr~l~k~~lpgip~~y~~~~~~~~~~i 457 (569)
T PRK04778 378 YSELQEELEEILKQLEEIEKEQEKLSEMLQGLRKDELEAREKLERYRNKLHEIKRYLEKSNLPGLPEDYLEMFFEVSDEI 457 (569)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCcHHHHHHHHHHHHHH
Confidence 345556666666666655555555555555443333333222222 2221 334555555566666666666
Q ss_pred HHHHHHhccCCCccchhccccchhHH-HHHHHHHHHHHHh
Q 027481 145 GRLAEVLCECPGEYYRFHNDWRSETQ-TVVSLLAFMHWLE 183 (223)
Q Consensus 145 ~~La~~l~~~p~~yYRY~~~ws~~lQ-E~VEalsf~~yLe 183 (223)
..|...+..-|-+. .+++ +|-++-.-+.+|.
T Consensus 458 ~~l~~~L~~g~VNm--------~ai~~e~~e~~~~~~~L~ 489 (569)
T PRK04778 458 EALAEELEEKPINM--------EAVNRLLEEATEDVETLE 489 (569)
T ss_pred HHHHHHhccCCCCH--------HHHHHHHHHHHHHHHHHH
Confidence 66776666433222 2444 6666666666664
No 30
>PF00015 MCPsignal: Methyl-accepting chemotaxis protein (MCP) signalling domain; InterPro: IPR004089 Methyl-accepting chemotaxis proteins (MCPs) are a family of bacterial receptors that mediate chemotaxis to diverse signals, responding to changes in the concentration of attractants and repellents in the environment by altering swimming behaviour []. Environmental diversity gives rise to diversity in bacterial signalling receptors, and consequently there are many genes encoding MCPs []. For example, there are four well-characterised MCPs found in Escherichia coli: Tar (taxis towards aspartate and maltose, away from nickel and cobalt), Tsr (taxis towards serine, away from leucine, indole and weak acids), Trg (taxis towards galactose and ribose) and Tap (taxis towards dipeptides). MCPs share similar topology and signalling mechanisms. MCPs either bind ligands directly or interact with ligand-binding proteins, transducing the signal to downstream signalling proteins in the cytoplasm. MCPs undergo two covalent modifications: deamidation and reversible methylation at a number of glutamate residues. Attractants increase the level of methylation, while repellents decrease it. The methyl groups are added by the methyl-transferase cheR and are removed by the methylesterase cheB. Most MCPs are homodimers that contain the following organisation: an N-terminal signal sequence that acts as a transmembrane domain in the mature protein; a poorly-conserved periplasmic receptor (ligand-binding) domain; a second transmembrane domain; and a highly-conserved C-terminal cytoplasmic domain that interacts with downstream signalling components. The C-terminal domain contains the glycosylated glutamate residues. This entry represents the signalling domain found in several methyl-accepting chemotaxis proteins. This domain is thought to transduce the signal to CheA since it is highly conserved in very diverse MCPs.; GO: 0004871 signal transducer activity, 0007165 signal transduction, 0016020 membrane; PDB: 2CH7_A 3ZX6_B 1QU7_A 3G6B_B 3UR1_C 3G67_B.
Probab=36.11 E-value=1.4e+02 Score=24.43 Aligned_cols=27 Identities=7% Similarity=0.257 Sum_probs=16.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 027481 96 RERIRAVVNEIESITRLMHASLLHVHQ 122 (223)
Q Consensus 96 RErI~kisRdIe~~tr~sk~vI~~lHr 122 (223)
-++|++++.+....+..+..+|..++.
T Consensus 81 A~eir~LA~~t~~~~~~I~~~i~~i~~ 107 (213)
T PF00015_consen 81 ADEIRKLAEQTSESAKEISEIIEEIQE 107 (213)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHhhhhhhhHHHHHHHHHhhhhh
Confidence 455666666666666666666666654
No 31
>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=35.98 E-value=55 Score=26.63 Aligned_cols=31 Identities=13% Similarity=-0.030 Sum_probs=20.7
Q ss_pred HHHHHHHHHHHHHHhcCCccCHHHHHHHhCC
Q 027481 169 TQTVVSLLAFMHWLETGKLLMHTEAEEKLGM 199 (223)
Q Consensus 169 lQE~VEalsf~~yLe~g~Llt~eEv~~~Lgv 199 (223)
++++-..+.=++.+-+..+.+.|.+.++|..
T Consensus 89 v~els~~L~~~~~lL~~~v~~ie~LN~~LP~ 119 (131)
T PF10158_consen 89 VNELSQQLSRCQSLLNQTVPSIETLNEILPE 119 (131)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhCCh
Confidence 5566666666666666677777777777753
No 32
>PRK13502 transcriptional activator RhaR; Provisional
Probab=35.83 E-value=2.9e+02 Score=23.87 Aligned_cols=67 Identities=9% Similarity=0.030 Sum_probs=38.9
Q ss_pred HHHHHHhccCCCccchhccc-cchhHHHHHHHHHH---HHHHhcCCccCHHHHHHHhCCCC---------CccCcChhHH
Q 027481 145 GRLAEVLCECPGEYYRFHND-WRSETQTVVSLLAF---MHWLETGKLLMHTEAEEKLGMNQ---------AEFALDIEDY 211 (223)
Q Consensus 145 ~~La~~l~~~p~~yYRY~~~-ws~~lQE~VEalsf---~~yLe~g~Llt~eEv~~~Lgv~~---------~~f~L~~eDY 211 (223)
..+|..+.-++..+.|.-.. .....++|+--.-+ ...|.+. =.+..|||..+|+++ +.+.++|-+|
T Consensus 196 ~~lA~~~~iS~~~L~r~fk~~~G~t~~~yi~~~Rl~~A~~lL~~t-~~sI~eIA~~~GF~d~s~F~r~FKk~~G~tP~~y 274 (282)
T PRK13502 196 DAFCQQEQCSERVLRQQFRAQTGMTINQYLRQVRICHAQYLLQHS-PLMISEISMQCGFEDSNYFSVVFTRETGMTPSQW 274 (282)
T ss_pred HHHHHHHCcCHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHcC-CCCHHHHHHHcCCCCHHHHHHHHHHHHCcCHHHH
Confidence 56666554334333333232 23444555443333 3344443 469999999999987 4578888887
Q ss_pred h
Q 027481 212 L 212 (223)
Q Consensus 212 L 212 (223)
=
T Consensus 275 R 275 (282)
T PRK13502 275 R 275 (282)
T ss_pred H
Confidence 3
No 33
>PF10018 Med4: Vitamin-D-receptor interacting Mediator subunit 4; InterPro: IPR019258 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Members of this family represent the Med4 subunit of the Mediator (Med) complex [, ]. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=35.36 E-value=74 Score=26.94 Aligned_cols=43 Identities=19% Similarity=0.279 Sum_probs=31.0
Q ss_pred HHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 027481 80 KQFEDFRVKLDEAGSLRERIRAVVNEIESITRLMHASLLHVHQ 122 (223)
Q Consensus 80 ~~F~~fr~eLDe~~d~RErI~kisRdIe~~tr~sk~vI~~lHr 122 (223)
+.+...-+.|.+++++..+|..+-.+++..-..++.++..|..
T Consensus 12 ~~L~~~L~~l~~hq~~~~~I~~L~~e~~~ld~~i~~~~~~L~~ 54 (188)
T PF10018_consen 12 DELSSALEELQEHQENQARIQQLRAEIEELDEQIRDILKQLKE 54 (188)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3456666778888888888888888887666666666666543
No 34
>PLN00047 photosystem II biogenesis protein Psb29; Provisional
Probab=35.03 E-value=1.7e+02 Score=27.04 Aligned_cols=63 Identities=13% Similarity=0.225 Sum_probs=35.7
Q ss_pred HHHHHHHHHHHHHhccCCCccchhccccchhHHHHHHHHHHHHHHhcCCc---cCHHHHHHHhCCCCCccCcChhHH
Q 027481 138 DGLKELYGRLAEVLCECPGEYYRFHNDWRSETQTVVSLLAFMHWLETGKL---LMHTEAEEKLGMNQAEFALDIEDY 211 (223)
Q Consensus 138 ~~i~~~~~~La~~l~~~p~~yYRY~~~ws~~lQE~VEalsf~~yLe~g~L---lt~eEv~~~Lgv~~~~f~L~~eDY 211 (223)
.++...+..++.... .+..|+|++.. |+.++..|+.-.- -..+++.+.||++.+...=|++=|
T Consensus 169 ~~l~~~l~~IA~~a~--~~~~f~YSRlf---------AIGLf~LLe~a~~~d~~~l~~l~e~Lgls~~kv~KDLdlY 234 (283)
T PLN00047 169 GEIEGILKDIAERAG--SKGKFSYSRFF---------AIGLFRLLELANATEPTALEKLCAALNINKRSVDRDLDVY 234 (283)
T ss_pred hHHHHHHHHHHHhhc--cCCCcchHHHH---------HHHHHHHHHhcCCCCHHHHHHHHHHcCCCHHHHHhhHHHH
Confidence 445555666665443 33467788765 5555666652221 255677888888764444444444
No 35
>KOG3820 consensus Aromatic amino acid hydroxylase [Amino acid transport and metabolism]
Probab=34.93 E-value=75 Score=30.95 Aligned_cols=72 Identities=10% Similarity=0.221 Sum_probs=46.3
Q ss_pred HHHHHHHHHHHHHHHHHhccCCCccchhccccchhHHHHHHHHHHHHHHhcCCccCHHHHHHHhCCCCCcc-------Cc
Q 027481 134 KAQVDGLKELYGRLAEVLCECPGEYYRFHNDWRSETQTVVSLLAFMHWLETGKLLMHTEAEEKLGMNQAEF-------AL 206 (223)
Q Consensus 134 ~~~l~~i~~~~~~La~~l~~~p~~yYRY~~~ws~~lQE~VEalsf~~yLe~g~Llt~eEv~~~Lgv~~~~f-------~L 206 (223)
++.++.-+..|.+|..+.+.|. -.-|.+.| +-+|+++- .....++-+++|.+.|.-++ || .|
T Consensus 187 ~eEikTWg~Vf~~L~~Ly~~HA--C~ey~~~f-~lLe~~cg-------~~ednIPQLeDVs~FLk~~T-GF~lRPvAGlL 255 (461)
T KOG3820|consen 187 EEEIKTWGTVFRTLTDLYPTHA--CAEYLDNF-PLLEKYCG-------YREDNIPQLEDVSKFLKKKT-GFRLRPVAGLL 255 (461)
T ss_pred HHHHHHHHHHHHHHHHHhhhhh--HHHHHHHH-HHHHHhcC-------cCCCCcchHHHHHHHHHhcc-CceeecccccC
Confidence 4444455555666777666444 44455555 34554432 23578999999999887543 33 57
Q ss_pred ChhHHhhhhh
Q 027481 207 DIEDYLIGEH 216 (223)
Q Consensus 207 ~~eDYLlGL~ 216 (223)
+..|+|.||+
T Consensus 256 SaRDFLagLA 265 (461)
T KOG3820|consen 256 SARDFLAGLA 265 (461)
T ss_pred cHHHHHhhhh
Confidence 8999999986
No 36
>PF00804 Syntaxin: Syntaxin; InterPro: IPR006011 Syntaxins A and B are nervous system-specific proteins implicated in the docking of synaptic vesicles with the presynaptic plasma membrane. Syntaxins are a family of receptors for intracellular transport vesicles. Each target membrane may be identified by a specific member of the syntaxin family []. Members of the syntaxin family [, ] have a size ranging from 30 Kd to 40 Kd; a C-terminal extremity which is highly hydrophobic and anchors the protein on the cytoplasmic surface of cellular membranes; a central, well conserved region, which seems to be in a coiled-coil conformation. ; GO: 0016020 membrane; PDB: 1S94_B 1EZ3_A 3C98_B 1BR0_A 1FIO_A 2XHE_B.
Probab=34.49 E-value=1.7e+02 Score=20.92 Aligned_cols=65 Identities=22% Similarity=0.281 Sum_probs=34.3
Q ss_pred HHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHhhcc---C-CCchhHHhcHHHHHHHHHHHHHHHHHHh
Q 027481 87 VKLDEAGSLRERIRAVVNEIESITRLMHASLLHVHQ---S-RPLSEVLEKPKAQVDGLKELYGRLAEVL 151 (223)
Q Consensus 87 ~eLDe~~d~RErI~kisRdIe~~tr~sk~vI~~lHr---~-~~~~~~l~~A~~~l~~i~~~~~~La~~l 151 (223)
+-+++-+++++.|.++...|+.....-+..+...=. . .++..+..+....+..++..+..|....
T Consensus 4 ~f~~~v~~i~~~i~~i~~~~~~l~~l~~~~l~~~~~d~~~~~el~~l~~~i~~~~~~~~~~lk~l~~~~ 72 (103)
T PF00804_consen 4 EFFDEVQEIREDIDKIKEKLNELRKLHKKILSSPDQDSELKRELDELTDEIKQLFQKIKKRLKQLSKDN 72 (103)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 345566667777777777664433333333322210 0 1233444556666666777777776664
No 37
>cd07591 BAR_Rvs161p The Bin/Amphiphysin/Rvs (BAR) domain of Saccharomyces cerevisiae Reduced viability upon starvation protein 161 and similar proteins. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. This subfamily is composed of fungal proteins with similarity to Saccharomyces cerevisiae Reduced viability upon starvation protein 161 (Rvs161p) and Schizosaccharomyces pombe Hob3 (homolog of Bin3). S. cerevisiae Rvs161p plays a role in regulating cell polarity, actin cytoskeleton polarization, vesicle trafficking, endocytosis, bud formation, and the mating response. It forms a heterodimer with another BAR domain protein Rvs167p. Rvs161p and Rvs167p share common functions but are not interchangeable. Their BAR domains cannot be replaced with each other and the overexpression of one cannot suppress the mutant phenotypes of the other. S. pombe Hob3 is important in regulating filamentous actin localization an
Probab=33.23 E-value=3.3e+02 Score=23.77 Aligned_cols=75 Identities=19% Similarity=0.215 Sum_probs=39.6
Q ss_pred hHHhcHHHHHHHHHHHH----HHHHHHhccCCCccchhcccc-chhHHHHHHHHHHHHHHhcCCccCHHHHHHHhCCCCC
Q 027481 128 EVLEKPKAQVDGLKELY----GRLAEVLCECPGEYYRFHNDW-RSETQTVVSLLAFMHWLETGKLLMHTEAEEKLGMNQA 202 (223)
Q Consensus 128 ~~l~~A~~~l~~i~~~~----~~La~~l~~~p~~yYRY~~~w-s~~lQE~VEalsf~~yLe~g~Llt~eEv~~~Lgv~~~ 202 (223)
.-+.+|++.++..++.| ..|.+++| . +|.....+ .+.+|.++.+-.-+++.-.. ...++...+.
T Consensus 144 ~kL~kae~el~~a~~~Ye~lN~~Lk~ELP--~--l~~~r~~~l~~~f~s~~~iQ~~~~~~~y~---~l~~~~~~~~---- 212 (224)
T cd07591 144 TKLPRAEKELDEAKEVYETLNDQLKTELP--Q--LVDLRIPYLDPSFEAFVKIQLRFFTEGYE---RLAQVQRYLD---- 212 (224)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhH--H--HHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHhhcc----
Confidence 44677888888888877 45555666 3 44333333 34444444443333332221 3344444444
Q ss_pred ccCcChhHHhhhh
Q 027481 203 EFALDIEDYLIGE 215 (223)
Q Consensus 203 ~f~L~~eDYLlGL 215 (223)
.-+-+||.-|.
T Consensus 213 --~~~~~~y~~~~ 223 (224)
T cd07591 213 --AQTREDYANGQ 223 (224)
T ss_pred --hhhHHHHhccC
Confidence 24568888775
No 38
>cd07662 BAR_SNX6 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 6. 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. SNX6 forms a stable complex with SNX1 and may be a component of the retromer complex, a membrane coat multimeric complex required for endosomal retrieval of lysosomal hydrolase receptors to the Golgi, acting as a mammalian equivalent of yeast Vsp17p. It interacts with the receptor serine/threonine kinases from the transforming growth factor-beta family. It also plays
Probab=32.72 E-value=3.6e+02 Score=23.99 Aligned_cols=73 Identities=16% Similarity=0.089 Sum_probs=43.9
Q ss_pred hHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHhh-------ccC-CCchhHHhcHHHHHHHHHHHHHHHH
Q 027481 77 SMEKQFEDFRVKLDEAGSLRERIRAVVNEIESITRLMHASLLHV-------HQS-RPLSEVLEKPKAQVDGLKELYGRLA 148 (223)
Q Consensus 77 ~v~~~F~~fr~eLDe~~d~RErI~kisRdIe~~tr~sk~vI~~l-------Hr~-~~~~~~l~~A~~~l~~i~~~~~~La 148 (223)
.+.+-|+.=+.+|++.+ .+|++++..+|..++.=+.+.-.. +.. ..-...+.++-..+.++-+.+.+|-
T Consensus 20 d~D~wFe~ek~~l~~~~---~~Lk~~~~~~e~l~~~rk~la~~~~~~s~sl~~L~~~e~t~L~~~l~~laev~eki~~l~ 96 (218)
T cd07662 20 DVDDFFEHERTFLLEYH---NRVKDSSAKSDRMTRSHKSAADDYNRIGSSLYTLGTQDSTDICKFFLKVSELFDKTRKIE 96 (218)
T ss_pred chhHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccchhHHHHHHHHHHHHHHHHHHH
Confidence 44566888888888877 566777666666555544332221 111 1122346667777777777777777
Q ss_pred HHhc
Q 027481 149 EVLC 152 (223)
Q Consensus 149 ~~l~ 152 (223)
....
T Consensus 97 ~~~A 100 (218)
T cd07662 97 ARVA 100 (218)
T ss_pred HHHh
Confidence 6665
No 39
>PRK11100 sensory histidine kinase CreC; Provisional
Probab=32.49 E-value=2.3e+02 Score=25.76 Aligned_cols=45 Identities=16% Similarity=0.335 Sum_probs=26.0
Q ss_pred HHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 027481 78 MEKQFEDFRVKLDEAGSLRERIRAVVNEIESITRLMHASLLHVHQ 122 (223)
Q Consensus 78 v~~~F~~fr~eLDe~~d~RErI~kisRdIe~~tr~sk~vI~~lHr 122 (223)
+...|+.+++.|++.+.+++-+..++.++-.........+..++.
T Consensus 239 l~~~~~~m~~~l~~~~~~~~~~~~~~h~l~~pl~~i~~~~~~l~~ 283 (475)
T PRK11100 239 LAQALESMRVKLEGKAYVEQYVQTLTHELKSPLAAIRGAAELLQE 283 (475)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhhhcCcHHHHHHHHHHHhc
Confidence 444577777777766666665666666664434444444444443
No 40
>PF14735 HAUS4: HAUS augmin-like complex subunit 4
Probab=32.30 E-value=2.5e+02 Score=25.11 Aligned_cols=19 Identities=11% Similarity=0.202 Sum_probs=11.0
Q ss_pred HHHHHHHHHHHHHHHHHhc
Q 027481 134 KAQVDGLKELYGRLAEVLC 152 (223)
Q Consensus 134 ~~~l~~i~~~~~~La~~l~ 152 (223)
-..|+++...|..|...+.
T Consensus 208 g~~F~~ivreY~~l~~~ie 226 (238)
T PF14735_consen 208 GPEFEEIVREYTDLQQEIE 226 (238)
T ss_pred cHhHHHHHHHHHHHHHHHH
Confidence 3345566666666666665
No 41
>KOG4514 consensus Uncharacterized conserved protein [Function unknown]
Probab=31.80 E-value=2.3e+02 Score=24.89 Aligned_cols=11 Identities=9% Similarity=0.447 Sum_probs=4.1
Q ss_pred HHHHHHHHHHH
Q 027481 96 RERIRAVVNEI 106 (223)
Q Consensus 96 RErI~kisRdI 106 (223)
|..+-|++..+
T Consensus 167 r~aV~kl~d~~ 177 (222)
T KOG4514|consen 167 RNAVNKLTDTL 177 (222)
T ss_pred HHHHHHHHHHh
Confidence 33333333333
No 42
>PF06160 EzrA: Septation ring formation regulator, EzrA ; InterPro: IPR010379 During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerises into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation [].; GO: 0000921 septin ring assembly, 0005940 septin ring, 0016021 integral to membrane
Probab=31.62 E-value=2.6e+02 Score=27.80 Aligned_cols=39 Identities=18% Similarity=0.334 Sum_probs=16.2
Q ss_pred cHHHHHHHHHHHHHHHHHHh-----ccCCCccchhccccchhHH
Q 027481 132 KPKAQVDGLKELYGRLAEVL-----CECPGEYYRFHNDWRSETQ 170 (223)
Q Consensus 132 ~A~~~l~~i~~~~~~La~~l-----~~~p~~yYRY~~~ws~~lQ 170 (223)
.|++.+..++..+..++-.+ ||-|+.|.-|-...+..++
T Consensus 411 ~Ar~~l~~~~~~l~~ikR~lek~nLPGlp~~y~~~~~~~~~~i~ 454 (560)
T PF06160_consen 411 EAREKLQKLKQKLREIKRRLEKSNLPGLPEDYLDYFFDVSDEIE 454 (560)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHH
Confidence 44444444444444333333 4444444433333333333
No 43
>PF12205 GIT1_C: G protein-coupled receptor kinase-interacting protein 1 C term; InterPro: IPR022018 This domain family is found in eukaryotes, and is approximately 120 amino acids in length. The family is found in association with PF01412 from PFAM, PF00023 from PFAM, PF08518 from PFAM. GIT1 plays an important role in cell adhesion, motility, cytoskeletal remodeling and membrane trafficking. To perform this function, it localises p21-activated kinase (PAK) and PAK-interactive exchange factor to focal adhesions. Its activation is regulated by interaction between its paxillin-binding C-terminal and the LD motifs of paxillin. The C-terminal folds into a four helix bundle. ; PDB: 2JX0_A.
Probab=31.51 E-value=2.8e+02 Score=22.40 Aligned_cols=69 Identities=12% Similarity=0.115 Sum_probs=39.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhccCCCchhHHhcHHHHHHHHHHHHHHHHHHhccCCCccchhccccchhHHHHHHHH
Q 027481 97 ERIRAVVNEIESITRLMHASLLHVHQSRPLSEVLEKPKAQVDGLKELYGRLAEVLCECPGEYYRFHNDWRSETQTVVSLL 176 (223)
Q Consensus 97 ErI~kisRdIe~~tr~sk~vI~~lHr~~~~~~~l~~A~~~l~~i~~~~~~La~~l~~~p~~yYRY~~~ws~~lQE~VEal 176 (223)
|+++.-+..| ||.++.++....-. + .+.....-..|+..+.+|..++|+.+ +...++.+++.+..+.
T Consensus 12 e~Vi~~TE~v---Tk~IqeLl~aAQ~~-~----~~s~~pcae~I~~aV~~m~~LfP~~~-----~~e~vr~~L~~L~~~~ 78 (123)
T PF12205_consen 12 EDVIRRTEQV---TKRIQELLRAAQEG-R----HDSFAPCAERIRSAVTEMAALFPKDP-----RSETVRSSLRQLTSSA 78 (123)
T ss_dssp HHHHHHHHHH---HHHHHHHHHHHHTT------HHHHHHHHHHHHHHHHHHHHTS-SSB-------HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHH---HHHHHHHHHHHHhc-c----cccchhHHHHHHHHHHHHHHhCCCcc-----CChHHHHHHHHHHHHH
Confidence 4455555555 78888777776321 1 12222333557777788888888333 4677888888887665
Q ss_pred HH
Q 027481 177 AF 178 (223)
Q Consensus 177 sf 178 (223)
..
T Consensus 79 ~~ 80 (123)
T PF12205_consen 79 YR 80 (123)
T ss_dssp HH
T ss_pred HH
Confidence 43
No 44
>PF12825 DUF3818: Domain of unknown function in PX-proteins (DUF3818); InterPro: IPR024554 The function of this domain is not known, but it is almost always found C-terminal to a PX-domain (IPR001683 from INTERPRO).
Probab=31.03 E-value=3.8e+02 Score=25.18 Aligned_cols=94 Identities=20% Similarity=0.279 Sum_probs=47.3
Q ss_pred cchHHHHHHHHHHHHhhhhhHHH--HHHHHHHHHHHHHHHHHHH-------HHhhccCCCchhHHhcHHHHHHHHH----
Q 027481 75 PASMEKQFEDFRVKLDEAGSLRE--RIRAVVNEIESITRLMHAS-------LLHVHQSRPLSEVLEKPKAQVDGLK---- 141 (223)
Q Consensus 75 ~~~v~~~F~~fr~eLDe~~d~RE--rI~kisRdIe~~tr~sk~v-------I~~lHr~~~~~~~l~~A~~~l~~i~---- 141 (223)
...-...|..+++.|...-..|| .++++-.+ ...+...|.+ |-++|+..++..-+...+.-+.++-
T Consensus 201 ~~~~a~lf~~lk~yl~l~~r~RDk~~~~~l~~e-~~~~qllkd~v~ifYepl~rv~k~a~l~~~l~d~q~Fi~DlI~~~~ 279 (341)
T PF12825_consen 201 ENEDAWLFSDLKEYLKLYLRKRDKEQMIQLWCE-PELTQLLKDLVTIFYEPLVRVHKAADLSEALSDFQKFIDDLIKLVE 279 (341)
T ss_pred cchhhHHHHHHHHHHHHHHHHhhHHHHHHHHcC-hhHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHH
Confidence 33444557777777766555544 45554443 3334444433 3356765444444443333333332
Q ss_pred ------------HHHHHHHHHhccCCCccchhccccchhH
Q 027481 142 ------------ELYGRLAEVLCECPGEYYRFHNDWRSET 169 (223)
Q Consensus 142 ------------~~~~~La~~l~~~p~~yYRY~~~ws~~l 169 (223)
..+..+..++..|.+.+|+|-+.+-..-
T Consensus 280 ~~~~~~~~~~~~~~V~~~v~Ll~rH~~~~y~FvH~v~~~d 319 (341)
T PF12825_consen 280 KLRNGSGSSDPFPSVEDFVDLLDRHEQSFYKFVHEVHKND 319 (341)
T ss_pred HhhcccccCCchhHHHHHHHHHHHHHHHHHHHHHHHHHcC
Confidence 2344455555555556666655554333
No 45
>KOG1666 consensus V-SNARE [Intracellular trafficking, secretion, and vesicular transport]
Probab=30.62 E-value=1.7e+02 Score=26.16 Aligned_cols=63 Identities=11% Similarity=0.154 Sum_probs=41.2
Q ss_pred HHHHHHHHHhhccC--CCchhHHhcHHHHHHHHHHHHHHHHHHhccCCCccchhccccchhHHHHHHH
Q 027481 110 TRLMHASLLHVHQS--RPLSEVLEKPKAQVDGLKELYGRLAEVLCECPGEYYRFHNDWRSETQTVVSL 175 (223)
Q Consensus 110 tr~sk~vI~~lHr~--~~~~~~l~~A~~~l~~i~~~~~~La~~l~~~p~~yYRY~~~ws~~lQE~VEa 175 (223)
+.++++.|..+|+. ++..+.|.+.++.++++.+.+.+...++.+-|.++ ++.+..-+++|=.-
T Consensus 16 ~a~it~k~~~~~~~~~~ekk~~l~~i~~~leEa~ell~qMdlEvr~lp~~~---Rs~~~~KlR~yksd 80 (220)
T KOG1666|consen 16 SAEITKKIGRALSLPGSEKKQLLSEIDSKLEEANELLDQMDLEVRELPPNF---RSSYLSKLREYKSD 80 (220)
T ss_pred HHHHHHhHHHHhcCCchHHHHHHHHHHHhHHHHHHHHHHHHHHHHhCCchh---hhHHHHHHHHHHHH
Confidence 44455566666665 45666788888888888888888877775544333 45555556655443
No 46
>smart00150 SPEC Spectrin repeats.
Probab=30.18 E-value=1.9e+02 Score=20.05 Aligned_cols=59 Identities=17% Similarity=0.274 Sum_probs=33.2
Q ss_pred HHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCchhHHhcHHHHHHHHHHHHHHHHHHhc
Q 027481 78 MEKQFEDFRVKLDEAGSLRERIRAVVNEIESITRLMHASLLHVHQSRPLSEVLEKPKAQVDGLKELYGRLAEVLC 152 (223)
Q Consensus 78 v~~~F~~fr~eLDe~~d~RErI~kisRdIe~~tr~sk~vI~~lHr~~~~~~~l~~A~~~l~~i~~~~~~La~~l~ 152 (223)
....|..|+.+++...+.-+.|.+..+++ +..-|.. .......+.++...|..|...+.
T Consensus 36 ~~~~~~~~~~e~~~~~~~v~~~~~~~~~L----------~~~~~~~------~~~i~~~~~~l~~~w~~l~~~~~ 94 (101)
T smart00150 36 LLKKHEALEAELEAHEERVEALNELGEQL----------IEEGHPD------AEEIEERLEELNERWEELKELAE 94 (101)
T ss_pred HHHHHHHHHHHHHHhHHHHHHHHHHHHHH----------HHcCCCc------HHHHHHHHHHHHHHHHHHHHHHH
Confidence 44447777777777777777776666666 2222211 23344455566666666555443
No 47
>PF13427 DUF4111: Domain of unknown function (DUF4111)
Probab=29.86 E-value=2.1e+02 Score=22.11 Aligned_cols=49 Identities=20% Similarity=0.228 Sum_probs=31.2
Q ss_pred HHHHHHHHHHHHHHHHhccCCCccchhccccchhHHHHHHHHHHHHHHhcCCccCHHHHHHH
Q 027481 135 AQVDGLKELYGRLAEVLCECPGEYYRFHNDWRSETQTVVSLLAFMHWLETGKLLMHTEAEEK 196 (223)
Q Consensus 135 ~~l~~i~~~~~~La~~l~~~p~~yYRY~~~ws~~lQE~VEalsf~~yLe~g~Llt~eEv~~~ 196 (223)
..++.|...+..+...+. .+++| + ..-++=.++++++|.++|+++.++.
T Consensus 12 ~~~~ai~~~l~~~~~~~~--~~~~~--------~---vL~LcR~~~tl~tg~i~SK~~aa~W 60 (106)
T PF13427_consen 12 DYRDAIRDDLPEWEADIE--GDPRY--------V---VLNLCRILYTLRTGEIVSKDEAAEW 60 (106)
T ss_pred HHHHHHHHHHHHHHHhhc--cChHH--------H---HHHHHHHHHHHHhCCcccHHHHHHH
Confidence 344556666666666666 33343 1 2223335678899999999999874
No 48
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=29.86 E-value=32 Score=21.60 Aligned_cols=25 Identities=20% Similarity=0.341 Sum_probs=16.6
Q ss_pred cCHHHHHHHhCCCC--------CccCcChhHHh
Q 027481 188 LMHTEAEEKLGMNQ--------AEFALDIEDYL 212 (223)
Q Consensus 188 lt~eEv~~~Lgv~~--------~~f~L~~eDYL 212 (223)
++.++|++.+|++. ..+.+++-+|+
T Consensus 9 ~~l~~iA~~~g~S~~~f~r~Fk~~~g~tp~~y~ 41 (42)
T PF00165_consen 9 LTLEDIAEQAGFSPSYFSRLFKKETGMTPKQYR 41 (42)
T ss_dssp --HHHHHHHHTS-HHHHHHHHHHHTSS-HHHHH
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHCcCHHHHh
Confidence 78899999999854 35677777776
No 49
>PF10398 DUF2443: Protein of unknown function (DUF2443); InterPro: IPR019469 This entry represents a small group of highly conserved proteins from bacteria, in particular Helicobacter species. The structure is a bundle of alpha helices. The function is not known. ; PDB: 1ZKE_F.
Probab=29.74 E-value=2.4e+02 Score=21.14 Aligned_cols=53 Identities=23% Similarity=0.337 Sum_probs=27.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhc----------cC-CCchh-----HHhcHHHHHHHHHHHHHHHHH
Q 027481 97 ERIRAVVNEIESITRLMHASLLHVH----------QS-RPLSE-----VLEKPKAQVDGLKELYGRLAE 149 (223)
Q Consensus 97 ErI~kisRdIe~~tr~sk~vI~~lH----------r~-~~~~~-----~l~~A~~~l~~i~~~~~~La~ 149 (223)
|+|..+-++||.+-.++.-+|...+ |+ -+.|+ .+.+..+.+.++++++..|.+
T Consensus 3 Ekid~I~k~IE~~~~eIe~LL~~AkiSl~DyImiKRGS~DmPe~l~~~~~~QideeV~~LKe~IdaLNK 71 (79)
T PF10398_consen 3 EKIDLILKNIENAQEEIEILLKIAKISLVDYIMIKRGSQDMPEHLNMAFLAQIDEEVEKLKEHIDALNK 71 (79)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHT--HHHHHHHHTTSS---TTS-HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHhhccHHHHHHhcccCCcCcccccHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5666666666665555554444333 44 33443 455666666666666554443
No 50
>PF15011 CK2S: Casein Kinase 2 substrate
Probab=28.49 E-value=1.5e+02 Score=24.87 Aligned_cols=36 Identities=17% Similarity=0.356 Sum_probs=29.9
Q ss_pred chHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHH
Q 027481 76 ASMEKQFEDFRVKLDEAGSLRERIRAVVNEIESITR 111 (223)
Q Consensus 76 ~~v~~~F~~fr~eLDe~~d~RErI~kisRdIe~~tr 111 (223)
..++.+|..+++.|++-+++|+.+-+.+++..+...
T Consensus 67 ~ale~vl~~L~e~l~~l~~v~~~l~~~~~~~~~l~~ 102 (168)
T PF15011_consen 67 EALETVLAKLRETLEELQKVRDSLSRQVRDVFQLYE 102 (168)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 457788999999999999999999999998865544
No 51
>PF05633 DUF793: Protein of unknown function (DUF793); InterPro: IPR008511 This entry includes Protein BYPASS 1 which is required for normal root and shoot development. Prevents constitutive production of a root mobile carotenoid-derived signaling compound that is capable of arresting shoot and leaf development [, ].
Probab=28.27 E-value=3.5e+02 Score=26.14 Aligned_cols=73 Identities=18% Similarity=0.207 Sum_probs=41.3
Q ss_pred HHHHHHHHHHHhhhhhHHHHH-----HHHHHHHHHHHHHHHHHHHhhccCCCchhHHhcHHHHHHHHHHHHHHHHHHhc
Q 027481 79 EKQFEDFRVKLDEAGSLRERI-----RAVVNEIESITRLMHASLLHVHQSRPLSEVLEKPKAQVDGLKELYGRLAEVLC 152 (223)
Q Consensus 79 ~~~F~~fr~eLDe~~d~RErI-----~kisRdIe~~tr~sk~vI~~lHr~~~~~~~l~~A~~~l~~i~~~~~~La~~l~ 152 (223)
..-|..+|+.+.++-++|++= .+--..+|...+....++..++... -.+..++.++..+++.+....|.+-+.
T Consensus 288 A~s~~~LQ~rI~eEikkk~~kgs~gLLkEl~~ve~~vr~L~el~d~~~~p~-~~e~~~ev~~~V~EL~~~~~~L~~GLd 365 (389)
T PF05633_consen 288 APSFISLQERINEEIKKKERKGSCGLLKELQQVEASVRELHELIDSFQFPL-EEEKEEEVREAVEELARVCEALSQGLD 365 (389)
T ss_pred chHHHHHHHHHHHHHhhccccCcchHHHHHHHHHHHHHHHHHHHHhccCCc-chhHHHHHHHHHHHHHHHHHHHHcccH
Confidence 344777788777777776643 3444445556667777777776541 112234444555555555555555554
No 52
>PF01369 Sec7: Sec7 domain; InterPro: IPR000904 The SEC7 domain was named after the first protein found to contain such a region []. It has been shown to be linked with guanine nucleotide exchange function [, ]. The 3D structure of the domain displays several alpha-helices []. It was found to be associated with other domains involved in guanine nucleotide exchange (e.g., CDC25, Dbl) in mammalian factors [].; GO: 0005086 ARF guanyl-nucleotide exchange factor activity, 0032012 regulation of ARF protein signal transduction, 0005622 intracellular; PDB: 3SWV_A 3L8N_A 2R09_A 2R0D_B 1RE0_B 3LTL_A 1KU1_A 1XSZ_A 1XT0_B 1R8Q_E ....
Probab=27.50 E-value=62 Score=27.31 Aligned_cols=44 Identities=18% Similarity=0.107 Sum_probs=29.8
Q ss_pred HHHHHHHhcCCccCHHHHHHHhCCCCCccCcChhHHhhhhhhccc
Q 027481 176 LAFMHWLETGKLLMHTEAEEKLGMNQAEFALDIEDYLIGEHSDEC 220 (223)
Q Consensus 176 lsf~~yLe~g~Llt~eEv~~~Lgv~~~~f~L~~eDYLlGL~DLtG 220 (223)
.....||....-+.+..+++.||-+ +.+...+-.+.+..+|+.|
T Consensus 39 ~~iA~fL~~~~~l~k~~ige~Lg~~-~~~n~~vL~~y~~~fdf~~ 82 (190)
T PF01369_consen 39 KSIAKFLFQTPGLDKKKIGEYLGKD-NPFNRDVLKEYISLFDFSG 82 (190)
T ss_dssp HHHHHHHHHTTTS-HHHHHHHHTSS-SHHHHHHHHHHHHTSS-TT
T ss_pred HHHHHHHHhCCCCCHHHHHHHHhcc-chHHHHHHHHHHHHcCCcC
Confidence 3466778777889999999999963 3455555555556677665
No 53
>PF04355 SmpA_OmlA: SmpA / OmlA family; InterPro: IPR007450 This is a bacterial outer membrane lipoprotein, possibly involved in maintaining the structural integrity of the cell envelope []. The lipid attachment site is a conserved N-terminal cysteine residue sometimes found adjacent to the OmpA domain (IPR006665 from INTERPRO).; GO: 0019867 outer membrane; PDB: 4DM5_C 2PXG_A 2YH9_B 2KXX_A 2KM7_A.
Probab=27.16 E-value=25 Score=24.66 Aligned_cols=30 Identities=17% Similarity=0.278 Sum_probs=21.3
Q ss_pred hcCCccCHHHHHHHhCCCC--CccCcChhHHhhh
Q 027481 183 ETGKLLMHTEAEEKLGMNQ--AEFALDIEDYLIG 214 (223)
Q Consensus 183 e~g~Llt~eEv~~~Lgv~~--~~f~L~~eDYLlG 214 (223)
+.| +|.+||..+||-|. +.|+-...+|+.-
T Consensus 13 ~~G--mTk~qV~~lLG~P~~~~~~~~~~W~Y~~~ 44 (71)
T PF04355_consen 13 KPG--MTKDQVRALLGSPSLRDPFDPNRWYYVYS 44 (71)
T ss_dssp -TT--SBHHHHHHHHTS-SEE-CTTSSEEEEEEE
T ss_pred cCC--CCHHHHHHhcCCCCccccccCCEEEEEEE
Confidence 455 89999999999887 6677777777643
No 54
>PRK10404 hypothetical protein; Provisional
Probab=27.13 E-value=3e+02 Score=21.32 Aligned_cols=21 Identities=10% Similarity=0.276 Sum_probs=12.2
Q ss_pred hhhHHHHHHHHHHHHHHHHHH
Q 027481 92 AGSLRERIRAVVNEIESITRL 112 (223)
Q Consensus 92 ~~d~RErI~kisRdIe~~tr~ 112 (223)
..++++.|..++.|+|...+.
T Consensus 7 ~~~l~~dl~~L~~dle~Ll~~ 27 (101)
T PRK10404 7 DTRIDDDLTLLSETLEEVLRS 27 (101)
T ss_pred hhHHHHHHHHHHHHHHHHHHH
Confidence 345566666666666554443
No 55
>PF09548 Spore_III_AB: Stage III sporulation protein AB (spore_III_AB); InterPro: IPR014198 This entry represents the stage III sporulation protein AB, which is encoded in a spore formation operon: spoIIIAABCDEFGH that is under sigma G regulation []. A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species.
Probab=27.06 E-value=1.7e+02 Score=24.22 Aligned_cols=48 Identities=25% Similarity=0.444 Sum_probs=34.8
Q ss_pred CCchhHHhcHHHHH-HHHHHHHHHHHHHhccCCCccchhccccchhHHHHH
Q 027481 124 RPLSEVLEKPKAQV-DGLKELYGRLAEVLCECPGEYYRFHNDWRSETQTVV 173 (223)
Q Consensus 124 ~~~~~~l~~A~~~l-~~i~~~~~~La~~l~~~p~~yYRY~~~ws~~lQE~V 173 (223)
++.++.+.++-... ..+...+..+++.+.+.. -..+...|..++.++-
T Consensus 49 tpL~eal~~i~~~~~~~~~~~f~~~a~~L~~~~--~~~~~~~w~~~~~~~~ 97 (170)
T PF09548_consen 49 TPLPEALERISRRSEGPIGEFFERVAERLEKNE--GESFAEAWEEAVEKLL 97 (170)
T ss_pred CCHHHHHHHHHhcccchHHHHHHHHHHHHHcCC--CCCHHHHHHHHHHhhh
Confidence 67888888866655 468888999999998433 3457788877766543
No 56
>PF13713 BRX_N: Transcription factor BRX N-terminal domain
Probab=26.97 E-value=85 Score=20.55 Aligned_cols=24 Identities=21% Similarity=0.178 Sum_probs=21.3
Q ss_pred HHhcHHHHHHHHHHHHHHHHHHhc
Q 027481 129 VLEKPKAQVDGLKELYGRLAEVLC 152 (223)
Q Consensus 129 ~l~~A~~~l~~i~~~~~~La~~l~ 152 (223)
-+..|++.++.+..+++.+++.++
T Consensus 6 k~kaaKe~IKsLt~QlK~maekl~ 29 (39)
T PF13713_consen 6 KCKAAKEVIKSLTAQLKDMAEKLP 29 (39)
T ss_pred ccHHHHHHHHHHHHHHHHHHHhCc
Confidence 367789999999999999999998
No 57
>KOG0201 consensus Serine/threonine protein kinase [Signal transduction mechanisms]
Probab=26.70 E-value=51 Score=32.35 Aligned_cols=80 Identities=18% Similarity=0.281 Sum_probs=51.8
Q ss_pred HHhcHHHHHHHHHHHHHHHHHHhccCCCccchhccccchhHHHHHHHHHHHHHHhcCCccCHHHHHHHhCCCCCccCcCh
Q 027481 129 VLEKPKAQVDGLKELYGRLAEVLCECPGEYYRFHNDWRSETQTVVSLLAFMHWLETGKLLMHTEAEEKLGMNQAEFALDI 208 (223)
Q Consensus 129 ~l~~A~~~l~~i~~~~~~La~~l~~~p~~yYRY~~~ws~~lQE~VEalsf~~yLe~g~Llt~eEv~~~Lgv~~~~f~L~~ 208 (223)
.+++++..+++|++-+.-|+..=. ++ .=+|++.+-.+. ..+.+++|+..|.+...-+....+ +....++-+
T Consensus 47 ~Le~~~deIediqqei~~Ls~~~~--~~-it~yygsyl~g~----~LwiiMey~~gGsv~~lL~~~~~~--~E~~i~~il 117 (467)
T KOG0201|consen 47 DLEEAEDEIEDIQQEISVLSQCDS--PN-ITEYYGSYLKGT----KLWIIMEYCGGGSVLDLLKSGNIL--DEFEIAVIL 117 (467)
T ss_pred chhhcchhhHHHHHHHHHHHhcCc--ch-HHhhhhheeecc----cHHHHHHHhcCcchhhhhccCCCC--ccceeeeeh
Confidence 367788888888888877776533 31 225666665443 567899999999888777744333 223455556
Q ss_pred hHHhhhhhh
Q 027481 209 EDYLIGEHS 217 (223)
Q Consensus 209 eDYLlGL~D 217 (223)
-|-|+||--
T Consensus 118 re~l~~l~y 126 (467)
T KOG0201|consen 118 REVLKGLDY 126 (467)
T ss_pred HHHHHHhhh
Confidence 666666643
No 58
>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=26.58 E-value=2.2e+02 Score=19.70 Aligned_cols=62 Identities=15% Similarity=0.247 Sum_probs=28.7
Q ss_pred HHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCchhHHhcHHHHHHHHHHHHHHHHHHhc
Q 027481 85 FRVKLDEAGSLRERIRAVVNEIESITRLMHASLLHVHQSRPLSEVLEKPKAQVDGLKELYGRLAEVLC 152 (223)
Q Consensus 85 fr~eLDe~~d~RErI~kisRdIe~~tr~sk~vI~~lHr~~~~~~~l~~A~~~l~~i~~~~~~La~~l~ 152 (223)
++..+.+...+.+.|...-..|+........++..-|.. -...+..+..+...|..|...+.
T Consensus 36 ~~~~~~~~~~~~~ei~~~~~~l~~l~~~~~~L~~~~~~~------~~~i~~~~~~l~~~w~~l~~~~~ 97 (105)
T PF00435_consen 36 LEEQLKKHKELQEEIESRQERLESLNEQAQQLIDSGPED------SDEIQEKLEELNQRWEALCELVE 97 (105)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHTT------HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHcCCCc------HHHHHHHHHHHHHHHHHHHHHHH
Confidence 333444444444444444444444444444443333321 23445555666666666655543
No 59
>PF10234 Cluap1: Clusterin-associated protein-1; InterPro: IPR019366 This protein of 413 amino acids contains a central coiled-coil domain, possibly the region that binds to clusterin. Cluap1 expression is highest in the nucleus and gradually increases during late S to G2/M phases of the cell cycle and returns to the basal level in the G0/G1 phases. In addition, it is upregulated in colon cancer tissues compared to corresponding non-cancerous mucosa. It thus plays a crucial role in the life of the cell [].
Probab=26.46 E-value=2.5e+02 Score=25.62 Aligned_cols=55 Identities=18% Similarity=0.247 Sum_probs=35.2
Q ss_pred HhcHHHHHHHHHHHHHHHHHHhccCCCccchhccccchhHHHHHHHHHHHHHHhc
Q 027481 130 LEKPKAQVDGLKELYGRLAEVLCECPGEYYRFHNDWRSETQTVVSLLAFMHWLET 184 (223)
Q Consensus 130 l~~A~~~l~~i~~~~~~La~~l~~~p~~yYRY~~~ws~~lQE~VEalsf~~yLe~ 184 (223)
+++-+..++.-++.+..|...=|.|-++|=+...-...-.+.|++-.==..||++
T Consensus 199 Iekkk~ELER~qKRL~sLq~vRPAfmdEyEklE~EL~~lY~~Y~~kfRNl~yLe~ 253 (267)
T PF10234_consen 199 IEKKKQELERNQKRLQSLQSVRPAFMDEYEKLEEELQKLYEIYVEKFRNLDYLEH 253 (267)
T ss_pred HHHHHHHHHHHHHHHHHHHhcChHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHH
Confidence 3334444555566667777666655566666666666677777777777777763
No 60
>PRK04778 septation ring formation regulator EzrA; Provisional
Probab=26.40 E-value=3.6e+02 Score=26.76 Aligned_cols=61 Identities=11% Similarity=0.168 Sum_probs=33.3
Q ss_pred hhHHhcHHHHHHHHHHHHHHHHHH-----hccCCCccchhccccchhHHHHHHHHHHHHHHhcCCccCHHHHH
Q 027481 127 SEVLEKPKAQVDGLKELYGRLAEV-----LCECPGEYYRFHNDWRSETQTVVSLLAFMHWLETGKLLMHTEAE 194 (223)
Q Consensus 127 ~~~l~~A~~~l~~i~~~~~~La~~-----l~~~p~~yYRY~~~ws~~lQE~VEalsf~~yLe~g~Llt~eEv~ 194 (223)
.+.-.+|+..+..++..+..+... +||-|..|.-|-..++..+++ +..=|+. .=+..+.|.
T Consensus 410 rk~E~eAr~kL~~~~~~L~~ikr~l~k~~lpgip~~y~~~~~~~~~~i~~------l~~~L~~-g~VNm~ai~ 475 (569)
T PRK04778 410 RKDELEAREKLERYRNKLHEIKRYLEKSNLPGLPEDYLEMFFEVSDEIEA------LAEELEE-KPINMEAVN 475 (569)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCcHHHHHHHHHHHHHHHH------HHHHhcc-CCCCHHHHH
Confidence 334456777787777777777644 355555554444444433333 3334555 335555555
No 61
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=26.05 E-value=51 Score=23.17 Aligned_cols=18 Identities=33% Similarity=0.516 Sum_probs=13.3
Q ss_pred hcCCccCHHHHHHHhCCC
Q 027481 183 ETGKLLMHTEAEEKLGMN 200 (223)
Q Consensus 183 e~g~Llt~eEv~~~Lgv~ 200 (223)
+.|+-+|.+||++.||++
T Consensus 16 ~lgr~Pt~eEiA~~lgis 33 (78)
T PF04539_consen 16 ELGREPTDEEIAEELGIS 33 (78)
T ss_dssp HHSS--BHHHHHHHHTS-
T ss_pred HhCCCCCHHHHHHHHccc
Confidence 468899999999999975
No 62
>PF10475 DUF2450: Protein of unknown function N-terminal domain (DUF2450) ; InterPro: IPR019515 This entry represents Vacuolar protein sorting-associated protein 54, and is thought to be involved in retrograde transport from early and late endosomes to late Golgi found in eukaryotes, but its function is not known.
Probab=25.69 E-value=3.9e+02 Score=23.95 Aligned_cols=25 Identities=8% Similarity=0.173 Sum_probs=14.4
Q ss_pred HHHHHHHHhhhhhHHHHHHHHHHHH
Q 027481 82 FEDFRVKLDEAGSLRERIRAVVNEI 106 (223)
Q Consensus 82 F~~fr~eLDe~~d~RErI~kisRdI 106 (223)
.++|-+.|...+++++.+......+
T Consensus 59 s~~f~~a~~~v~el~~~l~~a~~~~ 83 (291)
T PF10475_consen 59 SDSFFQAMSSVQELQDELEEALVIC 83 (291)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5555556666666666555555544
No 63
>PF05667 DUF812: Protein of unknown function (DUF812); InterPro: IPR008530 This family consists of several eukaryotic proteins of unknown function.
Probab=25.41 E-value=1.9e+02 Score=29.21 Aligned_cols=19 Identities=5% Similarity=0.263 Sum_probs=8.7
Q ss_pred cchhccccchhHHHHHHHH
Q 027481 158 YYRFHNDWRSETQTVVSLL 176 (223)
Q Consensus 158 yYRY~~~ws~~lQE~VEal 176 (223)
-|||--.....++++|+++
T Consensus 552 aYK~La~lh~~c~~Li~~v 570 (594)
T PF05667_consen 552 AYKLLASLHENCSQLIETV 570 (594)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 3444444444444444443
No 64
>PRK11637 AmiB activator; Provisional
Probab=25.14 E-value=4.9e+02 Score=24.58 Aligned_cols=17 Identities=6% Similarity=0.167 Sum_probs=8.4
Q ss_pred hHHHHHHHHHHHHhhhh
Q 027481 77 SMEKQFEDFRVKLDEAG 93 (223)
Q Consensus 77 ~v~~~F~~fr~eLDe~~ 93 (223)
...+..++++.++++.+
T Consensus 44 ~~~~~l~~l~~qi~~~~ 60 (428)
T PRK11637 44 DNRDQLKSIQQDIAAKE 60 (428)
T ss_pred hhHHHHHHHHHHHHHHH
Confidence 34444555555554443
No 65
>PF08700 Vps51: Vps51/Vps67; InterPro: IPR014812 The VFT tethering complex (also known as GARP complex, Golgi associated retrograde protein complex, Vps53 tethering complex) is a conserved eukaryotic docking complex which is involved in recycling of proteins from endosomes to the late Golgi. Vps51 (also known as Vps67) is a subunit of VFT and interacts with the SNARE Tlg1 [].
Probab=24.91 E-value=2.6e+02 Score=19.91 Aligned_cols=74 Identities=14% Similarity=0.217 Sum_probs=35.0
Q ss_pred hHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHhhccC-CCchhHHhcHHHHHHHHHHHHHHHHHHh
Q 027481 77 SMEKQFEDFRVKLDEAGSLRERIRAVVNEIESITRLMHASLLHVHQS-RPLSEVLEKPKAQVDGLKELYGRLAEVL 151 (223)
Q Consensus 77 ~v~~~F~~fr~eLDe~~d~RErI~kisRdIe~~tr~sk~vI~~lHr~-~~~~~~l~~A~~~l~~i~~~~~~La~~l 151 (223)
.+...|..+-.... ..+++..-.++.++|+......+.+++.=++- -...+.+...+..+.+++..+.+|...+
T Consensus 7 d~~~~~~~~l~~~s-~~~i~~~~~~L~~~i~~~~~eLr~~V~~nY~~fI~as~~I~~m~~~~~~l~~~l~~l~~~~ 81 (87)
T PF08700_consen 7 DVDEYFKDLLKNSS-IKEIRQLENKLRQEIEEKDEELRKLVYENYRDFIEASDEISSMENDLSELRNLLSELQQSI 81 (87)
T ss_pred CHHHHHHHHHhhCC-HHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444554444333 23444555555566665567777776654432 1122223333444444555555444443
No 66
>PF10498 IFT57: Intra-flagellar transport protein 57 ; InterPro: IPR019530 Eukaryotic cilia and flagella are specialised organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bi-directional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated []. This protein is known as Huntington-interacting protein-1 in humans.
Probab=24.45 E-value=2.5e+02 Score=26.56 Aligned_cols=22 Identities=23% Similarity=0.404 Sum_probs=8.4
Q ss_pred hhhhhHHHHHHHHHHHHHHHHH
Q 027481 90 DEAGSLRERIRAVVNEIESITR 111 (223)
Q Consensus 90 De~~d~RErI~kisRdIe~~tr 111 (223)
++..+.+++....+..|+..++
T Consensus 280 ~~ls~~~~~y~~~s~~V~~~t~ 301 (359)
T PF10498_consen 280 DELSEVQEKYKQASEGVSERTR 301 (359)
T ss_pred HHHHHHHHHHHHHhhHHHHHHH
Confidence 3333334444444444433333
No 67
>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=24.26 E-value=3e+02 Score=20.65 Aligned_cols=30 Identities=20% Similarity=0.161 Sum_probs=16.7
Q ss_pred hHHHHHHHHHHHHhhhhhHHHHHHHHHHHH
Q 027481 77 SMEKQFEDFRVKLDEAGSLRERIRAVVNEI 106 (223)
Q Consensus 77 ~v~~~F~~fr~eLDe~~d~RErI~kisRdI 106 (223)
.+.+.....++-..+-+++|.+--.+++.|
T Consensus 30 ~i~~ld~~~r~l~~~~e~lr~~rN~~sk~I 59 (108)
T PF02403_consen 30 EIIELDQERRELQQELEELRAERNELSKEI 59 (108)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhHHHHHH
Confidence 344445555555555555565555555555
No 68
>cd07604 BAR_ASAPs The Bin/Amphiphysin/Rvs (BAR) domain of ArfGAP with SH3 domain, 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 ASAPs (ArfGAP with SH3 domain, ANK repeat and PH domain containing proteins), which are Arf GTPase activating proteins (GAPs) with similarity to ACAPs (ArfGAP with Coiled-coil, ANK repeat and PH domain containing proteins) in that they contain an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, an Arf GAP domain, and ankyrin (ANK) repeats. However, ASAPs contain an additional C-terminal SH3 domain. ASAPs function in regulating cell growth, migration, and invasion. Vertebrates contain at least three members, ASAP1, ASAP2, and ASAP3. ASAP1 and ASAP2 shows GTPase activating protein (GAP) activity towards Arf1 and Arf5. They do not show GAP activity towards Arf6, but is able to mediate
Probab=24.23 E-value=3.8e+02 Score=23.46 Aligned_cols=66 Identities=18% Similarity=0.171 Sum_probs=39.2
Q ss_pred hHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHhhccC--CCchhHHhcHHHHHHHHHHHHHHHHHHh
Q 027481 77 SMEKQFEDFRVKLDEAGSLRERIRAVVNEIESITRLMHASLLHVHQS--RPLSEVLEKPKAQVDGLKELYGRLAEVL 151 (223)
Q Consensus 77 ~v~~~F~~fr~eLDe~~d~RErI~kisRdIe~~tr~sk~vI~~lHr~--~~~~~~l~~A~~~l~~i~~~~~~La~~l 151 (223)
.|...|..|..-+.+..+.|+.++.-+.++ +++.+++. .++..+..++++.++...+.|....+.+
T Consensus 60 ~i~~~l~kF~~~l~El~~~~~~L~~~~~~~---------i~~pL~~f~k~dL~~~k~e~KK~fdK~s~~ye~~~~k~ 127 (215)
T cd07604 60 DLGAAFLKFSVFTKELAALFKNLMQNLNNI---------IMFPLDSLLKGDLKGSKGDLKKPFDKAWKDYETKASKI 127 (215)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---------HHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 466778888888888888888887666554 44444433 2333333455555655555444333333
No 69
>PF12728 HTH_17: Helix-turn-helix domain
Probab=23.77 E-value=60 Score=21.03 Aligned_cols=14 Identities=43% Similarity=0.548 Sum_probs=12.4
Q ss_pred ccCHHHHHHHhCCC
Q 027481 187 LLMHTEAEEKLGMN 200 (223)
Q Consensus 187 Llt~eEv~~~Lgv~ 200 (223)
++|.+|+++.||++
T Consensus 1 ~lt~~e~a~~l~is 14 (51)
T PF12728_consen 1 YLTVKEAAELLGIS 14 (51)
T ss_pred CCCHHHHHHHHCcC
Confidence 47899999999986
No 70
>TIGR02492 flgK_ends flagellar hook-associated protein FlgK. The flagellar hook-associated protein FlgK of bacterial flagella has conserved N- and C-terminal domains. The central region is highly variable in length and sequence, and often contains substantial runs of low-complexity sequence. This model is built from an alignment of FlgK sequences with the central region excised. Note that several other proteins of the flagellar apparatus also are homologous in the N- and C-terminal regions to FlgK, but are excluded from this model.
Probab=23.53 E-value=5.2e+02 Score=23.53 Aligned_cols=71 Identities=7% Similarity=0.163 Sum_probs=39.0
Q ss_pred CCcchHHHHHHHHHHHHhh--hhhHHHHHHHHHHHHHHHHHHHHHHHHhhccC--CCchhHHhcHHHHHHHHHHH
Q 027481 73 DAPASMEKQFEDFRVKLDE--AGSLRERIRAVVNEIESITRLMHASLLHVHQS--RPLSEVLEKPKAQVDGLKEL 143 (223)
Q Consensus 73 ~~~~~v~~~F~~fr~eLDe--~~d~RErI~kisRdIe~~tr~sk~vI~~lHr~--~~~~~~l~~A~~~l~~i~~~ 143 (223)
.....+.+.|..+++--.. ....|+.++.....+....+....-|..+... .++...++++...+++|.+.
T Consensus 104 gl~~~l~~ff~a~~~ls~~P~~~~~r~~vl~~a~~l~~~~n~~~~~L~~~~~~~~~~i~~~V~~iN~ll~~Ia~l 178 (322)
T TIGR02492 104 GLSTYLNNFFNALQELAKNPDSEALRQAVLESAQALANSFNQTSNELQDLRKGINAEIKSAVTEINSLLKQIASL 178 (322)
T ss_pred cHHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445566667777665442 45567888888877755555555556655433 22333334444444333333
No 71
>KOG4796 consensus RNA polymerase II elongation factor [Transcription]
Probab=22.88 E-value=4.7e+02 Score=26.60 Aligned_cols=33 Identities=21% Similarity=0.391 Sum_probs=26.4
Q ss_pred HHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHH
Q 027481 82 FEDFRVKLDEAGSLRERIRAVVNEIESITRLMH 114 (223)
Q Consensus 82 F~~fr~eLDe~~d~RErI~kisRdIe~~tr~sk 114 (223)
|..|.++-+|..++.+||-++++...+...+.+
T Consensus 507 k~dF~~eY~EYreLharve~vs~rF~~Lea~L~ 539 (604)
T KOG4796|consen 507 KKDFEAEYDEYRELHARVETVSRRFRQLEAQLK 539 (604)
T ss_pred HHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 888999999999999999999998844333333
No 72
>PF07182 DUF1402: Protein of unknown function (DUF1402); InterPro: IPR009842 This family consists of several hypothetical bacterial proteins of around 310 residues in length. Members of this family seem to be found exclusively in Agrobacterium, Rhizobium and Brucella species. The function of this family is unknown.
Probab=22.83 E-value=2e+02 Score=26.58 Aligned_cols=59 Identities=20% Similarity=0.296 Sum_probs=40.2
Q ss_pred CCCCCCCCCccccccccCCCcccccCCCCCCCCCcchHHHHHHHHHHHHhhhhhHHHHHHHHHHHH
Q 027481 41 SLVSPSKPETFRFRRRSSPLRVRYSSMTGGETDAPASMEKQFEDFRVKLDEAGSLRERIRAVVNEI 106 (223)
Q Consensus 41 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~F~~fr~eLDe~~d~RErI~kisRdI 106 (223)
..+-|.-+ |+..-|. .+..| +..|-..+...+.-|+.+.+-|..+..++-+|++++.--
T Consensus 11 ~~~VP~GN-----R~~eQP~-IP~AS-~rRT~a~~ttyd~Ky~Kv~~lL~~D~~L~~kIk~~a~~Y 69 (303)
T PF07182_consen 11 ATVVPPGN-----RNAEQPP-IPGAS-ARRTKAFKTTYDAKYEKVRDLLARDRKLRGKIKKVAAAY 69 (303)
T ss_pred ceecCCCC-----CCccCCC-CCchh-hhhhhcccccHHHHHHHHHHHHhhcHHHHHHHHHHHHHc
Confidence 34555543 3334455 44444 344445666888889999999999999999998887643
No 73
>PRK10807 paraquat-inducible protein B; Provisional
Probab=22.83 E-value=7.7e+02 Score=24.58 Aligned_cols=46 Identities=11% Similarity=0.052 Sum_probs=20.8
Q ss_pred HHHHHHHHHHHHHhccCCCccchhccccchhHHHHH----HHHHHHHHHhc
Q 027481 138 DGLKELYGRLAEVLCECPGEYYRFHNDWRSETQTVV----SLLAFMHWLET 184 (223)
Q Consensus 138 ~~i~~~~~~La~~l~~~p~~yYRY~~~ws~~lQE~V----Ealsf~~yLe~ 184 (223)
.++++.+.++...+.+....-- -+......+|++- ++-.+..+|+.
T Consensus 476 ~~L~~TL~~l~~~l~~~~~~s~-~~~~l~~tl~~l~~~~r~lr~l~~~L~~ 525 (547)
T PRK10807 476 ADMQKTLRELNRSMQGFQPGSP-AYNKMVADMQRLDQVLRELQPVLKTLNE 525 (547)
T ss_pred HHHHHHHHHHHHHHhhcCCCCh-HHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 4556666666665553111110 1123334444443 33456666653
No 74
>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=22.76 E-value=3.8e+02 Score=21.06 Aligned_cols=63 Identities=21% Similarity=0.254 Sum_probs=29.9
Q ss_pred HHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCchhHHhcHHHHHHHHHHHHHHHHHHh
Q 027481 84 DFRVKLDEAGSLRERIRAVVNEIESITRLMHASLLHVHQSRPLSEVLEKPKAQVDGLKELYGRLAEVL 151 (223)
Q Consensus 84 ~fr~eLDe~~d~RErI~kisRdIe~~tr~sk~vI~~lHr~~~~~~~l~~A~~~l~~i~~~~~~La~~l 151 (223)
.+++.+++..+.++.|......|+........++...+... .......+..+...+..|...+
T Consensus 140 ~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-----~~~~~~~l~~l~~~~~~l~~~~ 202 (213)
T cd00176 140 SVEELLKKHKELEEELEAHEPRLKSLNELAEELLEEGHPDA-----DEEIEEKLEELNERWEELLELA 202 (213)
T ss_pred HHHHHHHHHHHHHHHHHhchHHHHHHHHHHHHHHHcCCCCc-----HHHHHHHHHHHHHHHHHHHHHH
Confidence 34445555555555555555555444555555555554331 0223334444444444444443
No 75
>PF12732 YtxH: YtxH-like protein; InterPro: IPR024623 This family of uncharacterised proteins is found in bacteria. Proteins in this family are typically between 100 and 143 amino acids in length. The N-terminal region is the most conserved.
Probab=22.43 E-value=2.9e+02 Score=19.57 Aligned_cols=14 Identities=14% Similarity=0.449 Sum_probs=8.2
Q ss_pred hhHHHHHHHHHHHH
Q 027481 93 GSLRERIRAVVNEI 106 (223)
Q Consensus 93 ~d~RErI~kisRdI 106 (223)
.+.|++|.+.+.++
T Consensus 25 ~e~R~~l~~~~~~~ 38 (74)
T PF12732_consen 25 KETREKLKDKAEDL 38 (74)
T ss_pred HHHHHHHHHHHHHH
Confidence 35566666666655
No 76
>cd03345 eu_TyrOH Eukaryotic tyrosine hydroxylase (TyrOH); a member of the biopterin-dependent aromatic amino acid hydroxylase family of non-heme, iron(II)-dependent enzymes that also includes prokaryotic and eukaryotic phenylalanine-4-hydroxylase (PheOH) and eukaryotic tryptophan hydroxylase (TrpOH). TyrOH catalyzes the conversion of tyrosine to L-dihydroxyphenylalanine (L-DOPA), the rate-limiting step in the biosynthesis of the catecholamines dopamine, noradrenaline, and adrenaline.
Probab=22.42 E-value=4.6e+02 Score=24.44 Aligned_cols=70 Identities=14% Similarity=0.213 Sum_probs=48.4
Q ss_pred HHHHHHHHHHHHHHHHHhccCCCccchhccccchhHHHHHHHHHHHH---HHhcCCccCHHHHHHHhCCCC-------Cc
Q 027481 134 KAQVDGLKELYGRLAEVLCECPGEYYRFHNDWRSETQTVVSLLAFMH---WLETGKLLMHTEAEEKLGMNQ-------AE 203 (223)
Q Consensus 134 ~~~l~~i~~~~~~La~~l~~~p~~yYRY~~~ws~~lQE~VEalsf~~---yLe~g~Llt~eEv~~~Lgv~~-------~~ 203 (223)
.+..+.=+..++++.+.++ . .+.++|.+.+.... =+...+++..+||.+.|.-.+ .|
T Consensus 62 ~eE~~~W~~l~~r~~~l~~--~-----------~Ac~eyl~gl~~L~~~~gl~~d~IPql~dvn~~L~~~TGw~~~pV~G 128 (298)
T cd03345 62 AEEIATWKEVYKTLKDLHA--T-----------HACKEYLDAFQLLEKECGYSEDRIPQLEDVSEFLKERTGFQLRPVAG 128 (298)
T ss_pred HHHHHHHHHHHHHHHHHHh--h-----------hhhHHHHHHHHHHHhccCCCCCCCCCHHHHHHHHHhccCCEEEecCc
Confidence 3334445566777777777 2 36788888887763 356789999999999887432 12
Q ss_pred cCcChhHHhhhhhh
Q 027481 204 FALDIEDYLIGEHS 217 (223)
Q Consensus 204 f~L~~eDYLlGL~D 217 (223)
.|+..|++-||++
T Consensus 129 -li~~~~Ff~~LA~ 141 (298)
T cd03345 129 -LLSARDFLASLAF 141 (298)
T ss_pred -cCCHHHHHHHHhc
Confidence 4677888888764
No 77
>PF04136 Sec34: Sec34-like family ; InterPro: IPR007265 Sec34 and Sec35 form a sub-complex in a seven-protein complex that includes Dor1. This complex is thought to be important for tethering vesicles to the Golgi [].; GO: 0006886 intracellular protein transport, 0005801 cis-Golgi network, 0016020 membrane
Probab=21.90 E-value=4.6e+02 Score=21.63 Aligned_cols=19 Identities=11% Similarity=0.312 Sum_probs=10.9
Q ss_pred ccccchhHHHHHHHHHHHH
Q 027481 162 HNDWRSETQTVVSLLAFMH 180 (223)
Q Consensus 162 ~~~ws~~lQE~VEalsf~~ 180 (223)
.+.+...++++=+++.|+.
T Consensus 94 ~~~F~~~L~~LD~cl~Fl~ 112 (157)
T PF04136_consen 94 SDSFKPMLSRLDECLEFLE 112 (157)
T ss_pred chHHHHHHHHHHHHHHHHH
Confidence 4455556666666666553
No 78
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=21.67 E-value=1.7e+02 Score=20.70 Aligned_cols=43 Identities=21% Similarity=0.084 Sum_probs=26.0
Q ss_pred HHHHHHHHHHHHHhcCCccCHHHHHHHhCCCCCccCcChhHHhhhh
Q 027481 170 QTVVSLLAFMHWLETGKLLMHTEAEEKLGMNQAEFALDIEDYLIGE 215 (223)
Q Consensus 170 QE~VEalsf~~yLe~g~Llt~eEv~~~Lgv~~~~f~L~~eDYLlGL 215 (223)
|.=|....--++-++|-=+|..|+++.+|+.. .=++.+||-.|
T Consensus 8 Q~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S---~~tv~~~L~~L 50 (65)
T PF01726_consen 8 QKEVLEFIREYIEENGYPPTVREIAEALGLKS---TSTVQRHLKAL 50 (65)
T ss_dssp HHHHHHHHHHHHHHHSS---HHHHHHHHTSSS---HHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCC---hHHHHHHHHHH
Confidence 44455555566678999999999999999863 12244555444
No 79
>TIGR02833 spore_III_AB stage III sporulation protein AB. A comparative genome analysis of all sequenced genomes of shows a number of proteins conserved strictly among the endospore-forming subset of the Firmicutes. This protein, a member of this panel, is designated stage III sporulation protein AB.
Probab=21.67 E-value=2.9e+02 Score=23.10 Aligned_cols=61 Identities=21% Similarity=0.321 Sum_probs=39.1
Q ss_pred HHHHHHHHhhccC-----CCchhHHhcHHHHHH-HHHHHHHHHHHHhccCCCccchhccccchhHHHHH
Q 027481 111 RLMHASLLHVHQS-----RPLSEVLEKPKAQVD-GLKELYGRLAEVLCECPGEYYRFHNDWRSETQTVV 173 (223)
Q Consensus 111 r~sk~vI~~lHr~-----~~~~~~l~~A~~~l~-~i~~~~~~La~~l~~~p~~yYRY~~~ws~~lQE~V 173 (223)
++.+.+|+.+..- ++.++.+.+...+.+ .+...+..+++.+.+..+ -.+...|..++.++-
T Consensus 31 ~~l~~~l~~L~~EI~Y~~tpL~ea~~~i~~~~~~~~~~~f~~~a~~L~~~~g--~s~~~~w~~~~~~~~ 97 (170)
T TIGR02833 31 RQLINALQSLEAEIVYGHTPLPEAFKKIALKSPKPVNLLFESASERLKEGEG--LTVYEAWKKALNEVW 97 (170)
T ss_pred HHHHHHHHHHHHHHhhcCCcHHHHHHHHHhhcchhHHHHHHHHHHHHHhCCC--CCHHHHHHHHHHHhh
Confidence 3444445544421 567788887666654 588888999999974332 235688887776653
No 80
>PRK09940 transcriptional regulator YdeO; Provisional
Probab=21.59 E-value=4.8e+02 Score=23.41 Aligned_cols=31 Identities=10% Similarity=0.031 Sum_probs=24.3
Q ss_pred HHhcCCccCHHHHHHHhCCCC---------CccCcChhHHhh
Q 027481 181 WLETGKLLMHTEAEEKLGMNQ---------AEFALDIEDYLI 213 (223)
Q Consensus 181 yLe~g~Llt~eEv~~~Lgv~~---------~~f~L~~eDYLl 213 (223)
.|.++ . +..||+..+|+.. ..+..+|.+|.-
T Consensus 193 LL~~~-~-sI~eIA~~~GF~s~S~Fsr~FKr~~G~TPs~yRk 232 (253)
T PRK09940 193 LIRVE-G-SVNKIAEQCGYASTSYFIYAFRKHFGNSPKRVSK 232 (253)
T ss_pred HHccC-C-CHHHHHHHhCCCCHHHHHHHHHHHHCcCHHHHHH
Confidence 35554 3 9999999999987 457899998865
No 81
>smart00753 PAM PCI/PINT associated module.
Probab=21.47 E-value=1.6e+02 Score=20.97 Aligned_cols=44 Identities=14% Similarity=0.226 Sum_probs=31.2
Q ss_pred hHHHHHHHHHHHHHHhcCCccCHHHHHHHhCCCCCccCcChhHHhhhh
Q 027481 168 ETQTVVSLLAFMHWLETGKLLMHTEAEEKLGMNQAEFALDIEDYLIGE 215 (223)
Q Consensus 168 ~lQE~VEalsf~~yLe~g~Llt~eEv~~~Lgv~~~~f~L~~eDYLlGL 215 (223)
.+++-+--..+..|.+..+-++.+++++.++++.+ ++|+++..+
T Consensus 5 ~l~~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~~~----~vE~~i~~~ 48 (88)
T smart00753 5 RLQRKIRLTNLLQLSEPYSSISLSDLAKLLGLSVP----EVEKLVSKA 48 (88)
T ss_pred HHHHHHHHHHHHHHhHHhceeeHHHHHHHhCcCHH----HHHHHHHHH
Confidence 34555556667777788888999999999998642 356666554
No 82
>smart00088 PINT motif in proteasome subunits, Int-6, Nip-1 and TRIP-15. Also called the PCI (Proteasome, COP9, Initiation factor 3) domain. Unknown function.
Probab=21.47 E-value=1.6e+02 Score=20.97 Aligned_cols=44 Identities=14% Similarity=0.226 Sum_probs=31.2
Q ss_pred hHHHHHHHHHHHHHHhcCCccCHHHHHHHhCCCCCccCcChhHHhhhh
Q 027481 168 ETQTVVSLLAFMHWLETGKLLMHTEAEEKLGMNQAEFALDIEDYLIGE 215 (223)
Q Consensus 168 ~lQE~VEalsf~~yLe~g~Llt~eEv~~~Lgv~~~~f~L~~eDYLlGL 215 (223)
.+++-+--..+..|.+..+-++.+++++.++++.+ ++|+++..+
T Consensus 5 ~l~~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~~~----~vE~~i~~~ 48 (88)
T smart00088 5 RLQRKIRLTNLLQLSEPYSSISLSDLAKLLGLSVP----EVEKLVSKA 48 (88)
T ss_pred HHHHHHHHHHHHHHhHHhceeeHHHHHHHhCcCHH----HHHHHHHHH
Confidence 34555556667777788888999999999998642 356666554
No 83
>PF04799 Fzo_mitofusin: fzo-like conserved region; InterPro: IPR006884 This entry represents the heptad repeat domain which is conserved at the C terminus of Fzo/mitofusion family of GTPases. Fzo is a mediator of mitochondrial fusion during spermatogenesis []. This conserved region is also found in the human mitofusin protein []. This domain forms a dimeric antiparallel coiled coil structure, which has been proposed to act as a mitochodrial tether before vesicle fusion [].; GO: 0003924 GTPase activity, 0006184 GTP catabolic process, 0008053 mitochondrial fusion, 0005741 mitochondrial outer membrane, 0016021 integral to membrane; PDB: 1T3J_A.
Probab=21.42 E-value=2.5e+02 Score=24.11 Aligned_cols=34 Identities=18% Similarity=0.414 Sum_probs=14.0
Q ss_pred CCcchHHHHHHHHHHHHhhh-hhHHHHHHHHHHHH
Q 027481 73 DAPASMEKQFEDFRVKLDEA-GSLRERIRAVVNEI 106 (223)
Q Consensus 73 ~~~~~v~~~F~~fr~eLDe~-~d~RErI~kisRdI 106 (223)
+....+...|..+.+..|+- .|+.++|.++.++|
T Consensus 102 QVqqeL~~tf~rL~~~Vd~~~~eL~~eI~~L~~~i 136 (171)
T PF04799_consen 102 QVQQELSSTFARLCQQVDQTKNELEDEIKQLEKEI 136 (171)
T ss_dssp --------HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44455555566666665543 34555555555554
No 84
>cd00171 Sec7 Sec7 domain; Domain named after the S. cerevisiae SEC7 gene product. The Sec7 domain is the central domain of the guanine-nucleotide-exchange factors (GEFs) of the ADP-ribosylation factor family of small GTPases (ARFs) . It carries the exchange factor activity.
Probab=21.35 E-value=1.7e+02 Score=24.74 Aligned_cols=45 Identities=18% Similarity=0.085 Sum_probs=31.9
Q ss_pred HHHHHHHHhcCCccCHHHHHHHhCCCCCccCcChhHHhhhhhhccc
Q 027481 175 LLAFMHWLETGKLLMHTEAEEKLGMNQAEFALDIEDYLIGEHSDEC 220 (223)
Q Consensus 175 alsf~~yLe~g~Llt~eEv~~~Lgv~~~~f~L~~eDYLlGL~DLtG 220 (223)
.-.+..||.+..=++++.+++.||-+. .+...+-+..+.++|+.|
T Consensus 34 ~~~iA~fl~~~~~l~k~~ig~~L~~~~-~~~~~vL~~y~~~f~f~~ 78 (185)
T cd00171 34 PKEIAKFLYETEGLNKKAIGEYLGENN-EFNSLVLHEFVDLFDFSG 78 (185)
T ss_pred HHHHHHHHHhCCCCCHHHHHHHHcCCc-hHHHHHHHHHHHhcCCCC
Confidence 345778888888899999999999652 355555555555666655
No 85
>PF04136 Sec34: Sec34-like family ; InterPro: IPR007265 Sec34 and Sec35 form a sub-complex in a seven-protein complex that includes Dor1. This complex is thought to be important for tethering vesicles to the Golgi [].; GO: 0006886 intracellular protein transport, 0005801 cis-Golgi network, 0016020 membrane
Probab=21.31 E-value=4.7e+02 Score=21.55 Aligned_cols=22 Identities=14% Similarity=0.143 Sum_probs=9.1
Q ss_pred HHHHHhhhhhHHHHHHHHHHHH
Q 027481 85 FRVKLDEAGSLRERIRAVVNEI 106 (223)
Q Consensus 85 fr~eLDe~~d~RErI~kisRdI 106 (223)
+.++|+...+.-+.|..-+.++
T Consensus 5 y~~~L~~~~~~~~~ll~~~~~~ 26 (157)
T PF04136_consen 5 YLDYLQQYREECDQLLDQTDEI 26 (157)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 4444444444334444333333
No 86
>PF10146 zf-C4H2: Zinc finger-containing protein ; InterPro: IPR018482 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a family of proteins which appears to have a highly conserved zinc finger domain at the C-terminal end, described as -C-X2-CH-X3-H-X5-C-X2-C-. The structure is predicted to contain a coiled coil. Members of this family are annotated as being tumour-associated antigen HCA127 in humans, but this could not be confirmed.
Probab=21.18 E-value=5.6e+02 Score=22.74 Aligned_cols=69 Identities=20% Similarity=0.299 Sum_probs=0.0
Q ss_pred HHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHH-----------------HHhhccC-CCchhHHhcHHHHHHHHHHHH
Q 027481 83 EDFRVKLDEAGSLRERIRAVVNEIESITRLMHAS-----------------LLHVHQS-RPLSEVLEKPKAQVDGLKELY 144 (223)
Q Consensus 83 ~~fr~eLDe~~d~RErI~kisRdIe~~tr~sk~v-----------------I~~lHr~-~~~~~~l~~A~~~l~~i~~~~ 144 (223)
..++...++.+.++.+|++.+..++.....+... |..||.= ..+..++.+++..-....+.+
T Consensus 4 ~~ir~K~~~lek~k~~i~~e~~~~e~ee~~L~e~~kE~~~L~~Er~~h~eeLrqI~~DIn~lE~iIkqa~~er~~~~~~i 83 (230)
T PF10146_consen 4 KEIRNKTLELEKLKNEILQEVESLENEEKCLEEYRKEMEELLQERMAHVEELRQINQDINTLENIIKQAESERNKRQEKI 83 (230)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_pred HHHHHHh
Q 027481 145 GRLAEVL 151 (223)
Q Consensus 145 ~~La~~l 151 (223)
..+.+++
T Consensus 84 ~r~~eey 90 (230)
T PF10146_consen 84 QRLYEEY 90 (230)
T ss_pred HHHHHHH
No 87
>KOG4025 consensus Putative apoptosis related protein [Function unknown]
Probab=21.08 E-value=3.1e+02 Score=23.82 Aligned_cols=17 Identities=12% Similarity=0.190 Sum_probs=10.4
Q ss_pred HHHHHHHHHHHHHHHhh
Q 027481 104 NEIESITRLMHASLLHV 120 (223)
Q Consensus 104 RdIe~~tr~sk~vI~~l 120 (223)
+|+.+..+..|.+|.+|
T Consensus 96 qeLn~ka~aLk~iLSri 112 (207)
T KOG4025|consen 96 QELNKKAIALKRILSRI 112 (207)
T ss_pred HHHHHHHHHHHHHHHhC
Confidence 45555556667777766
No 88
>PF04108 APG17: Autophagy protein Apg17 ; InterPro: IPR007240 Macroautophagy is a bulk degradation process induced by starvation in eukaryotic cells. In yeast, 15 Apg proteins coordinate the formation of autophagosomes. No molecule involved in autophagy has yet been identified in higher eukaryotes []. The pre-autophagosomal structure contains at least five Apg proteins: Apg1p, Apg2p, Apg5p, Aut7p/Apg8p and Apg16p. It is found in the vacuole []. The C-terminal glycine of Apg12p is conjugated to a lysine residue of Apg5p via an isopeptide bond. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. Auotphagy protein 16 (Apg16) has been shown to be bind to Apg5 and is required for the function of the Apg12p-Apg5p conjugate []. Autophagy protein 5 (Apg5) is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway []. Autophagy protein 17 (Apg17) is required for activating Apg1 protein kinases. This entry also contains Autophagy protein 11 which is involved in cytoplasm to vacuole transport (Cvt) and pexophagy. ; GO: 0006914 autophagy
Probab=21.02 E-value=4.1e+02 Score=25.30 Aligned_cols=13 Identities=23% Similarity=0.192 Sum_probs=6.3
Q ss_pred hccccchhHHHHH
Q 027481 161 FHNDWRSETQTVV 173 (223)
Q Consensus 161 Y~~~ws~~lQE~V 173 (223)
|...|..-+.|+.
T Consensus 344 F~~aY~~LL~Ev~ 356 (412)
T PF04108_consen 344 FLSAYDSLLLEVE 356 (412)
T ss_pred HHHHHHHHHHHHH
Confidence 5555554444443
No 89
>PF08668 HDOD: HDOD domain; InterPro: IPR013976 This domain is found in a superfamily of enzymes with a predicted or known phosphohydrolase activity. These members appear to be involved in the nucleic acid metabolism and signal transduction or possibly other functions and are restricted to bacteria, primarily the proteobacteria. The fact that all the highly conserved residues in the HD superfamily are histidines or aspartates suggests that coordination of divalent cations is essential for the activity of these proteins [].; PDB: 1VQR_D 3LJX_A 3P3Q_B 3MEM_A 3M1T_A 3HC1_A 3I7A_A.
Probab=20.91 E-value=4.6e+02 Score=21.30 Aligned_cols=119 Identities=17% Similarity=0.191 Sum_probs=60.0
Q ss_pred HHHHHHHHHHhhhh-hHHHHHHHHHHHHHHHHHHHHHHHHhhccC----CCchhHHhcHHHHH--HHHHHHH--HHHHHH
Q 027481 80 KQFEDFRVKLDEAG-SLRERIRAVVNEIESITRLMHASLLHVHQS----RPLSEVLEKPKAQV--DGLKELY--GRLAEV 150 (223)
Q Consensus 80 ~~F~~fr~eLDe~~-d~RErI~kisRdIe~~tr~sk~vI~~lHr~----~~~~~~l~~A~~~l--~~i~~~~--~~La~~ 150 (223)
+....+++.++..+ +.+|=..-+.+| -..+.++|....+. ...-..+++|-..+ +.++... ..+...
T Consensus 6 ~~~~~l~~~l~~~~~~~~~l~~~i~~D----p~L~~~lL~~aNs~~~~~~~~i~sl~~Ai~~LG~~~i~~l~~~~~~~~~ 81 (196)
T PF08668_consen 6 EVARRLLSLLNDPEASIDELAELIESD----PALAARLLRLANSAYFGLRRPISSLEQAISRLGLDRIRNLALALSLRSL 81 (196)
T ss_dssp HHHHHHHHHHHSTTS-HHHHHHHHHTS----HHHHHHHHHHHHSTTTTSTST--SHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCCCCHHHHHHHHHHC----HHHHHHHHHHHhhhhcCCCCCCCCHHHHHHHhCHHHHHHHHHHHHHHHH
Confidence 34566677776543 455533334444 35566666666554 11222466666665 4566654 223333
Q ss_pred hccCCCccchhccccchhHHHHHHHHHHHHHHhcCCccCHHHHHHHhCCCCCccCcChhHHhhhhhhccccC
Q 027481 151 LCECPGEYYRFHNDWRSETQTVVSLLAFMHWLETGKLLMHTEAEEKLGMNQAEFALDIEDYLIGEHSDECHI 222 (223)
Q Consensus 151 l~~~p~~yYRY~~~ws~~lQE~VEalsf~~yLe~g~Llt~eEv~~~Lgv~~~~f~L~~eDYLlGL~DLtGEi 222 (223)
.+..+.....+.+.|..++.-...+-.++..+.... . -+-|+.||+--.|++
T Consensus 82 ~~~~~~~~~~~~~~~~~s~~~a~~a~~la~~~~~~~---~-----------------~~a~~~gLL~~iG~l 133 (196)
T PF08668_consen 82 FPSSPPYQFNLERFWRHSLAAAAIARRLARELGFDD---P-----------------DEAYLAGLLHDIGKL 133 (196)
T ss_dssp SCTTSCTTSCHHHHHHHHHHHHHHHHHHHHHCTCCH---H-----------------HHHHHHHHHTTHHHH
T ss_pred ccccchhhhhHHHHHHHHHHHHHHHHHHHHHcCCCC---H-----------------HHHHHHHHHHHHhHH
Confidence 442221123456677766666655555444442111 1 356777777766654
No 90
>PF10504 DUF2452: Protein of unknown function (DUF2452); InterPro: IPR019534 This entry contains proteins that have no known function.
Probab=20.90 E-value=1.5e+02 Score=25.11 Aligned_cols=38 Identities=11% Similarity=0.186 Sum_probs=17.4
Q ss_pred hhHHhcHHHHHHHHHH--HHHHHHHHhccCCCc-cchhccc
Q 027481 127 SEVLEKPKAQVDGLKE--LYGRLAEVLCECPGE-YYRFHND 164 (223)
Q Consensus 127 ~~~l~~A~~~l~~i~~--~~~~La~~l~~~p~~-yYRY~~~ 164 (223)
..+-++|++.+++... .+-..+--+..-|++ ||-|.+.
T Consensus 62 ~~Lq~QA~~ile~~~~~~~l~~A~cnF~pipG~iYhLY~r~ 102 (159)
T PF10504_consen 62 RFLQEQARKILEEAERNEELHHAKCNFEPIPGQIYHLYRRE 102 (159)
T ss_pred HHHHHHHHHHHHHHHHhHHHhhcccCceecCCCEEEEEECC
Confidence 3334455555554322 233333333333444 8777664
No 91
>PRK11637 AmiB activator; Provisional
Probab=20.76 E-value=6.5e+02 Score=23.76 Aligned_cols=11 Identities=0% Similarity=0.006 Sum_probs=4.7
Q ss_pred HHHHHHHHHHh
Q 027481 80 KQFEDFRVKLD 90 (223)
Q Consensus 80 ~~F~~fr~eLD 90 (223)
......++++.
T Consensus 54 ~qi~~~~~~i~ 64 (428)
T PRK11637 54 QDIAAKEKSVR 64 (428)
T ss_pred HHHHHHHHHHH
Confidence 33444444444
No 92
>PF09756 DDRGK: DDRGK domain; InterPro: IPR019153 This is a family of proteins of approximately 300 residues. They contain a highly conserved DDRGK motif. The function is unknown. ; PDB: 1WI9_A.
Probab=20.63 E-value=22 Score=30.77 Aligned_cols=28 Identities=14% Similarity=0.413 Sum_probs=21.9
Q ss_pred HHHHHHHHHhcCCccCHHHHHHHhCCCC
Q 027481 174 SLLAFMHWLETGKLLMHTEAEEKLGMNQ 201 (223)
Q Consensus 174 Ealsf~~yLe~g~Llt~eEv~~~Lgv~~ 201 (223)
....|+.|++..+++.+++++..+|+.+
T Consensus 100 lL~~Fi~yIK~~Kvv~ledla~~f~l~t 127 (188)
T PF09756_consen 100 LLQEFINYIKEHKVVNLEDLAAEFGLRT 127 (188)
T ss_dssp HHHHHHHHHHH-SEE-HHHHHHHH-S-H
T ss_pred HHHHHHHHHHHcceeeHHHHHHHcCCCH
Confidence 6778999999999999999999999864
No 93
>KOG0977 consensus Nuclear envelope protein lamin, intermediate filament superfamily [Cell cycle control, cell division, chromosome partitioning; Nuclear structure]
Probab=20.55 E-value=8.1e+02 Score=24.78 Aligned_cols=51 Identities=14% Similarity=0.124 Sum_probs=39.2
Q ss_pred CCCCcchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 027481 71 ETDAPASMEKQFEDFRVKLDEAGSLRERIRAVVNEIESITRLMHASLLHVH 121 (223)
Q Consensus 71 ~~~~~~~v~~~F~~fr~eLDe~~d~RErI~kisRdIe~~tr~sk~vI~~lH 121 (223)
+..+..++..-=+.=+.+|.+.+|+=...|+-||-+|...+....=|..+-
T Consensus 26 ~~~~as~ir~sR~rEK~El~~LNDRLA~YIekVR~LEaqN~~L~~di~~lr 76 (546)
T KOG0977|consen 26 ASNAASPIRDSREREKKELQELNDRLAVYIEKVRFLEAQNRKLEHDINLLR 76 (546)
T ss_pred cccchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345556666666777889999999999999999999988877766665554
No 94
>PRK15361 pathogenicity island 2 effector protein SseD; Provisional
Probab=20.43 E-value=1.3e+02 Score=26.35 Aligned_cols=49 Identities=18% Similarity=0.223 Sum_probs=0.0
Q ss_pred CCCCCCCCCCCCccccccccCCCcccccCCCCCCCCCc-------chHHHHHHHHHHHHhhhhhHHHHH
Q 027481 38 PPSSLVSPSKPETFRFRRRSSPLRVRYSSMTGGETDAP-------ASMEKQFEDFRVKLDEAGSLRERI 99 (223)
Q Consensus 38 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~v~~~F~~fr~eLDe~~d~RErI 99 (223)
|+.+.+.|... |++|+-.|..++-= ..+.++|..+|+-|.+.+..+.++
T Consensus 11 ~~~~~~~~~~~-------------~~~~~~~md~~s~l~~fddii~kL~eLfKKLRDvl~~YnqkqQ~l 66 (195)
T PRK15361 11 PAPSLLTPSST-------------PSPSGEGMGTESMLLLFDDIWMKLMELAKKLRDIMRSYNVEKQRL 66 (195)
T ss_pred cCccccCCCCC-------------CCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
No 95
>PF03962 Mnd1: Mnd1 family; InterPro: IPR005647 This family of proteins includes meiotic nuclear division protein 1 (MND1) from Saccharomyces cerevisiae (Baker's yeast). The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair [].
Probab=20.36 E-value=5.4e+02 Score=21.88 Aligned_cols=25 Identities=8% Similarity=0.256 Sum_probs=22.0
Q ss_pred HHHHHHHhcCCccCHHHHHHHhCCC
Q 027481 176 LAFMHWLETGKLLMHTEAEEKLGMN 200 (223)
Q Consensus 176 lsf~~yLe~g~Llt~eEv~~~Lgv~ 200 (223)
.++..|+....-+..+++...+|+|
T Consensus 159 ~~l~~~~~~k~~~~~~~i~k~f~Ip 183 (188)
T PF03962_consen 159 FSLKSYLKKKFGMDEEDIRKEFGIP 183 (188)
T ss_pred HHHHHHHHHhcCCCHHHHHHHcCCc
Confidence 3577899999999999999999987
No 96
>PRK08307 stage III sporulation protein SpoAB; Provisional
Probab=20.13 E-value=2.9e+02 Score=23.06 Aligned_cols=84 Identities=21% Similarity=0.279 Sum_probs=48.7
Q ss_pred HHHHHHHHhhccC-----CCchhHHhcHHHHHH-HHHHHHHHHHHHhccCCCccchhccccchhHHHHHHHHHHHHHHhc
Q 027481 111 RLMHASLLHVHQS-----RPLSEVLEKPKAQVD-GLKELYGRLAEVLCECPGEYYRFHNDWRSETQTVVSLLAFMHWLET 184 (223)
Q Consensus 111 r~sk~vI~~lHr~-----~~~~~~l~~A~~~l~-~i~~~~~~La~~l~~~p~~yYRY~~~ws~~lQE~VEalsf~~yLe~ 184 (223)
++.+.+|+.+..- ++.++.+.+...+.+ .+...+..+++.+.+..+ -.+...|..++.++-.. ..|..
T Consensus 32 ~~l~~~l~~L~~EI~Y~~tpL~ea~~~i~~~~~~~~~~~f~~~a~~L~~~~g--~s~~eaw~~~~~~~~~~----~~L~~ 105 (171)
T PRK08307 32 RELKAALQSLEAEIMYGHTPLPEALENIAKQSPKPISTLFQRFSERLESGEG--ETAYEAWEKALEENWKN----TALKK 105 (171)
T ss_pred HHHHHHHHHHHHHHhhcCCcHHHHHHHHHHccchhHHHHHHHHHHHHHhCCC--CCHHHHHHHHHHHhhhc----cCCCH
Confidence 3444445544421 567788887666654 588888999999974332 23568887777665332 22333
Q ss_pred CCccCHHHHHHHhCCC
Q 027481 185 GKLLMHTEAEEKLGMN 200 (223)
Q Consensus 185 g~Llt~eEv~~~Lgv~ 200 (223)
+.+--..+++..||..
T Consensus 106 ~d~eiL~~lg~~LG~~ 121 (171)
T PRK08307 106 EDIEILLQFGKTLGQS 121 (171)
T ss_pred HHHHHHHHHHHHHCcC
Confidence 3333334456666654
No 97
>PRK11548 outer membrane biogenesis protein BamE; Provisional
Probab=20.06 E-value=51 Score=25.71 Aligned_cols=31 Identities=16% Similarity=0.279 Sum_probs=25.0
Q ss_pred HHhcCCccCHHHHHHHhCCCC--CccCcChhHHhh
Q 027481 181 WLETGKLLMHTEAEEKLGMNQ--AEFALDIEDYLI 213 (223)
Q Consensus 181 yLe~g~Llt~eEv~~~Lgv~~--~~f~L~~eDYLl 213 (223)
=++.| .|++||..+||-|. +.|+-...+|+.
T Consensus 45 ~l~~G--mTk~qV~~lLGtP~~~~~f~~~~W~Yi~ 77 (113)
T PRK11548 45 KIHVG--MTQQQVAYTLGTPMMQDPFGTNTWFYVF 77 (113)
T ss_pred HhcCC--CCHHHHHHHcCCCccccCCCCceEEEEE
Confidence 35667 59999999999887 677777888875
Done!