Query 029325
Match_columns 195
No_of_seqs 22 out of 24
Neff 2.1
Searched_HMMs 46136
Date Fri Mar 29 11:06:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029325.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029325hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF14812 PBP1_TM: Transmembran 89.0 0.1 2.2E-06 39.6 -0.4 22 105-127 52-73 (81)
2 PF11269 DUF3069: Protein of u 67.8 5.1 0.00011 32.7 2.7 34 86-119 75-108 (121)
3 KOG0943 Predicted ubiquitin-pr 61.1 5.4 0.00012 43.9 2.1 15 87-101 1758-1772(3015)
4 KOG3540 Beta amyloid precursor 59.3 7.2 0.00016 38.6 2.5 16 137-152 288-303 (615)
5 KOG2229 Protein required for a 55.6 10 0.00023 37.7 2.9 47 68-119 157-205 (616)
6 PF04615 Utp14: Utp14 protein; 55.4 9.6 0.00021 36.9 2.6 28 86-113 12-39 (735)
7 KOG2475 CDC45 (cell division c 54.5 17 0.00036 36.1 4.1 22 33-54 106-127 (587)
8 PF04871 Uso1_p115_C: Uso1 / p 54.4 9.1 0.0002 30.4 1.9 6 70-75 113-118 (136)
9 PF04889 Cwf_Cwc_15: Cwf15/Cwc 54.2 28 0.00061 30.3 5.0 18 90-108 143-160 (244)
10 PF02724 CDC45: CDC45-like pro 51.6 9.1 0.0002 36.9 1.8 43 10-54 55-104 (622)
11 PF08595 RXT2_N: RXT2-like, N- 50.0 10 0.00022 31.2 1.6 14 142-155 134-147 (149)
12 KOG1824 TATA-binding protein-i 49.9 12 0.00026 39.7 2.4 27 147-173 382-408 (1233)
13 KOG1122 tRNA and rRNA cytosine 46.3 21 0.00046 34.5 3.3 20 98-117 38-57 (460)
14 PF13324 GCIP: Grap2 and cycli 45.7 21 0.00045 30.4 2.9 19 144-162 231-249 (275)
15 PF11942 Spt5_N: Spt5 transcri 45.5 10 0.00023 28.2 1.0 10 71-80 1-10 (97)
16 PF03115 Astro_capsid: Astrovi 45.0 7.2 0.00016 39.5 0.0 17 112-128 725-741 (787)
17 PF13324 GCIP: Grap2 and cycli 43.1 27 0.00058 29.7 3.1 6 106-111 200-205 (275)
18 PF04281 Tom22: Mitochondrial 42.9 1.5E+02 0.0032 24.3 7.2 31 142-172 78-108 (137)
19 PF06624 RAMP4: Ribosome assoc 42.7 31 0.00066 24.9 2.9 42 119-169 21-62 (63)
20 KOG1999 RNA polymerase II tran 42.5 13 0.00028 39.0 1.3 13 119-131 156-168 (1024)
21 COG5414 TATA-binding protein-a 42.1 33 0.00073 32.4 3.8 31 90-120 330-360 (392)
22 PF08568 Kinetochor_Ybp2: Unch 41.4 24 0.00051 33.5 2.8 20 92-111 132-155 (633)
23 PF07524 Bromo_TP: Bromodomain 39.1 42 0.00091 23.4 3.1 26 96-121 33-58 (77)
24 TIGR00993 3a0901s04IAP86 chlor 38.6 22 0.00047 36.3 2.2 8 97-104 437-444 (763)
25 smart00576 BTP Bromodomain tra 37.6 60 0.0013 23.0 3.8 27 92-118 25-51 (77)
26 PF14459 Prok-E2_C: Prokaryoti 35.1 52 0.0011 27.3 3.5 34 91-124 11-56 (131)
27 PLN03196 MOC1-like protein; Pr 35.0 24 0.00052 33.1 1.8 10 66-75 448-457 (487)
28 PF06143 Baculo_11_kDa: Baculo 34.1 48 0.0011 25.4 3.0 22 145-168 31-52 (84)
29 KOG0699 Serine/threonine prote 33.9 20 0.00044 34.9 1.2 23 74-96 291-313 (542)
30 PF10904 DUF2694: Protein of u 33.6 43 0.00093 26.8 2.7 18 136-153 46-63 (101)
31 PF11571 Med27: Mediator compl 33.6 57 0.0012 24.0 3.2 19 104-122 12-30 (90)
32 PLN03088 SGT1, suppressor of 32.8 27 0.00059 30.6 1.7 22 97-118 296-317 (356)
33 PF11190 DUF2976: Protein of u 32.5 1.2E+02 0.0027 23.1 5.0 39 145-183 17-55 (87)
34 PRK05244 Der GTPase activator; 31.8 34 0.00074 29.3 2.0 12 91-102 157-168 (177)
35 PF04147 Nop14: Nop14-like fam 31.3 36 0.00078 34.1 2.4 19 109-127 405-423 (840)
36 TIGR02170 thyX thymidylate syn 30.4 93 0.002 25.6 4.3 32 113-145 145-176 (209)
37 cd03509 DesA_FADS-like Fatty a 30.1 1.8E+02 0.004 25.4 6.3 13 102-114 139-151 (288)
38 PF11702 DUF3295: Protein of u 30.0 22 0.00048 34.6 0.7 11 105-115 331-341 (507)
39 KOG1631 Translocon-associated 29.8 30 0.00066 31.4 1.5 23 73-95 33-55 (261)
40 PF10161 DDDD: Putative mitoch 29.7 21 0.00045 27.3 0.3 17 72-91 63-79 (79)
41 PF11705 RNA_pol_3_Rpc31: DNA- 29.7 35 0.00077 28.5 1.8 7 33-39 115-121 (233)
42 PF09770 PAT1: Topoisomerase I 29.3 18 0.00039 35.2 0.0 9 70-78 27-35 (808)
43 PF15539 CAF1-p150_C2: CAF1 co 28.6 34 0.00074 31.5 1.6 19 38-56 201-219 (292)
44 PF04277 OAD_gamma: Oxaloaceta 28.3 80 0.0017 21.9 3.1 21 159-179 13-33 (79)
45 PF02511 Thy1: Thymidylate syn 27.7 90 0.0019 25.0 3.7 40 105-145 120-161 (190)
46 KOG3491 Predicted membrane pro 27.3 60 0.0013 24.2 2.4 42 119-169 21-62 (65)
47 PF11085 YqhR: Conserved membr 27.1 85 0.0018 27.0 3.6 20 136-155 72-91 (173)
48 PF04220 YihI: Der GTPase acti 26.8 35 0.00075 28.9 1.2 12 91-102 157-168 (169)
49 PF15103 G0-G1_switch_2: G0/G1 26.6 95 0.0021 24.8 3.6 31 125-156 18-48 (102)
50 COG3428 Predicted membrane pro 26.3 85 0.0018 30.8 3.9 50 84-135 161-227 (494)
51 TIGR02762 TraL_TIGR type IV co 25.5 2.9E+02 0.0063 20.6 6.9 53 127-183 12-64 (95)
52 PF03286 Pox_Ag35: Pox virus A 25.2 94 0.002 26.9 3.6 59 91-159 126-186 (200)
53 PF15088 NADH_dh_m_C1: NADH de 25.2 39 0.00085 24.0 1.1 19 151-169 15-33 (49)
54 PF12785 VESA1_N: Variant eryt 25.1 52 0.0011 32.0 2.2 9 170-178 262-270 (462)
55 PF03729 DUF308: Short repeat 24.6 2E+02 0.0043 18.4 5.5 23 159-181 25-47 (72)
56 PF10661 EssA: WXG100 protein 23.8 85 0.0018 25.5 2.9 24 146-172 121-144 (145)
57 PF06643 DUF1158: Protein of u 23.4 1.9E+02 0.0042 22.4 4.6 12 135-146 11-22 (82)
58 PTZ00415 transmission-blocking 22.2 61 0.0013 37.1 2.3 6 47-52 128-133 (2849)
59 PF15176 LRR19-TM: Leucine-ric 22.2 80 0.0017 25.2 2.4 42 35-76 45-92 (102)
60 PRK10983 putative inner membra 22.1 1.6E+02 0.0034 26.5 4.5 13 135-147 224-236 (368)
61 PF13875 DUF4202: Domain of un 21.8 84 0.0018 27.1 2.6 24 97-120 150-173 (185)
62 COG5192 BMS1 GTP-binding prote 21.5 93 0.002 32.4 3.3 63 53-115 487-571 (1077)
63 PHA02608 67 prohead core prote 21.4 58 0.0013 25.2 1.4 6 61-66 47-52 (80)
64 PF01267 F-actin_cap_A: F-acti 21.4 77 0.0017 27.8 2.4 23 103-125 232-254 (271)
65 KOG1999 RNA polymerase II tran 21.3 1.1E+02 0.0024 32.5 3.8 21 144-170 167-187 (1024)
66 COG3079 Uncharacterized protei 21.3 50 0.0011 28.8 1.2 20 86-105 145-164 (186)
67 PRK12766 50S ribosomal protein 21.0 43 0.00094 29.7 0.8 11 116-126 163-173 (232)
68 TIGR00986 3a0801s05tom22 mitoc 20.7 3.1E+02 0.0067 23.0 5.7 55 117-178 57-111 (145)
69 PF13821 DUF4187: Domain of un 20.5 49 0.0011 23.0 0.8 20 88-107 8-27 (55)
70 PF04395 Poxvirus_B22R: Poxvir 20.3 87 0.0019 27.1 2.5 21 105-125 178-198 (205)
71 KOG4672 Uncharacterized conser 20.2 64 0.0014 31.6 1.8 13 83-95 279-291 (487)
72 KOG3555 Ca2+-binding proteogly 20.1 50 0.0011 31.8 1.0 14 84-97 416-429 (434)
73 KOG0299 U3 snoRNP-associated p 20.0 49 0.0011 32.3 1.0 16 54-70 35-50 (479)
No 1
>PF14812 PBP1_TM: Transmembrane domain of transglycosylase PBP1 at N-terminal; PDB: 3FWL_A 3VMA_A.
Probab=89.05 E-value=0.1 Score=39.58 Aligned_cols=22 Identities=27% Similarity=0.179 Sum_probs=1.3
Q ss_pred HHHHHHHHHHHHhhhhccCCccC
Q 029325 105 ATFKKVSKRAKKASRSILPAAIS 127 (195)
Q Consensus 105 s~fkKvSkRArKA~RsvLP~~is 127 (195)
.|=||..+| .+.-|..|=.-|.
T Consensus 52 ~m~rK~k~r-~rkKrrwlwLlik 73 (81)
T PF14812_consen 52 PMPRKGKKR-PRKKRRWLWLLIK 73 (81)
T ss_dssp --------------------TTT
T ss_pred ccccccccC-ccccchhHHHHHH
Confidence 577887776 5555555544444
No 2
>PF11269 DUF3069: Protein of unknown function (DUF3069); InterPro: IPR021422 This family of proteins with unknown function appear to be restricted to Gammaproteobacteria. ; PDB: 2PV4_A.
Probab=67.82 E-value=5.1 Score=32.72 Aligned_cols=34 Identities=32% Similarity=0.492 Sum_probs=26.4
Q ss_pred CCCCcccchhHHHHHHHHHHHHHHHHHHHHHhhh
Q 029325 86 SDDEDDMDSSVDLLIRFLQATFKKVSKRAKKASR 119 (195)
Q Consensus 86 ~ddede~d~SlDLLvrFl~s~fkKvSkRArKA~R 119 (195)
+++++++|-.--||-|.+++-.|.+.|.-|||=|
T Consensus 75 ~~~~~~~EY~~~lld~vl~~~lKd~vKqLKKAR~ 108 (121)
T PF11269_consen 75 MEEEEEQEYRAQLLDRVLHNCLKDMVKQLKKARR 108 (121)
T ss_dssp TTTS-HHHHHH-HHHHHHHTHHHHHHHHHHHHTT
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcc
Confidence 3455666777779999999999999999999865
No 3
>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=61.07 E-value=5.4 Score=43.86 Aligned_cols=15 Identities=40% Similarity=0.543 Sum_probs=8.9
Q ss_pred CCCcccchhHHHHHH
Q 029325 87 DDEDDMDSSVDLLIR 101 (195)
Q Consensus 87 ddede~d~SlDLLvr 101 (195)
||||++|.-+|++.+
T Consensus 1758 dDdDdeD~d~~aea~ 1772 (3015)
T KOG0943|consen 1758 DDDDDEDMDLDAEAA 1772 (3015)
T ss_pred ccccccccccchhhh
Confidence 344556666777654
No 4
>KOG3540 consensus Beta amyloid precursor protein [General function prediction only]
Probab=59.28 E-value=7.2 Score=38.58 Aligned_cols=16 Identities=19% Similarity=-0.004 Sum_probs=9.0
Q ss_pred hHHHHHHHHHHHHHHH
Q 029325 137 GILLLASLSILKALLE 152 (195)
Q Consensus 137 GvllLa~L~ilKAlLE 152 (195)
-.|.--|-.++++|-|
T Consensus 288 qalnqhFQ~~v~sLEe 303 (615)
T KOG3540|consen 288 QALNQHFQKTVSSLEE 303 (615)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 3445556666666654
No 5
>KOG2229 consensus Protein required for actin cytoskeleton organization and cell cycle progression [Cell cycle control, cell division, chromosome partitioning; Cytoskeleton]
Probab=55.64 E-value=10 Score=37.66 Aligned_cols=47 Identities=38% Similarity=0.397 Sum_probs=23.1
Q ss_pred cccccCCCCCCCCcccCCCCCCccc-chhH-HHHHHHHHHHHHHHHHHHHHhhh
Q 029325 68 GEAFFDEGVDGGAIMDDISDDEDDM-DSSV-DLLIRFLQATFKKVSKRAKKASR 119 (195)
Q Consensus 68 ~e~~fd~~~D~~~~~~~~~ddede~-d~Sl-DLLvrFl~s~fkKvSkRArKA~R 119 (195)
.-+||=|+ |..+. ||++|.|+|+ +.-+ +|+++. ++||-.||-+|-.|
T Consensus 157 ~l~FfL~~-D~~de-e~dsd~~~d~dg~~~~~l~~~~---vnkktkkr~~kl~~ 205 (616)
T KOG2229|consen 157 GLRFFLGA-DNEDE-EDDSDSESDEDGPDADALLHQR---VNKKTKKRQKKLLR 205 (616)
T ss_pred hhHHhccC-Ccccc-ccccccccccccccHHHHHHHH---HhccchhhHHHHHH
Confidence 56778766 42111 2222222222 2233 455544 88888887766433
No 6
>PF04615 Utp14: Utp14 protein; InterPro: IPR006709 A large ribonuclear protein complex is required for the processing of the small-ribosomal-subunit rRNA - the small-subunit (SSU) processome [, ]. This preribosomal complex contains the U3 snoRNA and at least 40 proteins, which have the following properties: They are nucleolar. They are able to coimmunoprecipitate with the U3 snoRNA and Mpp10 (a protein specific to the SSU processome). They are required for 18S rRNA biogenesis. There appears to be a linkage between polymerase I transcription and the formation of the SSU processome; as some, but not all, of the SSU processome components are required for pre-rRNA transcription initiation. These SSU processome components have been termed t-Utps. They form a pre-complex with pre-18S rRNA in the absence of snoRNA U3 and other SSU processome components. It has been proposed that the t-Utp complex proteins are both rDNA and rRNA binding proteins that are involved in the initiation of pre18S rRNA transcription. Initially binding to rDNA then associating with the 5' end of the nascent pre18S rRNA. The t-Utpcomplex forms the nucleus around which the rest of the SSU processome components, including snoRNA U3, assemble []. From electron microscopy the SSU processome may correspond to the terminal knobs visualized at the 5' ends of nascent 18S rRNA. This entry contains Utp14, a large ribonuclear protein associated with snoRNA U3 [].; GO: 0006364 rRNA processing, 0032040 small-subunit processome
Probab=55.43 E-value=9.6 Score=36.88 Aligned_cols=28 Identities=25% Similarity=0.399 Sum_probs=21.2
Q ss_pred CCCCcccchhHHHHHHHHHHHHHHHHHH
Q 029325 86 SDDEDDMDSSVDLLIRFLQATFKKVSKR 113 (195)
Q Consensus 86 ~ddede~d~SlDLLvrFl~s~fkKvSkR 113 (195)
|+||||+++..+=|+.++.++=++-.++
T Consensus 12 d~~~~~~~~~~~~L~~~i~~l~~~~~~~ 39 (735)
T PF04615_consen 12 DDDDEDDEEKHDKLLKAISSLDSKKRKK 39 (735)
T ss_pred ccccccChHHHHHHHHHHHhcccccccc
Confidence 3456677788888999999988777643
No 7
>KOG2475 consensus CDC45 (cell division cycle 45)-like protein [Replication, recombination and repair]
Probab=54.52 E-value=17 Score=36.14 Aligned_cols=22 Identities=9% Similarity=-0.171 Sum_probs=16.5
Q ss_pred cccCCcccccccCCcceeeccc
Q 029325 33 FHHNRHTNHNKTLSELSICHAQ 54 (195)
Q Consensus 33 f~hq~f~~~~~~~~~~~~~h~~ 54 (195)
=+|.|++..|--....|-|-++
T Consensus 106 DSHRP~nl~Niy~~~qi~~l~d 127 (587)
T KOG2475|consen 106 DSHRPFNLENIYEDNQIHLLDD 127 (587)
T ss_pred eCCCCcchhhcccCceEEEecC
Confidence 4799999888887777766544
No 8
>PF04871 Uso1_p115_C: Uso1 / p115 like vesicle tethering protein, C terminal region; InterPro: IPR006955 This domain identifies a group of proteins, which are described as: General vesicular transport factor, Transcytosis associate protein (TAP) and Vesicle docking protein. This myosin-shaped molecule consists of an N-terminal globular head region, a coiled-coil tail which mediates dimerisation, and a short C-terminal acidic region []. p115 tethers COP1 vesicles to the Golgi by binding the coiled coil proteins giantin (on the vesicles) and GM130 (on the Golgi), via its C-terminal acidic region. It is required for intercisternal transport in the Golgi stack. This domain is found in the acidic C-terminal region, which binds to the golgins giantin and GM130. p115 is thought to juxtapose two membranes by binding giantin with one acidic region, and GM130 with another [].; GO: 0008565 protein transporter activity, 0006886 intracellular protein transport, 0005737 cytoplasm, 0016020 membrane
Probab=54.37 E-value=9.1 Score=30.42 Aligned_cols=6 Identities=17% Similarity=0.219 Sum_probs=2.3
Q ss_pred cccCCC
Q 029325 70 AFFDEG 75 (195)
Q Consensus 70 ~~fd~~ 75 (195)
...+|.
T Consensus 113 eVSddE 118 (136)
T PF04871_consen 113 EVSDDE 118 (136)
T ss_pred CccCCc
Confidence 333333
No 9
>PF04889 Cwf_Cwc_15: Cwf15/Cwc15 cell cycle control protein; InterPro: IPR006973 This family represents Cwf15/Cwc15 (from Schizosaccharomyces pombe and Saccharomyces cerevisiae respectively) and their homologues. The function of these proteins is unknown, but they form part of the spliceosome and are thus thought to be involved in mRNA splicing [].; GO: 0000398 nuclear mRNA splicing, via spliceosome, 0005681 spliceosomal complex
Probab=54.16 E-value=28 Score=30.32 Aligned_cols=18 Identities=39% Similarity=0.460 Sum_probs=9.4
Q ss_pred cccchhHHHHHHHHHHHHH
Q 029325 90 DDMDSSVDLLIRFLQATFK 108 (195)
Q Consensus 90 de~d~SlDLLvrFl~s~fk 108 (195)
||+|.. -+|++=|+.+=|
T Consensus 143 ddeDd~-~~Ll~ELekIKk 160 (244)
T PF04889_consen 143 DDEDDT-AALLRELEKIKK 160 (244)
T ss_pred ccchHH-HHHHHHHHHHHH
Confidence 334444 455666766643
No 10
>PF02724 CDC45: CDC45-like protein; InterPro: IPR003874 CDC45 is an essential gene required for initiation of DNA replication in Saccharomyces cerevisiae (cell division control protein 45), forming a complex with MCM5/CDC46. Homologs of CDC45 have been identified in human [], mouse and the smut fungus, Melampsora spp., (tsd2 protein) among others.; GO: 0006270 DNA-dependent DNA replication initiation
Probab=51.59 E-value=9.1 Score=36.93 Aligned_cols=43 Identities=14% Similarity=0.130 Sum_probs=25.7
Q ss_pred ceeeeccc-cc-ccccCCCCCCCcc----cccCCcccccccC-Ccceeeccc
Q 029325 10 FIVINLSS-AK-LDHSSPSPTANLS----FHHNRHTNHNKTL-SELSICHAQ 54 (195)
Q Consensus 10 ~~~InL~~-s~-l~hf~~sp~~n~~----f~hq~f~~~~~~~-~~~~~~h~~ 54 (195)
.++||.-- -+ ...+. |..+.. =+|-|+++.|-.. ...++|=.+
T Consensus 55 vilIncGa~~dl~~~l~--~~~~~~iyViDshRP~~L~Nv~~~~~~v~v~dd 104 (622)
T PF02724_consen 55 VILINCGATVDLEEFLE--LDEDVTIYVIDSHRPWNLDNVFSDNDQVIVFDD 104 (622)
T ss_pred EEEEecCchhhHHHHhC--CCCceEEEEEeCCCCccHhhccCCCCcEEEEEC
Confidence 55666655 12 22222 334443 3788899888887 777777654
No 11
>PF08595 RXT2_N: RXT2-like, N-terminal; InterPro: IPR013904 The entry represents the N-terminal region of RXT2-like proteins. In Saccharomyces cerevisiae (Baker's yeast), RXT2 has been demonstrated to be involved in conjugation with cellular fusion (mating) and invasive growth []. A high throughput localisation study has localised RXT2 to the nucleus [].
Probab=50.00 E-value=10 Score=31.17 Aligned_cols=14 Identities=57% Similarity=0.531 Sum_probs=12.0
Q ss_pred HHHHHHHHHHHHHH
Q 029325 142 ASLSILKALLEVVC 155 (195)
Q Consensus 142 a~L~ilKAlLEVvC 155 (195)
..||-+|-||||+|
T Consensus 134 ~~l~~~~kLl~vll 147 (149)
T PF08595_consen 134 NSLWRLKKLLEVLL 147 (149)
T ss_pred HHHHHHHHHHHHHc
Confidence 47888999999987
No 12
>KOG1824 consensus TATA-binding protein-interacting protein [General function prediction only]
Probab=49.89 E-value=12 Score=39.69 Aligned_cols=27 Identities=15% Similarity=-0.102 Sum_probs=13.5
Q ss_pred HHHHHHHHHhcchHHHHHHHHHHHHHH
Q 029325 147 LKALLEVVCSIGGTVFVLILLLRFIWA 173 (195)
Q Consensus 147 lKAlLEVvCtlGs~VFv~ILl~R~iWs 173 (195)
.|-=-|-||+----+|+..|.=-..|-
T Consensus 382 fkEREEnVk~dvf~~yi~ll~qt~~~~ 408 (1233)
T KOG1824|consen 382 FKEREENVKADVFHAYIALLKQTRPVI 408 (1233)
T ss_pred HHHHhhhHHHHHHHHHHHHHHcCCCCc
Confidence 344445566554455555554444443
No 13
>KOG1122 consensus tRNA and rRNA cytosine-C5-methylase (nucleolar protein NOL1/NOP2) [RNA processing and modification]
Probab=46.32 E-value=21 Score=34.51 Aligned_cols=20 Identities=15% Similarity=0.350 Sum_probs=14.4
Q ss_pred HHHHHHHHHHHHHHHHHHHh
Q 029325 98 LLIRFLQATFKKVSKRAKKA 117 (195)
Q Consensus 98 LLvrFl~s~fkKvSkRArKA 117 (195)
+..+-...+++|+-||..+.
T Consensus 38 ~~~~~~e~~~~~l~~~~~~~ 57 (460)
T KOG1122|consen 38 IDLKLIERKSRKLRKRESLE 57 (460)
T ss_pred hhhhhhhhHHHHHHHhhccc
Confidence 33333899999999987654
No 14
>PF13324 GCIP: Grap2 and cyclin-D-interacting; PDB: 3AY5_A.
Probab=45.66 E-value=21 Score=30.39 Aligned_cols=19 Identities=11% Similarity=0.335 Sum_probs=9.4
Q ss_pred HHHHHHHHHHHHhcchHHH
Q 029325 144 LSILKALLEVVCSIGGTVF 162 (195)
Q Consensus 144 L~ilKAlLEVvCtlGs~VF 162 (195)
+...+.+-+-|=-+|+.+|
T Consensus 231 ~~~~~~i~~~VDel~~slY 249 (275)
T PF13324_consen 231 LDLCQEISPSVDELASSLY 249 (275)
T ss_dssp HHHHHHHHHHHHHHHHHHS
T ss_pred HHHHHHhhhHHHHHHHHhc
Confidence 3445555554544555444
No 15
>PF11942 Spt5_N: Spt5 transcription elongation factor, acidic N-terminal; InterPro: IPR022581 This is the very acidic N-terminal domain of the early transcription elongation factor Spt5 []. The Spt5-Spt4 complex regulates early transcription elongation by RNA polymerase II and has an imputed role in pre-mRNA processing via its physical association with mRNA capping enzymes. The actual function of this N-terminal domain is not known although it is dispensable for binding to Spt4 [], nor is it essential for RNA polymerase II binding [].
Probab=45.54 E-value=10 Score=28.21 Aligned_cols=10 Identities=20% Similarity=0.464 Sum_probs=4.7
Q ss_pred ccCCCCCCCC
Q 029325 71 FFDEGVDGGA 80 (195)
Q Consensus 71 ~fd~~~D~~~ 80 (195)
|+++.-++|+
T Consensus 1 Fid~EAeVDd 10 (97)
T PF11942_consen 1 FIDDEAEVDD 10 (97)
T ss_pred CchhhcccCC
Confidence 4555544444
No 16
>PF03115 Astro_capsid: Astrovirus capsid protein precursor; InterPro: IPR004337 The astrovirus genome is apparently organised with nonstructural proteins encoded at the 5' end and structural proteins at the 3' end []. Proteins in this family are encoded by astrovirus ORF2, one of the three astrovirus ORFs (1a, 1b, 2). The proteins contain a viral RNA-dependent RNA polymerase motif []. The 87kDa precursor polyprotein undergoes an intracellular cleavage to form a 79kDa protein. Subsequently, extracellular trypsin cleavage yields the three proteins forming the infectious virion [].; PDB: 3QSQ_A 3TS3_D.
Probab=44.98 E-value=7.2 Score=39.47 Aligned_cols=17 Identities=18% Similarity=0.401 Sum_probs=0.0
Q ss_pred HHHHHhhhhccCCccCc
Q 029325 112 KRAKKASRSILPAAISP 128 (195)
Q Consensus 112 kRArKA~RsvLP~~is~ 128 (195)
.||.+|+..-.|..--.
T Consensus 725 erAaria~RAfPT~aek 741 (787)
T PF03115_consen 725 ERAARIAKRAFPTLAEK 741 (787)
T ss_dssp -----------------
T ss_pred HHHHhhhhccCCCchhh
Confidence 46888888888864433
No 17
>PF13324 GCIP: Grap2 and cyclin-D-interacting; PDB: 3AY5_A.
Probab=43.08 E-value=27 Score=29.75 Aligned_cols=6 Identities=33% Similarity=0.451 Sum_probs=2.4
Q ss_pred HHHHHH
Q 029325 106 TFKKVS 111 (195)
Q Consensus 106 ~fkKvS 111 (195)
+.||+.
T Consensus 200 ~lk~~~ 205 (275)
T PF13324_consen 200 VLKKLL 205 (275)
T ss_dssp HHHHHH
T ss_pred HHHHHH
Confidence 344443
No 18
>PF04281 Tom22: Mitochondrial import receptor subunit Tom22 ; InterPro: IPR005683 The mitochondrial protein translocase family, which is responsible for movement of nuclear encoded pre-proteins into mitochondria, is very complex with at least 19 components. These proteins include several chaperone proteins, four proteins of the outer membrane translocase (Tom) import receptor, five proteins of the Tom channel complex, five proteins of the inner membrane translocase (Tim) and three "motor" proteins. This family represents the Tom22 proteins []. The N-terminal region of Tom22 has been shown to have chaperone-like activity, and the C-terminal region faces the intermembrane face []. ; GO: 0006886 intracellular protein transport, 0005741 mitochondrial outer membrane
Probab=42.94 E-value=1.5e+02 Score=24.25 Aligned_cols=31 Identities=23% Similarity=0.080 Sum_probs=20.0
Q ss_pred HHHHHHHHHHHHHHhcchHHHHHHHHHHHHH
Q 029325 142 ASLSILKALLEVVCSIGGTVFVLILLLRFIW 172 (195)
Q Consensus 142 a~L~ilKAlLEVvCtlGs~VFv~ILl~R~iW 172 (195)
..-|.+|.+.-..|..-=+++.+.||+=+-|
T Consensus 78 ~~~~~~k~~~~~~g~a~Wi~tTSallLgvPl 108 (137)
T PF04281_consen 78 TTSSAVKSLFSFSGKALWIVTTSALLLGVPL 108 (137)
T ss_pred HHHHHHHHHHHhcchhHHHHHHHHHHHHHHH
Confidence 3456677777777766666777766665444
No 19
>PF06624 RAMP4: Ribosome associated membrane protein RAMP4; InterPro: IPR010580 This entry contains Serp1/Ramp4, which has been shown to interacts with target proteins during their translocation into the lumen of the endoplasmic reticulum. It has also been shown to protect unfolded target proteins against degradation during ER stress. It may facilitate glycosylation of target proteins after termination of ER stress and may modulate the use of N-glycosylation sites on target proteins [, ].
Probab=42.67 E-value=31 Score=24.94 Aligned_cols=42 Identities=31% Similarity=0.595 Sum_probs=25.0
Q ss_pred hhccCCccCcceeeEeehhHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHH
Q 029325 119 RSILPAAISPKLVSFAVDGILLLASLSILKALLEVVCSIGGTVFVLILLLR 169 (195)
Q Consensus 119 RsvLP~~is~~LV~FsVnGvllLa~L~ilKAlLEVvCtlGs~VFv~ILl~R 169 (195)
|.-.|....++=-++.| |-.+|++ |+=||| ||.+|=.|=.+|
T Consensus 21 rG~v~~~~k~k~~k~pV-gp~~L~l------~iFVV~--Gs~ifqiir~i~ 62 (63)
T PF06624_consen 21 RGKVPKSLKKKEKKYPV-GPWLLGL------FIFVVC--GSAIFQIIRSIQ 62 (63)
T ss_pred cCCCccccccccccCCc-CHHHHhh------hheeeE--cHHHHHHHHHHh
Confidence 56667666666556777 3344443 233566 888887665543
No 20
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=42.53 E-value=13 Score=39.01 Aligned_cols=13 Identities=31% Similarity=0.677 Sum_probs=10.3
Q ss_pred hhccCCccCccee
Q 029325 119 RSILPAAISPKLV 131 (195)
Q Consensus 119 RsvLP~~is~~LV 131 (195)
|..||.+=.|.|-
T Consensus 156 ~~LLPsvkDP~LW 168 (1024)
T KOG1999|consen 156 QALLPSVKDPNLW 168 (1024)
T ss_pred HhhCCCCCCCCee
Confidence 5689999998863
No 21
>COG5414 TATA-binding protein-associated factor [Transcription]
Probab=42.09 E-value=33 Score=32.43 Aligned_cols=31 Identities=13% Similarity=0.260 Sum_probs=25.0
Q ss_pred cccchhHHHHHHHHHHHHHHHHHHHHHhhhh
Q 029325 90 DDMDSSVDLLIRFLQATFKKVSKRAKKASRS 120 (195)
Q Consensus 90 de~d~SlDLLvrFl~s~fkKvSkRArKA~Rs 120 (195)
+|-.|--.||..||...=+-+.+|-|++...
T Consensus 330 ~En~r~~~Ll~d~lnELE~~i~~~r~~~~~A 360 (392)
T COG5414 330 EENERHTELLADELNELEKGIEEKRRQMESA 360 (392)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 4456778899999999999999988887643
No 22
>PF08568 Kinetochor_Ybp2: Uncharacterised protein family, YAP/Alf4/glomulin; InterPro: IPR013877 This is a family of proteins integrally involved in the central kinetochore. In baker's yeast the protein seems to be part of a macromolecular kinetochore complex and appears to contribute to the proper associations among the central kinetochore sub-complexes and the kinetochore-specific nucleosome. The family is localised in such a way as to bridge the COMA and Ndc80 complexes onto the centromeric nucleosome []. This family also includes aberrant root formation protein 4 and glomulin. Aberrant root formation protein 4 (Alf4) of Arabidopsis thaliana (Mouse-ear cress) is required for the initiation of lateral roots independent from auxin signalling. It may also function in maintaining the pericycle in the mitotically competent state needed for lateral root formation []. Glomulin (FAP68) is essential for normal development of the vasculature and may represent a naturally occurring ligand of the immunophilins FKBP59 and FKBP12 [, ].
Probab=41.36 E-value=24 Score=33.49 Aligned_cols=20 Identities=30% Similarity=0.682 Sum_probs=16.5
Q ss_pred cchhHHH----HHHHHHHHHHHHH
Q 029325 92 MDSSVDL----LIRFLQATFKKVS 111 (195)
Q Consensus 92 ~d~SlDL----LvrFl~s~fkKvS 111 (195)
.+...++ |++.|+.++|++.
T Consensus 132 ~~~~~~~kf~~Ll~~l~~~l~ri~ 155 (633)
T PF08568_consen 132 IEEPFDLKFYCLLELLQIVLKRIQ 155 (633)
T ss_pred chhhhHHHHHHHHHHHHHHHHHhc
Confidence 4556788 9999999999985
No 23
>PF07524 Bromo_TP: Bromodomain associated; InterPro: IPR006565 This bromodomain is found in eukaryotic transcription factors and PHD domain containing proteins (IPR001965 from INTERPRO). The tandem PHD finger-bromodomain is found in many chromatin-associated proteins. It is involved in gene silencing by the human co-repressor KRAB-associated protein 1 (KAP1). The tandem PHD finger-bromodomain of KAP1 has a distinct structure that joins the two protein modules. The first helix, alpha(Z), of an atypical bromodomain forms the central hydrophobic core that anchors the other three helices of the bromodomain on one side and the zinc binding PHD finger on the other []. The Rap1 GTPase-activating protein, Sipa1, is modulated by the cellular bromodomain protein, Brd4. Brd4 belongs to the BET family and is a multifunctional protein involved in transcription, replication, the signal transduction pathway, and cell cycle progression. All of these functions are linked to its association with acetylated chromatin. It has tandem bromodomains []. The dysregulation of the Brd4-associated pathways may play an important role in breast cancer progression []. Bovine papillomavirus type 1 E2 also binds to chromosomes in a complex with Brd4. Interaction with Brd4 is additionally important for E2-mediated transcriptional regulation [, ].
Probab=39.08 E-value=42 Score=23.38 Aligned_cols=26 Identities=31% Similarity=0.437 Sum_probs=17.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhc
Q 029325 96 VDLLIRFLQATFKKVSKRAKKASRSI 121 (195)
Q Consensus 96 lDLLvrFl~s~fkKvSkRArKA~Rsv 121 (195)
-|++.+|++.+-+.+.+-|..|-|+.
T Consensus 33 tdi~~~yl~~l~~~~~~~ae~~gRt~ 58 (77)
T PF07524_consen 33 TDILQRYLQELGRTAKRYAEHAGRTE 58 (77)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCCC
Confidence 35566777777777777776777764
No 24
>TIGR00993 3a0901s04IAP86 chloroplast protein import component Toc86/159, G and M domains. The long precursor of the 86K protein originally described is proposed to have three domains. The N-terminal A-domain is acidic, repetitive, weakly conserved, readily removed by proteolysis during chloroplast isolation, and not required for protein translocation. The other domains are designated G (GTPase) and M (membrane anchor); this family includes most of the G domain and all of M.
Probab=38.62 E-value=22 Score=36.33 Aligned_cols=8 Identities=38% Similarity=0.708 Sum_probs=3.0
Q ss_pred HHHHHHHH
Q 029325 97 DLLIRFLQ 104 (195)
Q Consensus 97 DLLvrFl~ 104 (195)
|.=++.+|
T Consensus 437 dyr~kl~~ 444 (763)
T TIGR00993 437 DYRVKLLQ 444 (763)
T ss_pred HHHHHHHH
Confidence 33333333
No 25
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=37.62 E-value=60 Score=22.98 Aligned_cols=27 Identities=19% Similarity=0.354 Sum_probs=19.5
Q ss_pred cchhHHHHHHHHHHHHHHHHHHHHHhh
Q 029325 92 MDSSVDLLIRFLQATFKKVSKRAKKAS 118 (195)
Q Consensus 92 ~d~SlDLLvrFl~s~fkKvSkRArKA~ 118 (195)
.++.+|.|...++..++++.|.+++-+
T Consensus 25 ~~sale~ltdi~~~yl~~l~~~~~~~a 51 (77)
T smart00576 25 QESALETLTDILQSYIQELGRTAHSYA 51 (77)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 346777777777777777777777655
No 26
>PF14459 Prok-E2_C: Prokaryotic E2 family C
Probab=35.07 E-value=52 Score=27.26 Aligned_cols=34 Identities=26% Similarity=0.439 Sum_probs=25.7
Q ss_pred ccchhHHHHHHHHHHHH------------HHHHHHHHHhhhhccCC
Q 029325 91 DMDSSVDLLIRFLQATF------------KKVSKRAKKASRSILPA 124 (195)
Q Consensus 91 e~d~SlDLLvrFl~s~f------------kKvSkRArKA~RsvLP~ 124 (195)
|.--++||+||.|-..| ||++|.-..-+|||=|-
T Consensus 11 EGrA~lDL~vRLlARLYP~l~ilp~g~as~~~a~~l~~LA~sINp~ 56 (131)
T PF14459_consen 11 EGRASLDLVVRLLARLYPKLCILPSGEASSFQAQNLQSLARSINPR 56 (131)
T ss_pred cchhHHHHHHHHHHHhcceEEEeecchhHHHHHHHHHHHHHhcCCC
Confidence 45678999999999887 55666666677777664
No 27
>PLN03196 MOC1-like protein; Provisional
Probab=35.01 E-value=24 Score=33.08 Aligned_cols=10 Identities=30% Similarity=0.355 Sum_probs=4.1
Q ss_pred cccccccCCC
Q 029325 66 EIGEAFFDEG 75 (195)
Q Consensus 66 ~i~e~~fd~~ 75 (195)
++.-.|+.++
T Consensus 448 ~~~~~~~~~~ 457 (487)
T PLN03196 448 EMEPLFSMGG 457 (487)
T ss_pred ccCCCcccCC
Confidence 3433444443
No 28
>PF06143 Baculo_11_kDa: Baculovirus 11 kDa family; InterPro: IPR009313 This is a family of uncharacterised Baculovirus proteins that are all about 11 kDa in size.
Probab=34.10 E-value=48 Score=25.43 Aligned_cols=22 Identities=36% Similarity=0.842 Sum_probs=16.8
Q ss_pred HHHHHHHHHHHhcchHHHHHHHHH
Q 029325 145 SILKALLEVVCSIGGTVFVLILLL 168 (195)
Q Consensus 145 ~ilKAlLEVvCtlGs~VFv~ILl~ 168 (195)
+.+|-|+=|+|.+ +|||.|++.
T Consensus 31 sfirdFvLVic~~--lVfVii~lF 52 (84)
T PF06143_consen 31 SFIRDFVLVICCF--LVFVIIVLF 52 (84)
T ss_pred HHHHHHHHHHHHH--HHHHHHHHH
Confidence 3578888899976 888887654
No 29
>KOG0699 consensus Serine/threonine protein phosphatase [Signal transduction mechanisms]
Probab=33.86 E-value=20 Score=34.86 Aligned_cols=23 Identities=26% Similarity=0.359 Sum_probs=10.8
Q ss_pred CCCCCCCcccCCCCCCcccchhH
Q 029325 74 EGVDGGAIMDDISDDEDDMDSSV 96 (195)
Q Consensus 74 ~~~D~~~~~~~~~ddede~d~Sl 96 (195)
++.|+|+..++|+|||+.+|.+|
T Consensus 291 need~Ded~e~e~ddEE~~e~~m 313 (542)
T KOG0699|consen 291 NEEDDDEDAEDEQDDEEMVEGSM 313 (542)
T ss_pred cccccccccccccchhhhhhhcc
Confidence 33344444445555555555544
No 30
>PF10904 DUF2694: Protein of unknown function (DUF2694); InterPro: IPR024426 This family of proteins with unknown function appears to be restricted to Mycobacterium spp.
Probab=33.56 E-value=43 Score=26.79 Aligned_cols=18 Identities=50% Similarity=0.637 Sum_probs=17.0
Q ss_pred hhHHHHHHHHHHHHHHHH
Q 029325 136 DGILLLASLSILKALLEV 153 (195)
Q Consensus 136 nGvllLa~L~ilKAlLEV 153 (195)
++||+++-++-+||.|||
T Consensus 46 q~Il~~AdVa~Lra~lev 63 (101)
T PF10904_consen 46 QEILLTADVAYLRAQLEV 63 (101)
T ss_pred HHHHHHhHHHHHHHHHHH
Confidence 789999999999999997
No 31
>PF11571 Med27: Mediator complex subunit 27; InterPro: IPR021627 Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function []. Mediator exists in two major forms in human cells: a smaller form that interacts strongly with pol II and activates transcription, and a large form that does not interact strongly with pol II and does not directly activate transcription. The ubiquitous expression of Med27 mRNA suggests a universal requirement for Med27 in transcriptional initiation. Loss of Crsp34/Med27 decreases amacrine cell number, but increases the number of rod photoreceptor cells [].
Probab=33.56 E-value=57 Score=23.98 Aligned_cols=19 Identities=21% Similarity=0.391 Sum_probs=16.1
Q ss_pred HHHHHHHHHHHHHhhhhcc
Q 029325 104 QATFKKVSKRAKKASRSIL 122 (195)
Q Consensus 104 ~s~fkKvSkRArKA~RsvL 122 (195)
..||||++..|.+|.---+
T Consensus 12 ~~v~~~~t~~a~~al~~~~ 30 (90)
T PF11571_consen 12 YKVFRKITEHANTALLHFI 30 (90)
T ss_pred hhhhhhhhHHHHHHHHHhh
Confidence 7899999999999975444
No 32
>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional
Probab=32.78 E-value=27 Score=30.62 Aligned_cols=22 Identities=14% Similarity=0.428 Sum_probs=16.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHhh
Q 029325 97 DLLIRFLQATFKKVSKRAKKAS 118 (195)
Q Consensus 97 DLLvrFl~s~fkKvSkRArKA~ 118 (195)
+-|-.|+|.||+...--.|||.
T Consensus 296 ~~~~~~f~~iY~~~d~d~rram 317 (356)
T PLN03088 296 AALNKFFREIYQNADEDTRRAM 317 (356)
T ss_pred hHHHHHHHHHHhcCCHHHHHHH
Confidence 4556788888888887777773
No 33
>PF11190 DUF2976: Protein of unknown function (DUF2976); InterPro: IPR021356 Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in a region flanked by markers of conjugative transfer and/or transposition.
Probab=32.53 E-value=1.2e+02 Score=23.13 Aligned_cols=39 Identities=18% Similarity=0.147 Sum_probs=26.3
Q ss_pred HHHHHHHHHHHhcchHHHHHHHHHHHHHHHHHHHHhcCC
Q 029325 145 SILKALLEVVCSIGGTVFVLILLLRFIWAAISYFQSSGN 183 (195)
Q Consensus 145 ~ilKAlLEVvCtlGs~VFv~ILl~R~iWs~vsy~q~~~~ 183 (195)
-.+|+.+.=.-+++++++.++-.+-+.|++++=+.|-|+
T Consensus 17 ~~i~~y~~d~~~l~gLv~~a~afi~Va~~~i~~y~eir~ 55 (87)
T PF11190_consen 17 ETIKGYAKDGVLLLGLVLAAAAFIVVAKAAISTYNEIRD 55 (87)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 345666666667777777777777777777776666554
No 34
>PRK05244 Der GTPase activator; Provisional
Probab=31.79 E-value=34 Score=29.26 Aligned_cols=12 Identities=42% Similarity=0.509 Sum_probs=6.9
Q ss_pred ccchhHHHHHHH
Q 029325 91 DMDSSVDLLIRF 102 (195)
Q Consensus 91 e~d~SlDLLvrF 102 (195)
++++.=|||-+|
T Consensus 157 ~~~~~dDll~~f 168 (177)
T PRK05244 157 EEESDDDLLRLF 168 (177)
T ss_pred cccCHHHHHHHH
Confidence 455556666555
No 35
>PF04147 Nop14: Nop14-like family ; InterPro: IPR007276 Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production [].
Probab=31.30 E-value=36 Score=34.10 Aligned_cols=19 Identities=26% Similarity=0.410 Sum_probs=11.9
Q ss_pred HHHHHHHHhhhhccCCccC
Q 029325 109 KVSKRAKKASRSILPAAIS 127 (195)
Q Consensus 109 KvSkRArKA~RsvLP~~is 127 (195)
+..+.+.+..++=||..++
T Consensus 405 ~~~~~~~~~~~~elPftf~ 423 (840)
T PF04147_consen 405 KKKKESSESAKSELPFTFP 423 (840)
T ss_pred ccccccccccccCCCceec
Confidence 4445556667777777654
No 36
>TIGR02170 thyX thymidylate synthase, flavin-dependent. Two forms of microbial thymidylate synthase are known: ThyA (2.1.1.45) and ThyX (2.1.1.148). This model describes ThyX, a homotetrameric flavoprotein. Both enzymes convert dUMP to dTMP. Under oxygen-limiting conditions, thyX can complement a thyA mutation.
Probab=30.41 E-value=93 Score=25.56 Aligned_cols=32 Identities=25% Similarity=0.372 Sum_probs=25.4
Q ss_pred HHHHhhhhccCCccCcceeeEeehhHHHHHHHH
Q 029325 113 RAKKASRSILPAAISPKLVSFAVDGILLLASLS 145 (195)
Q Consensus 113 RArKA~RsvLP~~is~~LV~FsVnGvllLa~L~ 145 (195)
.|+..+|.+||.+.-++++ +++|.-=++-++.
T Consensus 145 ~a~E~AR~vLP~a~~t~~~-~t~N~r~l~hf~~ 176 (209)
T TIGR02170 145 IAREDARFVLPNALYTNIV-VTGNARALMHFLD 176 (209)
T ss_pred CCHHHHHHhCccccceEEE-EEEcHHHHHHHHH
Confidence 4578899999999988876 6788777666655
No 37
>cd03509 DesA_FADS-like Fatty acid desaturase protein family subgroup, a delta-12 acyl-lipid desaturase-like, DesA-like, yet uncharacterized subgroup of membrane fatty acid desaturase proteins found in alpha-, beta-, and gamma-proteobacteria. Sequences of this domain family appear to be structurally related to membrane fatty acid desaturases and alkane hydroxylases. They all share in common extensive hydrophobic regions that would be capable of spanning the membrane bilayer at least twice. Comparison of these sequences also reveals three regions of conserved histidine cluster motifs that contain eight histidine residues: HXXXH, HXXHH, and HXXHH. These histidine residues are reported to be catalytically essential and proposed to be the ligands for the iron atoms contained within homologs, stearoyl CoA desaturase and alkane hydroxylase.
Probab=30.12 E-value=1.8e+02 Score=25.36 Aligned_cols=13 Identities=15% Similarity=0.414 Sum_probs=5.6
Q ss_pred HHHHHHHHHHHHH
Q 029325 102 FLQATFKKVSKRA 114 (195)
Q Consensus 102 Fl~s~fkKvSkRA 114 (195)
+++.-++++.++.
T Consensus 139 ~~~~~~~~~~~~~ 151 (288)
T cd03509 139 FARDEFRALRAGD 151 (288)
T ss_pred HHHHHHHHhcccc
Confidence 3444444444433
No 38
>PF11702 DUF3295: Protein of unknown function (DUF3295); InterPro: IPR021711 This family is conserved in fungi but the function is not known.
Probab=30.01 E-value=22 Score=34.64 Aligned_cols=11 Identities=27% Similarity=0.607 Sum_probs=5.9
Q ss_pred HHHHHHHHHHH
Q 029325 105 ATFKKVSKRAK 115 (195)
Q Consensus 105 s~fkKvSkRAr 115 (195)
.||++|-.|+.
T Consensus 331 ~~FqRVdSrpn 341 (507)
T PF11702_consen 331 PLFQRVDSRPN 341 (507)
T ss_pred ccceeccCCCC
Confidence 35666655443
No 39
>KOG1631 consensus Translocon-associated complex TRAP, alpha subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=29.84 E-value=30 Score=31.38 Aligned_cols=23 Identities=30% Similarity=0.453 Sum_probs=12.5
Q ss_pred CCCCCCCCcccCCCCCCcccchh
Q 029325 73 DEGVDGGAIMDDISDDEDDMDSS 95 (195)
Q Consensus 73 d~~~D~~~~~~~~~ddede~d~S 95 (195)
++++++|+-.|||+|+|...|+|
T Consensus 33 ~~e~tddAv~eed~d~Dl~~~as 55 (261)
T KOG1631|consen 33 DGEVTDDAVKEEDEDDDLTIDAS 55 (261)
T ss_pred cccccccccccccccccccccCC
Confidence 34456666666555555445544
No 40
>PF10161 DDDD: Putative mitochondrial precursor protein; InterPro: IPR018782 This entry represents a family of small conserved proteins found from nematodes to humans. The C-terminal region is rich in asparagine. These proteins have been putatively designated as mitochondrial precursor proteins but this has not been confirmed.
Probab=29.67 E-value=21 Score=27.30 Aligned_cols=17 Identities=47% Similarity=0.581 Sum_probs=9.5
Q ss_pred cCCCCCCCCcccCCCCCCcc
Q 029325 72 FDEGVDGGAIMDDISDDEDD 91 (195)
Q Consensus 72 fd~~~D~~~~~~~~~ddede 91 (195)
|=++|| .+-.|||||||
T Consensus 63 fLEe~d---iFvP~DDDDDd 79 (79)
T PF10161_consen 63 FLEEND---IFVPEDDDDDD 79 (79)
T ss_pred HHHHhc---ccCCCcCCCCC
Confidence 344556 66666655554
No 41
>PF11705 RNA_pol_3_Rpc31: DNA-directed RNA polymerase III subunit Rpc31; InterPro: IPR024661 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and 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 []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. RNA polymerase III contains seventeen subunits in yeasts and in human cells. Twelve of these are akin to RNA polymerase I or II and the other five are RNA polymerase III-specific, and form the functionally distinct groups: (i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31, Rpc34 and Rpc82 form a cluster of enzyme-specific subunits that contribute to transcription initiation in Saccharomyces cerevisiae and Homo sapiens. There is evidence that these subunits are anchored at or near the N-terminal Zn-fold of Rpc1, itself prolonged by a highly conserved but RNA polymerase III-specific domain []. This entry represents the Rpc31 subunit.
Probab=29.66 E-value=35 Score=28.54 Aligned_cols=7 Identities=14% Similarity=0.207 Sum_probs=2.8
Q ss_pred cccCCcc
Q 029325 33 FHHNRHT 39 (195)
Q Consensus 33 f~hq~f~ 39 (195)
|....||
T Consensus 115 ~~~~~fP 121 (233)
T PF11705_consen 115 FDWEFFP 121 (233)
T ss_pred ccHhhCh
Confidence 3333444
No 42
>PF09770 PAT1: Topoisomerase II-associated protein PAT1; InterPro: IPR019167 Proteins in this entry are necessary for accurate chromosome transmission during cell division []. ; PDB: 2XER_C 2XES_B 2XEQ_D.
Probab=29.27 E-value=18 Score=35.21 Aligned_cols=9 Identities=33% Similarity=0.586 Sum_probs=0.0
Q ss_pred cccCCCCCC
Q 029325 70 AFFDEGVDG 78 (195)
Q Consensus 70 ~~fd~~~D~ 78 (195)
.-|+|.|||
T Consensus 27 ~dfedTYDG 35 (808)
T PF09770_consen 27 LDFEDTYDG 35 (808)
T ss_dssp ---------
T ss_pred ccccccccc
Confidence 457777776
No 43
>PF15539 CAF1-p150_C2: CAF1 complex subunit p150, region binding to CAF1-p60 at C-term
Probab=28.60 E-value=34 Score=31.51 Aligned_cols=19 Identities=21% Similarity=0.160 Sum_probs=9.4
Q ss_pred cccccccCCcceeeccccc
Q 029325 38 HTNHNKTLSELSICHAQLN 56 (195)
Q Consensus 38 f~~~~~~~~~~~~~h~~l~ 56 (195)
-|...+|++.-.-|-.|+-
T Consensus 201 tP~s~krksagsm~it~fm 219 (292)
T PF15539_consen 201 TPVSLKRKSAGSMCITKFM 219 (292)
T ss_pred CcccccccccCcccHHHHH
Confidence 3445555555455544443
No 44
>PF04277 OAD_gamma: Oxaloacetate decarboxylase, gamma chain ; InterPro: IPR005899 This family comprises distantly related, low complexity, hydrophobic small subunits of several related sodium ion-pumping decarboxylases. These include oxaloacetate decarboxylase gamma subunit and methylmalonyl-CoA decarboxylase delta subunit [].; GO: 0008948 oxaloacetate decarboxylase activity, 0015081 sodium ion transmembrane transporter activity, 0071436 sodium ion export, 0016020 membrane
Probab=28.31 E-value=80 Score=21.85 Aligned_cols=21 Identities=29% Similarity=0.589 Sum_probs=17.6
Q ss_pred hHHHHHHHHHHHHHHHHHHHH
Q 029325 159 GTVFVLILLLRFIWAAISYFQ 179 (195)
Q Consensus 159 s~VFv~ILl~R~iWs~vsy~q 179 (195)
++||+.++++=+++..++|+.
T Consensus 13 ~iVF~~L~lL~~~i~l~~~~~ 33 (79)
T PF04277_consen 13 GIVFLVLILLILVISLMSKLI 33 (79)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 578888888888899999983
No 45
>PF02511 Thy1: Thymidylate synthase complementing protein; InterPro: IPR003669 All cellular organisms need thymidylate (dTMP) for the replication of their chromosomes, as dTMP is required for the biosynthesis of dTTP, a building block of DNA. Cells can produce thymidylate either de novo from dUMP or incorporate thymidine using thymidine kinase. The de novo pathway of dTMP synthesis requires a specific enzyme, thymidylate synthase, which methylates dUMP at position 5 of the pyrimidine ring. There are two pathways for thymidylate synthesis, each utilising a different thymidylate synthase enzyme: ThyA (2.1.1.45 from EC) and ThyX (2.1.1.148 from EC) []. Both enzymes convert dUMP to dTMP, but there is no sequence identity between the two enzymes, and their mechanisms of action differ []. Only ThyX uses FAD as cofactor. The well studied thyA proteins catalyse the reductive methylation reaction of dUMP, with methylenetetrahydrofolate (CH(2)H(4)folate) serving as one-carbon donor and as source of reductive power. On the other hand the thyX family of thymidylate synthases contains FAD that is tightly bound by a novel fold. FAD mediates hydride transfer from NADPH during catalysis. Consequently, in the reaction catalysed by thyX, CH(2)H(4)folate serves only as a carbon donor and tetrahydrofolate (and not dihydrofolate as in the case of thyA) is produced [, ]. The thyX domain consists of a central alpha/beta domain and two alpha-helices located away from the central domain. The central domain is made up of a five-stranded antiparallel beta-sheet, flanked by six alpha-helices on one side of the sheet [, , ]. Sequence alignments reveal a specific sequence motif R-H-R-X(7)-S (thyX motif) common to this family of proteins []. This entry represents the flavin-dependent enzyme ThyX, which is a homotetramer bound to four FAD molecules. Under oxygen-limiting conditions, thyX can complement a thyA mutation [].; GO: 0050660 flavin adenine dinucleotide binding, 0050797 thymidylate synthase (FAD) activity, 0006231 dTMP biosynthetic process; PDB: 3N3Y_A 3GE9_A 3FNN_A 3AH5_E 3GWC_B 2AF6_D 2GQ2_B 3HZG_B 2CFA_A 3N0B_B ....
Probab=27.67 E-value=90 Score=25.00 Aligned_cols=40 Identities=23% Similarity=0.417 Sum_probs=27.8
Q ss_pred HHHHHHHH--HHHHhhhhccCCccCcceeeEeehhHHHHHHHH
Q 029325 105 ATFKKVSK--RAKKASRSILPAAISPKLVSFAVDGILLLASLS 145 (195)
Q Consensus 105 s~fkKvSk--RArKA~RsvLP~~is~~LV~FsVnGvllLa~L~ 145 (195)
..++++-+ .++..+|.+||.+..++++ +..|.--+.-++.
T Consensus 120 ~~Y~~ll~~g~~~E~AR~vLP~a~~t~~~-~t~n~r~l~~~~~ 161 (190)
T PF02511_consen 120 EAYEELLEKGVAKEDARYVLPNATKTRIV-VTMNARELMHFLE 161 (190)
T ss_dssp HHHHHHHHTCHHHHHHGGGSBTTBEEEEE-EEEEHHHHHHHHH
T ss_pred HHHHHHHhcCCCHHHHHHhccccceeEEE-EEEcHHHHHHHHH
Confidence 34444444 4889999999999888765 6677666555554
No 46
>KOG3491 consensus Predicted membrane protein [Function unknown]
Probab=27.30 E-value=60 Score=24.22 Aligned_cols=42 Identities=26% Similarity=0.371 Sum_probs=24.6
Q ss_pred hhccCCccCcceeeEeehhHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHH
Q 029325 119 RSILPAAISPKLVSFAVDGILLLASLSILKALLEVVCSIGGTVFVLILLLR 169 (195)
Q Consensus 119 RsvLP~~is~~LV~FsVnGvllLa~L~ilKAlLEVvCtlGs~VFv~ILl~R 169 (195)
|.-.|-...++=-...|.-.||- -|.=||| ||.+|-.|=-+|
T Consensus 21 RGnVakt~~~~e~kypvgPwLlg-------lFvFVVc--GSa~FqIIr~~~ 62 (65)
T KOG3491|consen 21 RGNVAKTTTKKEKKYPVGPWLLG-------LFVFVVC--GSALFQIIRTAT 62 (65)
T ss_pred cCCccccccCccccCCcchHHHH-------HHHHHhh--cHHHHHHHHHHh
Confidence 55555555555555666544332 3444677 899987765444
No 47
>PF11085 YqhR: Conserved membrane protein YqhR; InterPro: IPR024563 This family of proteins is conserved in the Bacillaceae family of the Firmicutes. Their function is not known.
Probab=27.10 E-value=85 Score=26.96 Aligned_cols=20 Identities=35% Similarity=0.463 Sum_probs=15.5
Q ss_pred hhHHHHHHHHHHHHHHHHHH
Q 029325 136 DGILLLASLSILKALLEVVC 155 (195)
Q Consensus 136 nGvllLa~L~ilKAlLEVvC 155 (195)
=|++++..+||+-|||=.+|
T Consensus 72 igi~~~gv~Si~aAllY~~~ 91 (173)
T PF11085_consen 72 IGIVFIGVFSIVAALLYYAL 91 (173)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 37788888888888887665
No 48
>PF04220 YihI: Der GTPase activator (YihI); InterPro: IPR007336 This entry contains Escherichia coli (strain K12) YihI. YihI activates the GTPase activity of Der, a 50S ribosomal subunit stability factor and can therefore be considered a GAP (GTPase activating)-like protein. The stimulation is specific to Der as YihI does not stimulate the GTPase activity of Era or ObgE. The interaction of YihI with Der requires only the C-terminal 78 amino acids of YihI []. A yihI deletion mutant is viable and shows a shorter lag period, but the same post-lag growth rate as a wild-type strain. yihI is expressed during the lag period. Overexpression of yihI inhibits cell growth and biogenesis of the 50S ribosomal subunit []. YihI is an unusual, highly hydrophilic protein with an uneven distribution of charged residues, resulting in an N-terminal region with high pI and a C-terminal region with low pI [].
Probab=26.79 E-value=35 Score=28.93 Aligned_cols=12 Identities=42% Similarity=0.612 Sum_probs=5.4
Q ss_pred ccchhHHHHHHH
Q 029325 91 DMDSSVDLLIRF 102 (195)
Q Consensus 91 e~d~SlDLLvrF 102 (195)
++++-=|||-+|
T Consensus 157 ~~~~~dDll~~f 168 (169)
T PF04220_consen 157 EEESDDDLLRQF 168 (169)
T ss_pred cccchhHHhhcc
Confidence 333334555444
No 49
>PF15103 G0-G1_switch_2: G0/G1 switch protein 2
Probab=26.59 E-value=95 Score=24.82 Aligned_cols=31 Identities=39% Similarity=0.532 Sum_probs=25.8
Q ss_pred ccCcceeeEeehhHHHHHHHHHHHHHHHHHHh
Q 029325 125 AISPKLVSFAVDGILLLASLSILKALLEVVCS 156 (195)
Q Consensus 125 ~is~~LV~FsVnGvllLa~L~ilKAlLEVvCt 156 (195)
-=|-++|+..|=|-+ ||+|-++=++.|.||.
T Consensus 18 kPsrkmvKlYvLGSv-LA~~Gvv~GLVEtVCs 48 (102)
T PF15103_consen 18 KPSRKMVKLYVLGSV-LAFFGVVIGLVETVCS 48 (102)
T ss_pred CCCCCeEeeehhhhH-HHHHHHHHHHHHHHhC
Confidence 345688999988864 6899999999999996
No 50
>COG3428 Predicted membrane protein [Function unknown]
Probab=26.33 E-value=85 Score=30.79 Aligned_cols=50 Identities=16% Similarity=0.129 Sum_probs=30.4
Q ss_pred CCCCCCcccchhHHHHHHHHHHHHHHH----------------HHHH-HHhhhhccCCccCcceeeEee
Q 029325 84 DISDDEDDMDSSVDLLIRFLQATFKKV----------------SKRA-KKASRSILPAAISPKLVSFAV 135 (195)
Q Consensus 84 ~~~ddede~d~SlDLLvrFl~s~fkKv----------------SkRA-rKA~RsvLP~~is~~LV~FsV 135 (195)
.|++.+|.++++.+.-.|. . |+||- +..+ --.+|.++|.+...+-++|-.
T Consensus 161 p~~~~~e~~~~~~~~~~r~-~-~~~~ell~aast~~~ig~~L~~~~~~~~~~re~ip~a~~~~~~~~v~ 227 (494)
T COG3428 161 PEEEVAEVLARSQSSVLRY-P-MNKGELLIAASTGGGIGTGLAVLLPLSGQLREAIPAAWLEGVFLFVP 227 (494)
T ss_pred CCcccccccccchhhHhhc-c-cccceEEEEEecCCceeeehhhhhhhHHHHHHhcchhhhhCeEEEEe
Confidence 3444557788999988877 3 76662 2222 345566666666666555544
No 51
>TIGR02762 TraL_TIGR type IV conjugative transfer system protein TraL. This protein is part of the type IV secretion system for conjugative plasmid transfer. The function of the TraL protein is unknown.
Probab=25.53 E-value=2.9e+02 Score=20.64 Aligned_cols=53 Identities=17% Similarity=0.310 Sum_probs=28.4
Q ss_pred CcceeeEeehhHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHHHHHHhcCC
Q 029325 127 SPKLVSFAVDGILLLASLSILKALLEVVCSIGGTVFVLILLLRFIWAAISYFQSSGN 183 (195)
Q Consensus 127 s~~LV~FsVnGvllLa~L~ilKAlLEVvCtlGs~VFv~ILl~R~iWs~vsy~q~~~~ 183 (195)
.|++++|.+|-.+.....-++=.++...+ -+ +.+++.+. .+|.++..+..++-
T Consensus 12 ~~~i~g~t~DE~i~~~~~~~~Gi~~~~~l--~g-~~lg~~~~-~~~~~lrr~K~g~~ 64 (95)
T TIGR02762 12 QPRILGLPLDEFLPGATLFGIGILSGKAL--IG-LILGAAVM-LIWKRLRRIKGGEG 64 (95)
T ss_pred CCeEEEeeHHHHHHHHHHHHHHHHHhhHH--HH-HHHHHHHH-HHHHHHHHHHcCCC
Confidence 46778899998744333222222222222 11 22333334 78988888877654
No 52
>PF03286 Pox_Ag35: Pox virus Ag35 surface protein; InterPro: IPR004966 The Pox virus Ag35 surface protein is an evelope protein known as protein H5.; GO: 0019031 viral envelope
Probab=25.24 E-value=94 Score=26.92 Aligned_cols=59 Identities=22% Similarity=0.199 Sum_probs=37.9
Q ss_pred ccchhHHHHHHHHHHHHHHHHHHHHHhhhhccCCccCcceeeEeehhHHHHHHHHHHHHHHH--HHHhcch
Q 029325 91 DMDSSVDLLIRFLQATFKKVSKRAKKASRSILPAAISPKLVSFAVDGILLLASLSILKALLE--VVCSIGG 159 (195)
Q Consensus 91 e~d~SlDLLvrFl~s~fkKvSkRArKA~RsvLP~~is~~LV~FsVnGvllLa~L~ilKAlLE--VvCtlGs 159 (195)
-+++-|.|-+.=+...||++..|- +|+++||--+ |..+.. =.|.++.|++=| -+|+.|.
T Consensus 126 ~d~Sdlklat~~I~kdlK~l~~rV-savstVLeDv---QAasv~------R~fs~L~K~i~~l~~l~~~Gk 186 (200)
T PF03286_consen 126 MDDSDLKLATANIIKDLKNLNARV-SAVSTVLEDV---QAASVS------RQFSSLSKAIEELKDLANGGK 186 (200)
T ss_pred cchHHHHHHHHHHHHHHHHHHHhh-hhHHHHHHHH---HHhccc------hHHHHHHHHHHHHHHHHhcCc
Confidence 356668888888999999999886 5888887321 222221 135667777643 4566554
No 53
>PF15088 NADH_dh_m_C1: NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
Probab=25.22 E-value=39 Score=24.04 Aligned_cols=19 Identities=37% Similarity=0.704 Sum_probs=16.4
Q ss_pred HHHHHhcchHHHHHHHHHH
Q 029325 151 LEVVCSIGGTVFVLILLLR 169 (195)
Q Consensus 151 LEVvCtlGs~VFv~ILl~R 169 (195)
|.|--|+|+.||.-++|++
T Consensus 15 lkVGLtlGts~flW~~L~k 33 (49)
T PF15088_consen 15 LKVGLTLGTSVFLWIYLIK 33 (49)
T ss_pred hheeeecchHHHHHHHHHH
Confidence 5677899999999998886
No 54
>PF12785 VESA1_N: Variant erythrocyte surface antigen-1; InterPro: IPR024751 This entry represents variant erythrocyte surface antigen 1, versions a and b, of Babesia. Babesia bovis is a tick-borne, intra-erythrocytic, protozoal parasite of cattle that shares many lifestyle parallels with the most virulent of the human malarial parasites, Plasmodium falciparum. Babesia uses antigenic variation to establish consistent infections of long duration. The two variants of VESA1, a and b, are expressed from different but closely related genes, and variation is achieved through the involvement of a segmental gene conversion mechanism and low-frequency epigenetic in situ switching of transcriptional activity from the VESA1 gene-pair to a possible other gene pair [].
Probab=25.13 E-value=52 Score=32.01 Aligned_cols=9 Identities=33% Similarity=1.313 Sum_probs=8.7
Q ss_pred HHHHHHHHH
Q 029325 170 FIWAAISYF 178 (195)
Q Consensus 170 ~iWs~vsy~ 178 (195)
+|||+++||
T Consensus 262 LIWSGLTym 270 (462)
T PF12785_consen 262 LIWSGLTYM 270 (462)
T ss_pred HHhcchhHh
Confidence 799999999
No 55
>PF03729 DUF308: Short repeat of unknown function (DUF308); InterPro: IPR005325 This represents a group of short repeats that occurs in a limited number of membrane proteins. It may divide further in short repeats of around 7-10 residues of the pattern G-#-X(2)-#(2)-X (#=hydrophobic).
Probab=24.61 E-value=2e+02 Score=18.42 Aligned_cols=23 Identities=22% Similarity=0.366 Sum_probs=19.4
Q ss_pred hHHHHHHHHHHHHHHHHHHHHhc
Q 029325 159 GTVFVLILLLRFIWAAISYFQSS 181 (195)
Q Consensus 159 s~VFv~ILl~R~iWs~vsy~q~~ 181 (195)
.+++...+++.+++..+.|+++.
T Consensus 25 ~~i~g~~~i~~Gi~~l~~~~~~~ 47 (72)
T PF03729_consen 25 AIILGIWLIISGIFQLISAFRRR 47 (72)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcc
Confidence 47788889999999999999943
No 56
>PF10661 EssA: WXG100 protein secretion system (Wss), protein EssA; InterPro: IPR018920 The Wss (WXG100 protein secretion system) in Staphylococcus aureus seems to be encoded by a locus of eight ORFs, called ess (eSAT-6 secretion system) []. This locus encodes, amongst several other proteins, EssA, a protein predicted to possess one transmembrane domain. Due to its predicted membrane location and its absolute requirement for WXG100 protein secretion, it has been speculated that EssA could form a secretion apparatus in conjunction with YukC and YukAB. Proteins homologous to EssA, YukC, EsaA and YukD were absent from mycobacteria []. Members of this family are associated with type VII secretion of WXG100 family targets in the Firmicutes, but not in the Actinobacteria. This highly divergent protein family consists largely of a central region of highly polar low-complexity sequence containing occasional LF motifs in weak repeats about 17 residues in length, flanked by hydrophobic N- and C-terminal regions.
Probab=23.77 E-value=85 Score=25.47 Aligned_cols=24 Identities=29% Similarity=0.715 Sum_probs=16.2
Q ss_pred HHHHHHHHHHhcchHHHHHHHHHHHHH
Q 029325 146 ILKALLEVVCSIGGTVFVLILLLRFIW 172 (195)
Q Consensus 146 ilKAlLEVvCtlGs~VFv~ILl~R~iW 172 (195)
|+-+++=+||+|++.+|+++ |=||
T Consensus 121 i~~~i~g~ll~i~~giy~~~---r~~~ 144 (145)
T PF10661_consen 121 ILLSIGGILLAICGGIYVVL---RKVW 144 (145)
T ss_pred HHHHHHHHHHHHHHHHHHHH---HHhh
Confidence 34445556777888887764 8777
No 57
>PF06643 DUF1158: Protein of unknown function (DUF1158); InterPro: IPR010590 This family consists of several enterobacterial YbdJ proteins. The function of this family is unknown
Probab=23.39 E-value=1.9e+02 Score=22.41 Aligned_cols=12 Identities=67% Similarity=0.764 Sum_probs=9.1
Q ss_pred ehhHHHHHHHHH
Q 029325 135 VDGILLLASLSI 146 (195)
Q Consensus 135 VnGvllLa~L~i 146 (195)
..|+|++++|+-
T Consensus 11 ~~giLll~~LS~ 22 (82)
T PF06643_consen 11 AGGILLLAFLSC 22 (82)
T ss_pred HHHHHHHHHHHH
Confidence 358899988874
No 58
>PTZ00415 transmission-blocking target antigen s230; Provisional
Probab=22.22 E-value=61 Score=37.06 Aligned_cols=6 Identities=17% Similarity=0.401 Sum_probs=2.4
Q ss_pred cceeec
Q 029325 47 ELSICH 52 (195)
Q Consensus 47 ~~~~~h 52 (195)
++++-.
T Consensus 128 d~~i~~ 133 (2849)
T PTZ00415 128 DMIIIK 133 (2849)
T ss_pred ceEEee
Confidence 444433
No 59
>PF15176 LRR19-TM: Leucine-rich repeat family 19 TM domain
Probab=22.17 E-value=80 Score=25.23 Aligned_cols=42 Identities=14% Similarity=0.217 Sum_probs=21.1
Q ss_pred cCCcccccccCCcc---eeecccccCCCCC---CCcccccccccCCCC
Q 029325 35 HNRHTNHNKTLSEL---SICHAQLNYGSAG---EDPDEIGEAFFDEGV 76 (195)
Q Consensus 35 hq~f~~~~~~~~~~---~~~h~~l~~~saG---~~p~~i~e~~fd~~~ 76 (195)
.-.+-|+|+|.+.. .-|.++-.+.+.| .+.+|=|+.|++|.|
T Consensus 45 k~~~SY~H~rL~e~e~~~~~~g~~~~p~~~~~~~~~~eDDDGFIEDnY 92 (102)
T PF15176_consen 45 KYLASYRHHRLPETEAETYEDGFTENPEVGSQIPDTNEDDDGFIEDNY 92 (102)
T ss_pred HHHhccccccCCcccccccccccCCCCCccccCCCCCCCCCccccccC
Confidence 33455888885532 3344444443333 223444556666665
No 60
>PRK10983 putative inner membrane protein; Provisional
Probab=22.15 E-value=1.6e+02 Score=26.54 Aligned_cols=13 Identities=31% Similarity=0.250 Sum_probs=6.5
Q ss_pred ehhHHHHHHHHHH
Q 029325 135 VDGILLLASLSIL 147 (195)
Q Consensus 135 VnGvllLa~L~il 147 (195)
+.|++....+|++
T Consensus 224 i~gvl~~ig~~i~ 236 (368)
T PRK10983 224 VQAVLGGIGLAIS 236 (368)
T ss_pred HHHHHHHHHHHHH
Confidence 3444555555554
No 61
>PF13875 DUF4202: Domain of unknown function (DUF4202)
Probab=21.84 E-value=84 Score=27.05 Aligned_cols=24 Identities=25% Similarity=0.524 Sum_probs=21.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhh
Q 029325 97 DLLIRFLQATFKKVSKRAKKASRS 120 (195)
Q Consensus 97 DLLvrFl~s~fkKvSkRArKA~Rs 120 (195)
+=+++-||..++|+|.+++.++-.
T Consensus 150 eK~v~Il~KTw~KMS~~g~~~AL~ 173 (185)
T PF13875_consen 150 EKIVDILRKTWRKMSERGHEAALK 173 (185)
T ss_pred HHHHHHHHHHHHHCCHHHHHHHHc
Confidence 347888999999999999999877
No 62
>COG5192 BMS1 GTP-binding protein required for 40S ribosome biogenesis [Translation, ribosomal structure and biogenesis]
Probab=21.50 E-value=93 Score=32.40 Aligned_cols=63 Identities=19% Similarity=0.392 Sum_probs=37.0
Q ss_pred ccccCCCCCCCcccccccccCCC---------CCCCCccc-CCCC-CCcccchhHH-----------HHHHHHHHHHHHH
Q 029325 53 AQLNYGSAGEDPDEIGEAFFDEG---------VDGGAIMD-DISD-DEDDMDSSVD-----------LLIRFLQATFKKV 110 (195)
Q Consensus 53 ~~l~~~saG~~p~~i~e~~fd~~---------~D~~~~~~-~~~d-dede~d~SlD-----------LLvrFl~s~fkKv 110 (195)
.||.++-.|.+.++|..-|+++. |-|.+... |+++ .+|++|..+| =+-+|+.+-|.++
T Consensus 487 ~kl~~sqs~kr~~ni~ki~y~e~lspeeci~e~kge~~~s~e~~~v~~D~~edff~vsk~~n~~~s~~~ek~~~~~fe~L 566 (1077)
T COG5192 487 SKLAYSQSGKRGRNIQKIFYDESLSPEECIEEYKGESAKSSESDLVVQDEPEDFFDVSKVANESISSNHEKLMESEFEEL 566 (1077)
T ss_pred hhhhhhhcccccccccceeccccCCHHHHHHHhccccccccccccccccCchhhhhhhhhcccccccchhhhchhHHHHH
Confidence 45777777888888888888875 22211111 2222 3455555555 2456777778777
Q ss_pred HHHHH
Q 029325 111 SKRAK 115 (195)
Q Consensus 111 SkRAr 115 (195)
+|.-+
T Consensus 567 ~kkw~ 571 (1077)
T COG5192 567 KKKWS 571 (1077)
T ss_pred HHHHh
Confidence 77654
No 63
>PHA02608 67 prohead core protein; Provisional
Probab=21.44 E-value=58 Score=25.16 Aligned_cols=6 Identities=50% Similarity=1.437 Sum_probs=2.6
Q ss_pred CCCccc
Q 029325 61 GEDPDE 66 (195)
Q Consensus 61 G~~p~~ 66 (195)
|+-|++
T Consensus 47 GEe~ed 52 (80)
T PHA02608 47 GEEPED 52 (80)
T ss_pred CCCCcc
Confidence 444443
No 64
>PF01267 F-actin_cap_A: F-actin capping protein alpha subunit; InterPro: IPR002189 This entry represents a component of the WASH complex. The WASH complex is present at the surface of endosomes and recruits and activates the Arp2/3 complex to induce actin polymerisation. The WASH complex plays a key role in the fission of tubules that serve as transport intermediates during endosome sorting []. The WASH complex's subunit structure: F-actin-capping protein subunit alpha (CAPZA1, CAPZA2 or CAPZA3), F-actin-capping protein subunit beta (CAPZB), WASH (WASH1, WASH2P, WASH3P, WASH4P, WASH5P or WASH6P), FAM21 (FAM21A, FAM21B or FAM21C), KIAA1033, KIAA0196 (strumpellin) and CCDC53. The actin filament system, a prominent part of the cytoskeleton in eukaryotic cells, is both a static structure and a dynamic network that can undergo rearrangements: it is thought to be involved in processes such as cell movement and phagocytosis [], as well as muscle contraction. The F-actin capping protein binds in a calcium-independent manner to the fast growing ends of actin filaments (barbed end) thereby blocking the exchange of subunits at these ends. Unlike gelsolin and severin this protein does not sever actin filaments. The F-actin capping protein is a heterodimer composed of two unrelated subunits: alpha and beta (see IPR001698 from INTERPRO). Neither of the subunits shows sequence similarity to other filament-capping proteins []. The alpha subunit is a protein of about 268 to 286 amino acid residues whose sequence is well conserved in eukaryotic species [].; GO: 0003779 actin binding, 0030036 actin cytoskeleton organization, 0008290 F-actin capping protein complex; PDB: 1MQ1_D 1MWN_X 2KBM_Y 2KZ7_A 3AAE_C 3AA6_A 3LK4_G 1IZN_A 3AA7_A 3AAA_A ....
Probab=21.37 E-value=77 Score=27.81 Aligned_cols=23 Identities=30% Similarity=0.530 Sum_probs=18.1
Q ss_pred HHHHHHHHHHHHHHhhhhccCCc
Q 029325 103 LQATFKKVSKRAKKASRSILPAA 125 (195)
Q Consensus 103 l~s~fkKvSkRArKA~RsvLP~~ 125 (195)
|..+|..++..+=|+.|..||.-
T Consensus 232 L~e~~~~ls~~tFK~LRR~LPVT 254 (271)
T PF01267_consen 232 LNESYNNLSEKTFKALRRQLPVT 254 (271)
T ss_dssp HHHHHHHHHHTHHHHHS-SS-TT
T ss_pred HHHHHHHhhHHHHHHhhhhCCCC
Confidence 45689999999999999999964
No 65
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=21.32 E-value=1.1e+02 Score=32.52 Aligned_cols=21 Identities=43% Similarity=0.553 Sum_probs=13.0
Q ss_pred HHHHHHHHHHHHhcchHHHHHHHHHHH
Q 029325 144 LSILKALLEVVCSIGGTVFVLILLLRF 170 (195)
Q Consensus 144 L~ilKAlLEVvCtlGs~VFv~ILl~R~ 170 (195)
||++| |-+|-===+++.|.|=
T Consensus 167 LW~VK------C~iG~Er~~a~~LMrK 187 (1024)
T KOG1999|consen 167 LWIVK------CKIGREREVAFCLMRK 187 (1024)
T ss_pred eeEEE------eccccHHHHHHHHHHH
Confidence 56665 7777665555556553
No 66
>COG3079 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.25 E-value=50 Score=28.79 Aligned_cols=20 Identities=15% Similarity=0.672 Sum_probs=15.2
Q ss_pred CCCCcccchhHHHHHHHHHH
Q 029325 86 SDDEDDMDSSVDLLIRFLQA 105 (195)
Q Consensus 86 ~ddede~d~SlDLLvrFl~s 105 (195)
|||++|.+.++.=.+.||+.
T Consensus 145 ded~EE~~~~leEiiEyvRv 164 (186)
T COG3079 145 DEDQEELEESLEEIIEYVRV 164 (186)
T ss_pred cccHHHHHHHHHHHHHHHHH
Confidence 45677778888888888864
No 67
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=21.04 E-value=43 Score=29.68 Aligned_cols=11 Identities=27% Similarity=0.389 Sum_probs=5.6
Q ss_pred HhhhhccCCcc
Q 029325 116 KASRSILPAAI 126 (195)
Q Consensus 116 KA~RsvLP~~i 126 (195)
|+.|.++|.-+
T Consensus 163 k~~R~l~PsG~ 173 (232)
T PRK12766 163 TAVRGKHPSGF 173 (232)
T ss_pred hhhcccCCCCC
Confidence 45555555443
No 68
>TIGR00986 3a0801s05tom22 mitochondrial import receptor subunit Tom22. translocase (Tom) import receptor, five proteins of the Tom channel complex, five proteins of the inner membrane translocase (Tim) and three "motor" proteins. This family is specific for the Tom22 proteins.
Probab=20.70 E-value=3.1e+02 Score=23.03 Aligned_cols=55 Identities=22% Similarity=0.193 Sum_probs=34.5
Q ss_pred hhhhccCCccCcceeeEeehhHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHHHHH
Q 029325 117 ASRSILPAAISPKLVSFAVDGILLLASLSILKALLEVVCSIGGTVFVLILLLRFIWAAISYF 178 (195)
Q Consensus 117 A~RsvLP~~is~~LV~FsVnGvllLa~L~ilKAlLEVvCtlGs~VFv~ILl~R~iWs~vsy~ 178 (195)
|.+-|+|+..-... +...-+..+.+|.++-.-|..-=+|.++-||+=+=|+ ++|.
T Consensus 57 ALkDm~Pp~~R~~i------~~~~s~t~s~~ks~~sfsGkalWivsTSaLLLgVPla-la~~ 111 (145)
T TIGR00986 57 ALKDIVPPTTRGWI------YHKYSTTTNFVKSTLSFAGRAAWAVSTSALLLGVPFA-ISFA 111 (145)
T ss_pred HHHhhCCHHHHHHH------HHHHHHHHHHHHHHHHhcCcchhhhHHHHHHHHHHHH-HHHH
Confidence 55556666543322 1233455677888888888888888888777765553 3443
No 69
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=20.51 E-value=49 Score=23.01 Aligned_cols=20 Identities=20% Similarity=0.409 Sum_probs=15.2
Q ss_pred CCcccchhHHHHHHHHHHHH
Q 029325 88 DEDDMDSSVDLLIRFLQATF 107 (195)
Q Consensus 88 dede~d~SlDLLvrFl~s~f 107 (195)
++-+...-|++|+.+|+..+
T Consensus 8 ~~l~~~e~L~~l~~YLR~~~ 27 (55)
T PF13821_consen 8 EELSPEERLDKLLSYLREEH 27 (55)
T ss_pred hccCHHHHHHHHHHHHHhhC
Confidence 34456678999999999875
No 70
>PF04395 Poxvirus_B22R: Poxvirus B22R protein; InterPro: IPR007490 This entry represents B22 proteins of Poxviruses [].
Probab=20.35 E-value=87 Score=27.15 Aligned_cols=21 Identities=24% Similarity=0.472 Sum_probs=19.1
Q ss_pred HHHHHHHHHHHHhhhhccCCc
Q 029325 105 ATFKKVSKRAKKASRSILPAA 125 (195)
Q Consensus 105 s~fkKvSkRArKA~RsvLP~~ 125 (195)
.+|.+|.+|||+++|+++|..
T Consensus 178 ~Iy~~vK~~~k~~~~~~mp~v 198 (205)
T PF04395_consen 178 EIYSNVKDRAKSLLKKYMPTV 198 (205)
T ss_pred HHHHHHHHHHHHHHHHhcCcC
Confidence 589999999999999999964
No 71
>KOG4672 consensus Uncharacterized conserved low complexity protein [Function unknown]
Probab=20.24 E-value=64 Score=31.58 Aligned_cols=13 Identities=31% Similarity=0.355 Sum_probs=5.5
Q ss_pred cCCCCCCcccchh
Q 029325 83 DDISDDEDDMDSS 95 (195)
Q Consensus 83 ~~~~ddede~d~S 95 (195)
+|+|||+.+||.+
T Consensus 279 ~d~~dds~~eden 291 (487)
T KOG4672|consen 279 PDNEDDSRPEDEN 291 (487)
T ss_pred Cccccccchhhhc
Confidence 3444444444443
No 72
>KOG3555 consensus Ca2+-binding proteoglycan Testican [General function prediction only]
Probab=20.08 E-value=50 Score=31.80 Aligned_cols=14 Identities=57% Similarity=0.677 Sum_probs=7.1
Q ss_pred CCCCCCcccchhHH
Q 029325 84 DISDDEDDMDSSVD 97 (195)
Q Consensus 84 ~~~ddede~d~SlD 97 (195)
|++||||++|.+.|
T Consensus 416 ddedded~~dg~aD 429 (434)
T KOG3555|consen 416 DDEDDEDSDDGSAD 429 (434)
T ss_pred ccccccccccCccc
Confidence 44455555555544
No 73
>KOG0299 consensus U3 snoRNP-associated protein (contains WD40 repeats) [RNA processing and modification]
Probab=20.02 E-value=49 Score=32.30 Aligned_cols=16 Identities=31% Similarity=0.428 Sum_probs=10.0
Q ss_pred cccCCCCCCCccccccc
Q 029325 54 QLNYGSAGEDPDEIGEA 70 (195)
Q Consensus 54 ~l~~~saG~~p~~i~e~ 70 (195)
+++ ...+++.+||.+.
T Consensus 35 ~~~-~~~~ed~eei~Sd 50 (479)
T KOG0299|consen 35 KKN-RDDDEDAEEIESD 50 (479)
T ss_pred ccc-CCchhhhhhhccc
Confidence 344 5666777777654
Done!