Query 026803
Match_columns 233
No_of_seqs 138 out of 344
Neff 5.9
Searched_HMMs 46136
Date Fri Mar 29 12:56:38 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026803.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026803hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04755 PAP_fibrillin: PAP_fi 100.0 2.8E-39 6.1E-44 274.5 19.2 158 65-227 1-198 (198)
2 PF08212 Lipocalin_2: Lipocali 74.0 32 0.0007 27.5 8.8 33 199-231 80-115 (143)
3 COG3040 Blc Bacterial lipocali 59.8 69 0.0015 27.4 8.2 95 119-231 35-143 (174)
4 PF14869 DUF4488: Domain of un 51.2 1.4E+02 0.003 24.6 9.7 63 119-184 2-71 (133)
5 PF12283 Protein_K: Bacterioph 40.6 45 0.00097 23.0 3.3 35 65-102 6-41 (56)
6 COG2026 RelE Cytotoxic transla 35.3 1.3E+02 0.0028 22.4 5.6 53 84-146 18-72 (90)
7 PF11010 DUF2848: Protein of u 33.4 46 0.001 29.0 3.2 29 87-115 6-34 (194)
8 TIGR02116 toxin_Txe_YoeB toxin 31.7 1.8E+02 0.0038 20.9 5.7 36 86-129 17-57 (80)
9 smart00550 Zalpha Z-DNA-bindin 30.5 1.1E+02 0.0024 21.5 4.3 40 64-103 4-50 (68)
10 cd03715 RT_ZFREV_like RT_ZFREV 28.2 99 0.0022 26.1 4.4 49 81-129 6-57 (210)
11 PF07624 PSD2: Protein of unkn 26.9 98 0.0021 22.3 3.6 41 63-103 8-59 (76)
12 cd01645 RT_Rtv RT_Rtv: Reverse 26.3 1.2E+02 0.0027 25.7 4.7 50 80-129 5-56 (213)
13 PHA00097 K protein K 25.9 1.1E+02 0.0024 21.1 3.3 35 65-102 6-41 (56)
14 TIGR02530 flg_new flagellar op 24.9 89 0.0019 24.3 3.1 25 79-103 27-51 (96)
15 COG2088 SpoVG Uncharacterized 23.4 81 0.0018 24.3 2.6 22 205-227 26-47 (95)
16 PF05973 Gp49: Phage derived p 23.0 2E+02 0.0043 20.9 4.7 39 84-128 6-46 (91)
17 PF04213 HtaA: Htaa; InterPro 22.1 3.5E+02 0.0077 22.5 6.5 26 202-228 75-100 (168)
18 PF07240 Turandot: Stress-indu 21.6 2.2E+02 0.0048 21.6 4.6 35 69-103 13-47 (85)
19 PF03076 GP3: Equine arteritis 20.5 73 0.0016 26.0 1.9 19 198-216 120-138 (160)
No 1
>PF04755 PAP_fibrillin: PAP_fibrillin; InterPro: IPR006843 This family identifies a conserved domain found in a number of plastid lipid-associated proteins (PAPs) that are thought to form together with other plastoglobulins a coat on the surface of the lipoprotein particle. The coat may contain receptors for attachment to the thylakoid membrane as well as regulatory proteins that may function in the transfer of lipids to and from the thylakoid membranes.). This entry also represents a number of putative fibrillin proteins.; GO: 0005198 structural molecule activity, 0009507 chloroplast
Probab=100.00 E-value=2.8e-39 Score=274.48 Aligned_cols=158 Identities=27% Similarity=0.463 Sum_probs=138.5
Q ss_pred HHHHHHHHHHhccCCCCccCChhhHHHHHHHHHHHHHhcCCCCCCCCcccCCCCCCCceeeeeecc------------c-
Q 026803 65 DDLVASILSKVNQSDGGVSLAKEEHKEVAEVAQELQKYCVEAPVKCPLIFGVPTSPGGGYRSAFGR------------L- 131 (233)
Q Consensus 65 ~~lK~~LL~aia~t~rG~~as~~~r~~I~~lI~~LEa~n~~~Pt~~Pl~~g~~~~l~G~WrL~lgr------------~- 131 (233)
+++|++||+++++++||+.++++++++|+++|++||++| |++.|+. +.++++|+|+|.+.. .
T Consensus 1 ~~~K~~Ll~~~~~~~rG~~~~~~~~~~i~~~v~~LE~~n---p~~~p~~--s~~~L~G~W~Lvytt~~~~~~~l~~~~~~ 75 (198)
T PF04755_consen 1 QDLKQELLQAVAGTNRGLRASPEDREEIEELVEELEALN---PTPDPAD--SLPLLDGRWELVYTTSPEIRSLLQRGRLP 75 (198)
T ss_pred ChHHHHHHHHHhccCCCccCCHHHHHHHHHHHHHHHHhC---CCCCCcC--CchhcCcEEEEEeecCCCccccccccccc
Confidence 479999999999999999999999999999999999999 9999996 458899999997422 1
Q ss_pred ceeccceEEEEcCCC-ceeEEEEeeeCCccceEEEEEEEEEEcCCcEEEEEEecceEee---------------------
Q 026803 132 FFKTKEMIQAVEAPD-TVRNKVSFTALGFLDGEVSLKGKLNALDEKWIQVVFEPPELKV--------------------- 189 (233)
Q Consensus 132 ~~~~g~v~Q~Id~~~-~v~N~V~~~~~g~l~G~v~v~a~~~~~~~~rv~V~F~~~~l~~--------------------- 189 (233)
.+..+++||+||.++ ++.|+|+|.++|++.|.+.+.+++++.+++|+.|+|+++.++.
T Consensus 76 ~~~~~~v~Q~id~~~~~~~N~v~~~~~~~~~~~~~v~a~~~~~~~~rv~v~f~~~~l~~~~~l~~~l~~~~~~~~~v~~~ 155 (198)
T PF04755_consen 76 GVRVGRVFQTIDADNGRVENVVELSGFPLLEGSVSVRASLEVRSPRRVEVTFERASLKPPSLLKGVLGPLKDALNNVPRG 155 (198)
T ss_pred cccccceEEEEECCCceEEEEEEEeccCceEEEEEEEEEEEEccccEEEEEEEeeEEcccceeeccchhhhhhhhhcccc
Confidence 345789999999999 9999999998888889999999999999999999999988843
Q ss_pred ----CceeeeeC-CCceeEEEEEEecCCeEEEeCCCCcEEEEE
Q 026803 190 ----GGLEFRYG-GQSEVKLQITYIDEKIRLGLGSRGSLFVFQ 227 (233)
Q Consensus 190 ----g~~~~~l~-~~~~GwldiTYLDe~lRIsRG~kGslFVl~ 227 (233)
.+++++++ ..++||||||||||||||+||++|++|||.
T Consensus 156 ~~~~~~~~~~~~~~~~~g~l~~tYLDedlRI~Rg~~G~~fVl~ 198 (198)
T PF04755_consen 156 ISDELPVPLPLPGGSPKGWLDTTYLDEDLRISRGNKGSLFVLK 198 (198)
T ss_pred cccccccccccCCCCCceEEEEEEECCCeEEEEcCCCCEEEeC
Confidence 11223333 578999999999999999999999999984
No 2
>PF08212 Lipocalin_2: Lipocalin-like domain; InterPro: IPR000566 Proteins which transport small hydrophobic molecules such as steroids, bilins, retinoids, and lipids share limited regions of sequence homology and a common tertiary structure architecture [, , , , ]. This is an eight stranded antiparallel beta-barrel with a repeated + 1 topology enclosing a internal ligand binding site [, ]. The name 'lipocalin' has been proposed [] for this protein family, but cytosolic fatty-acid binding proteins are also included. The sequences of most members of the family, the core or kernal lipocalins, are characterised by three short conserved stretches of residues, while others, the outlier lipocalin group, share only one or two of these [, ]. Proteins known to belong to this family include alpha-1-microglobulin (protein HC); alpha-1-acid glycoprotein (orosomucoid) []; aphrodisin; apolipoprotein D; beta-lactoglobulin; complement component C8 gamma chain []; crustacyanin []; epididymal-retinoic acid binding protein (E-RABP) []; insectacyanin; odorant-binding protein (OBP); human pregnancy-associated endometrial alpha-2 globulin; probasin (PB), a rat prostatic protein; prostaglandin D synthase (5.3.99.2 from EC) []; purpurin; Von Ebner's gland protein (VEGP) []; and lizard epididymal secretory protein IV (LESP IV) [].; GO: 0005488 binding; PDB: 3EBW_B 1QWD_A 2ACO_A 3MBT_A.
Probab=73.95 E-value=32 Score=27.50 Aligned_cols=33 Identities=21% Similarity=0.324 Sum_probs=26.9
Q ss_pred CceeEEEEEEecCC---eEEEeCCCCcEEEEEeccc
Q 026803 199 QSEVKLQITYIDEK---IRLGLGSRGSLFVFQRRTQ 231 (233)
Q Consensus 199 ~~~GwldiTYLDe~---lRIsRG~kGslFVl~R~~~ 231 (233)
...|-..|.|+|.+ .=|+-.++-.+|||.|...
T Consensus 80 ~~~~~YwVl~~D~dY~~~iv~~~~~~~~WILsR~p~ 115 (143)
T PF08212_consen 80 PPKGNYWVLYTDYDYSWAIVGSPDREYLWILSRTPQ 115 (143)
T ss_dssp TEEEEEEEEEEBTTSSEEEEEECCCCEEEEEESSSS
T ss_pred CCCcceEEEEEcCCccEEEEecCCCCEEEEEeCCCC
Confidence 56788899999988 4566678889999999764
No 3
>COG3040 Blc Bacterial lipocalin [Cell envelope biogenesis, outer membrane]
Probab=59.83 E-value=69 Score=27.43 Aligned_cols=95 Identities=17% Similarity=0.163 Sum_probs=55.5
Q ss_pred CCCceeeeeeccc--cee-----ccceEEEEcCCC-ceeEEEEeeeCCccceEEEEEEEEEEcCC---cEEEEEEecceE
Q 026803 119 SPGGGYRSAFGRL--FFK-----TKEMIQAVEAPD-TVRNKVSFTALGFLDGEVSLKGKLNALDE---KWIQVVFEPPEL 187 (233)
Q Consensus 119 ~l~G~WrL~lgr~--~~~-----~g~v~Q~Id~~~-~v~N~V~~~~~g~l~G~v~v~a~~~~~~~---~rv~V~F~~~~l 187 (233)
--.|+|-= +.|+ .|+ +-..|-..|... .|.|.-....-+.. =.++|+-.+.+. .++.|+|-.
T Consensus 35 ~Y~G~WyE-vaR~p~~f~~gc~~vtA~Y~l~d~~~I~V~n~c~~~~~~~~---~~ieGkA~i~~~~~~a~LkVsF~~--- 107 (174)
T COG3040 35 RYLGKWYE-VARLPMRFEKGCVQVTATYSLRDDGGISVINRCRTGDGGKW---SQIEGKAKIVDNATRAKLKVSFFG--- 107 (174)
T ss_pred hcceeeee-eecccchhhhcceeeEeEEEEecCCceEEEeccccCCCCCc---eeecceEEEecCccccEEEEEecC---
Confidence 45688843 3444 333 223455556555 77776544211101 145566665554 455555432
Q ss_pred eeCceeeeeCCCceeEEEEEEecCCeEEE---eCCCCcEEEEEeccc
Q 026803 188 KVGGLEFRYGGQSEVKLQITYIDEKIRLG---LGSRGSLFVFQRRTQ 231 (233)
Q Consensus 188 ~~g~~~~~l~~~~~GwldiTYLDe~lRIs---RG~kGslFVl~R~~~ 231 (233)
|.. |-..++|+|+|=+.. -.|+-.+|++.|...
T Consensus 108 ---------pF~--g~Y~Vl~~d~eYs~aiVgsPdr~ylWlLsRtP~ 143 (174)
T COG3040 108 ---------PFY--GDYWVLALDPEYSWAIVGSPDREYLWLLSRTPT 143 (174)
T ss_pred ---------Ccc--ccEEEEEECCCccEEEEeCCCcceEEEEecCCC
Confidence 122 788999999998865 458888999999763
No 4
>PF14869 DUF4488: Domain of unknown function (DUF4488)
Probab=51.24 E-value=1.4e+02 Score=24.58 Aligned_cols=63 Identities=11% Similarity=0.049 Sum_probs=42.9
Q ss_pred CCCceeeeeeccc-------ceeccceEEEEcCCCceeEEEEeeeCCccceEEEEEEEEEEcCCcEEEEEEec
Q 026803 119 SPGGGYRSAFGRL-------FFKTKEMIQAVEAPDTVRNKVSFTALGFLDGEVSLKGKLNALDEKWIQVVFEP 184 (233)
Q Consensus 119 ~l~G~WrL~lgr~-------~~~~g~v~Q~Id~~~~v~N~V~~~~~g~l~G~v~v~a~~~~~~~~rv~V~F~~ 184 (233)
.+.|.|++..... -++...++-++..++++.|+.-... ....+...|+++..++..+.-..++
T Consensus 2 ~l~GVWQ~c~~~~~~~~~~g~l~~~~~lKilS~Dgtf~Ni~~~~~---~~aiIt~~GtY~~~sD~~Y~E~IeK 71 (133)
T PF14869_consen 2 SLQGVWQLCHYVSESPEVPGKLKPSNVLKILSDDGTFVNITMIPK---SGAIITGYGTYEQPSDNIYVESIEK 71 (133)
T ss_pred CceEEEEEEEEeecCcccCceEeecccEEEEcCCCcEEEEEEeCC---CCcEEEEeEEEEEcCCccceeeecc
Confidence 3689999983221 2445677888988889999998532 2235678899998876654444443
No 5
>PF12283 Protein_K: Bacteriophage protein K; InterPro: IPR020962 This family of proteins is found in the microviridae (isometric ssDNA phages) and are approximately 60 amino acids in length. The function of these proteins are unknown. In phi X174 site-directed mutagenesis of gene K produces small plaques on su- hosts. The mutant phage has an identical latent period, but a more reduced burst size than that of the wild-type phi X174. The reduced burst size in the gene K mutant suggests that the gene K protein, although not essential, has a role in increasing infectivity by increasing the burst size three to six fold [].
Probab=40.61 E-value=45 Score=23.00 Aligned_cols=35 Identities=14% Similarity=0.247 Sum_probs=28.0
Q ss_pred HHHHHHHHHHhccCCC-CccCChhhHHHHHHHHHHHHHh
Q 026803 65 DDLVASILSKVNQSDG-GVSLAKEEHKEVAEVAQELQKY 102 (233)
Q Consensus 65 ~~lK~~LL~aia~t~r-G~~as~~~r~~I~~lI~~LEa~ 102 (233)
.-+||+||-.+...+| |+.+. -++|.....+||.+
T Consensus 6 tli~qellll~yelnrsgllve---ne~i~~~l~~le~l 41 (56)
T PF12283_consen 6 TLIKQELLLLTYELNRSGLLVE---NEEIQSQLKQLEKL 41 (56)
T ss_pred HHHHHHHHHHHHHhcccccccc---cHHHHHHHHHHHHH
Confidence 3579999999999988 77653 35688889999986
No 6
>COG2026 RelE Cytotoxic translational repressor of toxin-antitoxin stability system [Translation, ribosomal structure and biogenesis / Cell division and chromosome partitioning]
Probab=35.28 E-value=1.3e+02 Score=22.44 Aligned_cols=53 Identities=21% Similarity=0.271 Sum_probs=33.9
Q ss_pred CChhhHHHHHHHHHHHHHhcCCCCCC--CCcccCCCCCCCceeeeeecccceeccceEEEEcCCC
Q 026803 84 LAKEEHKEVAEVAQELQKYCVEAPVK--CPLIFGVPTSPGGGYRSAFGRLFFKTKEMIQAVEAPD 146 (233)
Q Consensus 84 as~~~r~~I~~lI~~LEa~n~~~Pt~--~Pl~~g~~~~l~G~WrL~lgr~~~~~g~v~Q~Id~~~ 146 (233)
+++..++.+.+.+.+++... +|-. .++. ....|.|++..|..- -+||+.|...
T Consensus 18 L~~~~~~~~~~~l~~~~~~~--~p~~~~k~~~----~~~~~~~R~RiG~YR----lIy~i~d~~~ 72 (90)
T COG2026 18 LDKKIRKKIKDKLKELLENP--PPIRHGKKLR----KGLSGKYRLRIGDYR----LIYEIDDETL 72 (90)
T ss_pred CCHHHHHHHHHHHHHhhccC--Cchhhceecc----cCCCCeEEEEecCEE----EEEEEECCce
Confidence 45677888888888888762 1433 3443 346899999988751 1466555433
No 7
>PF11010 DUF2848: Protein of unknown function (DUF2848); InterPro: IPR021269 This bacterial family of proteins has no known function.
Probab=33.45 E-value=46 Score=29.00 Aligned_cols=29 Identities=24% Similarity=0.458 Sum_probs=24.4
Q ss_pred hhHHHHHHHHHHHHHhcCCCCCCCCcccC
Q 026803 87 EEHKEVAEVAQELQKYCVEAPVKCPLIFG 115 (233)
Q Consensus 87 ~~r~~I~~lI~~LEa~n~~~Pt~~Pl~~g 115 (233)
.++++|+.-|++|++++++.|..-|+.+-
T Consensus 6 Rd~~av~~HI~EL~~lGVp~Ps~vP~~Y~ 34 (194)
T PF11010_consen 6 RDQEAVEHHIEELAALGVPPPSSVPLFYR 34 (194)
T ss_pred CCHHHHHHHHHHHHHhCCCCCCCCCEEEE
Confidence 46788999999999999988888887653
No 8
>TIGR02116 toxin_Txe_YoeB toxin-antitoxin system, toxin component, Txe/YoeB family. The Axe-Txe pair in Enterococcus faecium and the homologous YefM-YoeB pair in Escherichia coli have been shown to act as an antitoxin-toxin pair. This model describes the toxin component. Nearly every example found is next to an identifiable antitoxin, as indicated by matches to TIGR01552 and/or pfam02604.
Probab=31.68 E-value=1.8e+02 Score=20.87 Aligned_cols=36 Identities=22% Similarity=0.339 Sum_probs=23.6
Q ss_pred hhhHHHHHHHHHHHHHhcCCCCCC-----CCcccCCCCCCCceeeeeec
Q 026803 86 KEEHKEVAEVAQELQKYCVEAPVK-----CPLIFGVPTSPGGGYRSAFG 129 (233)
Q Consensus 86 ~~~r~~I~~lI~~LEa~n~~~Pt~-----~Pl~~g~~~~l~G~WrL~lg 129 (233)
++.++.|.+.|++|+ .| |.+ .++. . .++|-|++.++
T Consensus 17 ~~~~~~i~~~i~~l~-~~---P~~~~~~~~~L~---G-~~~g~~r~rig 57 (80)
T TIGR02116 17 KKLKKKINELIKDVR-RD---PFKGKGKPEPLK---G-DLSGYWSRRIT 57 (80)
T ss_pred HHHHHHHHHHHHHHH-cC---CCCCCCCcccCC---C-CCCCcEEEEcC
Confidence 457788999998886 35 543 2342 2 24566888877
No 9
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=30.54 E-value=1.1e+02 Score=21.48 Aligned_cols=40 Identities=28% Similarity=0.248 Sum_probs=29.9
Q ss_pred hHHHHHHHHHHhccCCC-CccCCh------hhHHHHHHHHHHHHHhc
Q 026803 64 PDDLVASILSKVNQSDG-GVSLAK------EEHKEVAEVAQELQKYC 103 (233)
Q Consensus 64 ~~~lK~~LL~aia~t~r-G~~as~------~~r~~I~~lI~~LEa~n 103 (233)
.+..++++|..+...+. |+.+.+ -.+..|..++..||..+
T Consensus 4 ~~~~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G 50 (68)
T smart00550 4 QDSLEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKKG 50 (68)
T ss_pred chHHHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence 56789999999987644 454432 23568999999999987
No 10
>cd03715 RT_ZFREV_like RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the intact endogenous retrovirus ZFERV from zebrafish and to Moloney murine leukemia virus RT. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs. Phylogenetic analysis suggests that ZFERV belongs to a distinct group of retroviruses.
Probab=28.24 E-value=99 Score=26.07 Aligned_cols=49 Identities=24% Similarity=0.356 Sum_probs=32.6
Q ss_pred CccCChhhHHHHHHHHHHHHHhcCCCCCCCCcccC--CCCCCCc-eeeeeec
Q 026803 81 GVSLAKEEHKEVAEVAQELQKYCVEAPVKCPLIFG--VPTSPGG-GYRSAFG 129 (233)
Q Consensus 81 G~~as~~~r~~I~~lI~~LEa~n~~~Pt~~Pl~~g--~~~~l~G-~WrL~lg 129 (233)
....++++++++.+.|++|+..+.=+|..+|-... --.+-+| .||+.++
T Consensus 6 ~~~~~~~~~~~~~~~v~~ll~~G~I~~~~s~~~sp~~~V~Kk~g~~~R~~vD 57 (210)
T cd03715 6 QYPLPREAREGITPHIQELLEAGILVPCQSPWNTPILPVKKPGGNDYRMVQD 57 (210)
T ss_pred CCCCCHHHHHHHHHHHHHHHHCCCeECCCCCCCCceEEEEeCCCCcceEEEE
Confidence 34568899999999999999987433444443210 1123378 9999754
No 11
>PF07624 PSD2: Protein of unknown function (DUF1585); InterPro: IPR011478 This entry represents a conserved region at the C terminus of a family of cytochrome-like proteins found in bacteria such as Rhodopirellula baltica and Solibacter usitatus. These proteins also contain IPR013036 from INTERPRO, IPR013039 from INTERPRO, IPR013042 from INTERPRO and IPR013043 from INTERPRO.
Probab=26.92 E-value=98 Score=22.34 Aligned_cols=41 Identities=12% Similarity=0.197 Sum_probs=28.4
Q ss_pred ChHHHHHHHHHH-----------hccCCCCccCChhhHHHHHHHHHHHHHhc
Q 026803 63 GPDDLVASILSK-----------VNQSDGGVSLAKEEHKEVAEVAQELQKYC 103 (233)
Q Consensus 63 ~~~~lK~~LL~a-----------ia~t~rG~~as~~~r~~I~~lI~~LEa~n 103 (233)
+..++|+.|++- +..-.-|...+..|+..|+++++++++.+
T Consensus 8 ~~~eLk~~L~~~~~~~~~~~~~kl~~YAlGR~~~~~D~~~i~~i~~~~~~~~ 59 (76)
T PF07624_consen 8 GAAELKQYLAERKDQFARCFAEKLLTYALGRPLEFSDRCEIDRIVEAFKANG 59 (76)
T ss_pred CHHHHHHHHHHCHHHHHHHHHHHHHHHHcCCCCCcchHHHHHHHHHHHHHcC
Confidence 456666666554 32223455667899999999999998765
No 12
>cd01645 RT_Rtv RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of single-stranded RNA into double-stranded viral DNA for integration into host chromosomes. Proteins in this subfamily contain long terminal repeats (LTRs) and are multifunctional enzymes with RNA-directed DNA polymerase, DNA directed DNA polymerase, and ribonuclease hybrid (RNase H) activities. The viral RNA genome enters the cytoplasm as part of a nucleoprotein complex, and the process of reverse transcription generates in the cytoplasm forming a linear DNA duplex via an intricate series of steps. This duplex DNA is colinear with its RNA template, but contains terminal duplications known as LTRs that are not present in viral RNA. It has been proposed that two specialized template switches, known as strand-transfer reactions or "jumps", are required to generate the LTRs.
Probab=26.31 E-value=1.2e+02 Score=25.74 Aligned_cols=50 Identities=20% Similarity=0.179 Sum_probs=33.6
Q ss_pred CCccCChhhHHHHHHHHHHHHHhcCCCCCCCCcccC--CCCCCCceeeeeec
Q 026803 80 GGVSLAKEEHKEVAEVAQELQKYCVEAPVKCPLIFG--VPTSPGGGYRSAFG 129 (233)
Q Consensus 80 rG~~as~~~r~~I~~lI~~LEa~n~~~Pt~~Pl~~g--~~~~l~G~WrL~lg 129 (233)
|....++++++++.+.|++|-..+.=.|..+|-... --..-+|.||+.++
T Consensus 5 ~~~p~~~~~~~~~~~~i~~ll~~g~I~~~~s~~~sp~~~v~K~~g~~R~~~D 56 (213)
T cd01645 5 KQWPLTEEKLEALTELVTEQLKEGHIEPSTSPWNTPVFVIKKKSGKWRLLHD 56 (213)
T ss_pred CccCCCHHHHHHHHHHHHHHHHCCceecCCCCCcCcEEEEEcCCCCeEEEec
Confidence 345678999999999999998876433444443200 11334799999855
No 13
>PHA00097 K protein K
Probab=25.91 E-value=1.1e+02 Score=21.08 Aligned_cols=35 Identities=14% Similarity=0.275 Sum_probs=27.5
Q ss_pred HHHHHHHHHHhccCCC-CccCChhhHHHHHHHHHHHHHh
Q 026803 65 DDLVASILSKVNQSDG-GVSLAKEEHKEVAEVAQELQKY 102 (233)
Q Consensus 65 ~~lK~~LL~aia~t~r-G~~as~~~r~~I~~lI~~LEa~ 102 (233)
.-++|+||-.....+| |+.+. -++|.....+||.+
T Consensus 6 tli~qelllltyelnrsgllve---neeiqs~lk~le~l 41 (56)
T PHA00097 6 TLILQELLLLTYELNRSGLLVE---NEEIQSQLKKLEKL 41 (56)
T ss_pred HHHHHHHHHHHHhhccccceec---cHHHHHHHHHHHHH
Confidence 3478999999999888 77653 35688888899886
No 14
>TIGR02530 flg_new flagellar operon protein. Members of this family are found in a subset of bacterial flagellar operons, generally between genes designated flgD and flgE, in species as diverse as Bacillus halodurans and various other Firmicutes, Geobacter sulfurreducens, and Bdellovibrio bacteriovorus. The specific molecular function is unknown.
Probab=24.90 E-value=89 Score=24.26 Aligned_cols=25 Identities=16% Similarity=0.328 Sum_probs=23.8
Q ss_pred CCCccCChhhHHHHHHHHHHHHHhc
Q 026803 79 DGGVSLAKEEHKEVAEVAQELQKYC 103 (233)
Q Consensus 79 ~rG~~as~~~r~~I~~lI~~LEa~n 103 (233)
.||+..++++-++|++.|++.+..+
T Consensus 27 ~R~I~l~~~~~~~i~~av~~A~~KG 51 (96)
T TIGR02530 27 ERNISINPDDWKKLLEAVEEAESKG 51 (96)
T ss_pred HcCCCCCHHHHHHHHHHHHHHHhcC
Confidence 6999999999999999999999987
No 15
>COG2088 SpoVG Uncharacterized protein, involved in the regulation of septum location [Cell envelope biogenesis, outer membrane]
Probab=23.35 E-value=81 Score=24.27 Aligned_cols=22 Identities=32% Similarity=0.499 Sum_probs=16.6
Q ss_pred EEEEecCCeEEEeCCCCcEEEEE
Q 026803 205 QITYIDEKIRLGLGSRGSLFVFQ 227 (233)
Q Consensus 205 diTYLDe~lRIsRG~kGslFVl~ 227 (233)
|--|+=.+|||-.|++| +||-.
T Consensus 26 D~efVvhdirVi~G~~G-lfVAM 47 (95)
T COG2088 26 DNEFVVHDIRVIEGNNG-LFVAM 47 (95)
T ss_pred cceEEEeccEEEeCCcc-eEEEc
Confidence 33345568999999999 88863
No 16
>PF05973 Gp49: Phage derived protein Gp49-like (DUF891); InterPro: IPR009241 This entry consists of several hypothetical viral and bacterial proteins some are annotated as addiction module killer proteins.
Probab=23.00 E-value=2e+02 Score=20.90 Aligned_cols=39 Identities=18% Similarity=0.252 Sum_probs=25.9
Q ss_pred CChhhHHHHHHHHHHHHHhcCCCCCCCCcccCCCCCC--Cceeeeee
Q 026803 84 LAKEEHKEVAEVAQELQKYCVEAPVKCPLIFGVPTSP--GGGYRSAF 128 (233)
Q Consensus 84 as~~~r~~I~~lI~~LEa~n~~~Pt~~Pl~~g~~~~l--~G~WrL~l 128 (233)
.++..+++|...++.|+..+. ....|.. ..+ +|-|+|..
T Consensus 6 L~~~~~~~i~~~l~~l~~~G~--~l~~~~~----k~l~~~~i~ElR~ 46 (91)
T PF05973_consen 6 LPDKERAKILAQLERLEEHGP--SLGEPLF----KHLKGDGIYELRV 46 (91)
T ss_pred CCHHHHHHHHHHHHHHHhcCC--ccCCCcc----cccCcCCeEEEEE
Confidence 456778889999999988771 1222322 223 69999985
No 17
>PF04213 HtaA: Htaa; InterPro: IPR007331 This domain is found in HtaA, a secreted protein implicated in iron acquisition and transport [].
Probab=22.06 E-value=3.5e+02 Score=22.49 Aligned_cols=26 Identities=23% Similarity=0.369 Sum_probs=19.6
Q ss_pred eEEEEEEecCCeEEEeCCCCcEEEEEe
Q 026803 202 VKLQITYIDEKIRLGLGSRGSLFVFQR 228 (233)
Q Consensus 202 GwldiTYLDe~lRIsRG~kGslFVl~R 228 (233)
|-||+|+-|-+|.|. |.+|.|++=.+
T Consensus 75 g~Ldlt~snp~I~~~-g~~g~L~adv~ 100 (168)
T PF04213_consen 75 GILDLTISNPRIVFD-GGTGTLYADVS 100 (168)
T ss_pred CeEEEEEeCCEEEEE-CCeEEEEEEEE
Confidence 778888888888876 66777776554
No 18
>PF07240 Turandot: Stress-inducible humoral factor Turandot; InterPro: IPR010825 This family consists of several Drosophila species specific Turandot proteins. The Turandot A (TotA) gene encodes a humoral factor, which is secreted from the fat body and accumulates in the body fluids. TotA is strongly induced upon bacterial challenge, as well as by other types of stress such as high temperature, mechanical pressure, dehydration, UV irradiation, and oxidative agents. It is also upregulated during metamorphosis and at high age. Flies that overexpress TotA show prolonged survival and retain normal activity at otherwise lethal temperatures. Although TotA is only induced by severe stress, it responds to a much wider range of stimuli than heat shock genes such as hsp70 or immune genes such as Cecropin A1 [].
Probab=21.63 E-value=2.2e+02 Score=21.58 Aligned_cols=35 Identities=3% Similarity=0.158 Sum_probs=26.7
Q ss_pred HHHHHHhccCCCCccCChhhHHHHHHHHHHHHHhc
Q 026803 69 ASILSKVNQSDGGVSLAKEEHKEVAEVAQELQKYC 103 (233)
Q Consensus 69 ~~LL~aia~t~rG~~as~~~r~~I~~lI~~LEa~n 103 (233)
++|+.--.....-+..++++++.+++.|.+-+..|
T Consensus 13 ~eLi~fY~ky~~~~~L~~~~r~~~d~~i~~y~~~~ 47 (85)
T PF07240_consen 13 QELIAFYEKYSPRLPLTPQDRQRIDRFIRRYKEEN 47 (85)
T ss_pred HHHHHHHHHcCccCCCCHHHHHHHHHHHHHHHHHh
Confidence 44444444444556789999999999999999988
No 19
>PF03076 GP3: Equine arteritis virus GP3; InterPro: IPR004310 This entry contains proteins encoded by ORF3 of Equine arteritis virus. They are possible envelope glcoproteins.
Probab=20.50 E-value=73 Score=26.03 Aligned_cols=19 Identities=32% Similarity=0.513 Sum_probs=15.3
Q ss_pred CCceeEEEEEEecCCeEEE
Q 026803 198 GQSEVKLQITYIDEKIRLG 216 (233)
Q Consensus 198 ~~~~GwldiTYLDe~lRIs 216 (233)
..+-|.+...|+|||||+-
T Consensus 120 ~~glg~~sfsfidedlrlh 138 (160)
T PF03076_consen 120 TAGLGQLSFSFIDEDLRLH 138 (160)
T ss_pred CCCcceEEEEEecccceee
Confidence 3455888999999999974
Done!