Query psy13898
Match_columns 185
No_of_seqs 152 out of 355
Neff 6.1
Searched_HMMs 46136
Date Fri Aug 16 23:14:54 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13898.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13898hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2219|consensus 99.9 4.3E-28 9.3E-33 224.5 7.4 88 7-94 700-793 (864)
2 cd01650 RT_nLTR_like RT_nLTR: 98.7 7.4E-09 1.6E-13 84.1 3.3 132 26-165 88-220 (220)
3 cd03487 RT_Bac_retron_II RT_Ba 98.2 3.1E-06 6.8E-11 69.8 5.3 79 80-182 134-213 (214)
4 PF00078 RVT_1: Reverse transc 98.0 2.1E-06 4.5E-11 68.4 1.6 60 80-165 155-214 (214)
5 cd01646 RT_Bac_retron_I RT_Bac 98.0 1.7E-06 3.6E-11 68.2 0.4 98 37-167 48-146 (158)
6 cd01651 RT_G2_intron RT_G2_int 97.9 4.5E-06 9.7E-11 67.7 1.9 94 46-164 126-225 (226)
7 cd01648 TERT TERT: Telomerase 97.8 8.7E-06 1.9E-10 61.7 1.1 99 46-165 19-118 (119)
8 cd00304 RT_like RT_like: Rever 97.4 0.0001 2.2E-09 52.6 2.3 46 80-133 40-85 (98)
9 cd03714 RT_DIRS1 RT_DIRS1: Rev 96.2 0.0062 1.3E-07 45.5 3.8 71 48-132 35-106 (119)
10 cd01645 RT_Rtv RT_Rtv: Reverse 96.0 0.0044 9.6E-08 51.2 2.4 72 48-131 130-201 (213)
11 cd01709 RT_like_1 RT_like_1: A 95.4 0.0036 7.8E-08 56.1 -0.6 78 41-138 82-162 (346)
12 cd03715 RT_ZFREV_like RT_ZFREV 94.7 0.029 6.3E-07 45.9 3.2 74 48-133 126-199 (210)
13 cd01647 RT_LTR RT_LTR: Reverse 90.6 0.18 3.9E-06 38.2 2.1 70 48-133 97-166 (177)
14 cd01644 RT_pepA17 RT_pepA17: R 52.4 43 0.00094 27.7 5.8 108 5-125 45-172 (213)
15 PF10865 DUF2703: Domain of un 47.3 19 0.00042 27.6 2.7 52 103-154 21-74 (120)
16 KOG4768|consensus 45.8 11 0.00023 36.9 1.3 46 83-134 503-548 (796)
17 PF05043 Mga: Mga helix-turn-h 39.5 29 0.00063 24.1 2.5 37 79-125 29-65 (87)
18 KOG2337|consensus 37.7 45 0.00097 32.2 4.0 88 11-120 358-450 (669)
19 COG0013 AlaS Alanyl-tRNA synth 36.6 9.5 0.00021 38.5 -0.6 61 3-66 220-287 (879)
20 PF12633 Adenyl_cycl_N: Adenyl 34.0 29 0.00064 29.1 2.0 24 104-127 132-155 (204)
21 PRK00252 alaS alanyl-tRNA synt 33.1 8.1 0.00018 38.8 -1.7 61 3-66 216-278 (865)
22 PF11273 DUF3073: Protein of u 29.8 65 0.0014 22.3 2.8 32 73-112 2-33 (65)
23 PF03755 YicC_N: YicC-like fam 28.8 1E+02 0.0022 24.2 4.3 100 14-128 6-105 (159)
24 cd03113 CTGs CTP synthetase (C 28.2 43 0.00093 29.1 2.1 33 151-183 96-128 (255)
25 PF13382 Adenine_deam_C: Adeni 26.7 96 0.0021 25.1 3.8 65 90-160 106-171 (171)
26 PRK01584 alanyl-tRNA synthetas 24.2 15 0.00032 35.5 -1.5 61 3-66 221-287 (594)
27 PF06418 CTP_synth_N: CTP synt 23.2 37 0.0008 29.8 0.8 34 151-184 97-130 (276)
28 COG0504 PyrG CTP synthase (UTP 22.2 60 0.0013 31.0 2.0 33 151-183 97-129 (533)
29 PF12944 DUF3840: Protein of u 20.6 64 0.0014 23.8 1.5 29 49-77 48-78 (104)
30 KOG4044|consensus 20.4 54 0.0012 27.1 1.2 50 79-135 40-89 (201)
No 1
>KOG2219|consensus
Probab=99.95 E-value=4.3e-28 Score=224.52 Aligned_cols=88 Identities=51% Similarity=0.762 Sum_probs=83.9
Q ss_pred CCCCcccceeeeeeceeceeeEEecccCCCceEEEEeccC------CCCCcccchhhHHHHHHHHHHHHHhhhhhhhHHH
Q psy13898 7 SYKTSSLNIQDDRSTGFLQDIEVTGDKDDSKCLHVTIQKT------NAGPLTQAKFIFDDHIRCMAAKQRLNRGRTQARL 80 (185)
Q Consensus 7 ~~~~~~~gw~~~~~~~~lqd~~~~~d~~dsr~l~i~i~~~------~~~~~~~a~f~F~d~i~c~~akq~l~~gr~~~r~ 80 (185)
.-|++++|||++||+|+|||.+|.||++|||+|||+||.. ...|++.|+|+||||||||+|||||+|||++||+
T Consensus 700 ePd~kr~gw~vvkf~Gllqd~~i~g~~dDsr~lhitv~~~ag~i~~r~~pvl~a~fif~DhiRcm~akQrltkgr~~ar~ 779 (864)
T KOG2219|consen 700 EPDTKRLGWGVVKFVGLLQDRWILGDRDDSRSLHITVHMVAGEIHLRCSPVLRAKFIFDDHIRCMAAKQRLTKGRQTARG 779 (864)
T ss_pred ccchhhcchheeeeeeeecceEEecccCcccceeEEEeccCCccccccchHHhhhccchHHHHHHHHHhHhhhhhHHHHH
Confidence 4589999999999999999999999999999999999993 2599999999999999999999999999999999
Q ss_pred HHHHHhhhhcCCCC
Q psy13898 81 AKMQQIAKLLDLPS 94 (185)
Q Consensus 81 ~k~~~~a~~l~i~~ 94 (185)
.||++||.+|++|+
T Consensus 780 ~kmq~ia~ll~vp~ 793 (864)
T KOG2219|consen 780 LKMQAIASLLGVPR 793 (864)
T ss_pred HHHHHHHHHhCCCC
Confidence 99999999999985
No 2
>cd01650 RT_nLTR_like RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.
Probab=98.72 E-value=7.4e-09 Score=84.09 Aligned_cols=132 Identities=21% Similarity=0.206 Sum_probs=86.1
Q ss_pred eeEEecccCCCceEEEEeccCCCCCcccchhhHHHHHHHHHHHHHhh-hhhhhHHHHHHHHhhhhcCCCCCCCCCCCCCc
Q psy13898 26 DIEVTGDKDDSKCLHVTIQKTNAGPLTQAKFIFDDHIRCMAAKQRLN-RGRTQARLAKMQQIAKLLDLPSSVQPCPSPPL 104 (185)
Q Consensus 26 d~~~~~d~~dsr~l~i~i~~~~~~~~~~a~f~F~d~i~c~~akq~l~-~gr~~~r~~k~~~~a~~l~i~~~~s~~~~s~~ 104 (185)
|++-.+|.-+...|.-.+ |.++..-.++++|.-.+..+...-.-. +...........+||||+.+.... + .
T Consensus 88 Di~~aFdsi~~~~l~~~l--GipQG~~lSp~l~~l~~~~l~~~~~~~~~~~~~~~~~~~~~yaDD~~i~~~~---~---~ 159 (220)
T cd01650 88 DFEKAFDSVDHEFLLKAL--GVRQGDPLSPLLFNLALDDLLRLLNKEEEIKLGGPGITHLAYADDIVLFSEG---K---S 159 (220)
T ss_pred EHHhhcCcCCHHHHHHHh--CCccCCcccHHHHHHHHHHHHHHHHhhccccCCCCccceEEeccceeeeccC---C---H
Confidence 666666654432221111 333333344444555555552211100 011123357789999999985421 1 1
Q ss_pred hhhhhHHHHHHHHHhhhCCccCcccceeeeccccccccceEEECCeeccccceeEeeccee
Q psy13898 105 YTLRGQINEWVTVANEYGLKFSAEKSEVVVLKCEEQVEGAIVMNGTTLKQVDHFKYLGSII 165 (185)
Q Consensus 105 ~~Lq~~l~~L~~~s~~~GL~IN~~KTKvM~~~~~~~~~~~i~I~g~~le~Ve~FkYLGs~I 165 (185)
..++..++.+..|+.+.||++|++||+++.++........+.+++..+..++.|+|||..+
T Consensus 160 ~~~~~~~~~~~~~~~~~gl~in~~Kt~~~~~~~~~~~~~~~~~~~~~~~~~~~~kyLG~~i 220 (220)
T cd01650 160 RKLQELLQRLQEWSKESGLKINPSKSKVMLIGNKKKRLKDITLNGTPIEAVETFKYLGVTI 220 (220)
T ss_pred HHHHHHHHHHHHHHHHcCCEEChhheEEEEecCCCcchhhhhhcCCcccCCCCCeeccccC
Confidence 4799999999999999999999999999998876544455788999999999999999753
No 3
>cd03487 RT_Bac_retron_II RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.
Probab=98.16 E-value=3.1e-06 Score=69.79 Aligned_cols=79 Identities=13% Similarity=0.141 Sum_probs=60.7
Q ss_pred HHHHHHhhhhcCCCCCCCCCCCCCchhhhhHHHHHHHHHhhhCCccCcccceeeeccccccccceEEECCeeccccceeE
Q psy13898 80 LAKMQQIAKLLDLPSSVQPCPSPPLYTLRGQINEWVTVANEYGLKFSAEKSEVVVLKCEEQVEGAIVMNGTTLKQVDHFK 159 (185)
Q Consensus 80 ~~k~~~~a~~l~i~~~~s~~~~s~~~~Lq~~l~~L~~~s~~~GL~IN~~KTKvM~~~~~~~~~~~i~I~g~~le~Ve~Fk 159 (185)
..+..+||||+.+... ++.. .++++.++.+..++++.||.+|++||+++... +.+.
T Consensus 134 ~~~~~RYaDD~~i~~~---~~~~--~~~~~~~~~i~~~l~~~gL~ln~~Kt~i~~~~-------------------~~~~ 189 (214)
T cd03487 134 GLTYTRYADDITFSSN---KKLK--EALDKLLEIIRSILSEEGFKINKSKTRISSKG-------------------SRQI 189 (214)
T ss_pred CCeEEEEeccEEEEcc---ccch--hHHHHHHHHHHHHHHHCCceeCCCceEEccCC-------------------CCcE
Confidence 4567899999988532 2210 26899999999999999999999999998742 3478
Q ss_pred eecceecCC-CCCHHHHHHHHHhh
Q psy13898 160 YLGSIISED-GTIDKEINRRIQQG 182 (185)
Q Consensus 160 YLGs~Is~d-~~~~~eI~~RI~~A 182 (185)
+||-.|+.+ .....+..+||+.+
T Consensus 190 ~~G~~i~~~~~~~~~~~~~~i~~~ 213 (214)
T cd03487 190 VTGLVVNNGKPSLPRKEKRKIRAL 213 (214)
T ss_pred EEEEEEeCCcCCCCHHHHHHHHhh
Confidence 899888865 56777888887653
No 4
>PF00078 RVT_1: Reverse transcriptase (RNA-dependent DNA polymerase); InterPro: IPR000477 The use of an RNA template to produce DNA, for integration into the host genome and exploitation of a host cell, is a strategy employed in the replication of retroid elements, such as the retroviruses and bacterial retrons. The enzyme catalysing polymerisation is an RNA-directed DNA-polymerase, or reverse trancriptase (RT) (2.7.7.49 from EC). Reverse transcriptase occurs in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. Retroviral reverse transcriptase is synthesised as part of the POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. The discovery of retroelements in the prokaryotes raises intriguing questions concerning their roles in bacteria and the origin and evolution of reverse transcriptases and whether the bacterial reverse transcriptases are older than eukaryotic reverse transcriptases [].; GO: 0003723 RNA binding, 0003964 RNA-directed DNA polymerase activity, 0006278 RNA-dependent DNA replication; PDB: 1MU2_B 3RWE_C 3DU6_B 3DU5_A 3KYL_A 2WOM_B 1DTQ_A 2OPS_A 3FFI_A 1VRU_B ....
Probab=98.02 E-value=2.1e-06 Score=68.44 Aligned_cols=60 Identities=22% Similarity=0.299 Sum_probs=48.8
Q ss_pred HHHHHHhhhhcCCCCCCCCCCCCCchhhhhHHHHHHHHHhhhCCccCcccceeeeccccccccceEEECCeeccccceeE
Q psy13898 80 LAKMQQIAKLLDLPSSVQPCPSPPLYTLRGQINEWVTVANEYGLKFSAEKSEVVVLKCEEQVEGAIVMNGTTLKQVDHFK 159 (185)
Q Consensus 80 ~~k~~~~a~~l~i~~~~s~~~~s~~~~Lq~~l~~L~~~s~~~GL~IN~~KTKvM~~~~~~~~~~~i~I~g~~le~Ve~Fk 159 (185)
.....++|||+.+. +.+++ +++..++.+.++++++||++|++||+.+. ..+.++
T Consensus 155 ~~~~~rY~DD~~i~---~~~~~----~~~~~~~~i~~~~~~~gl~ln~~Kt~~~~-------------------~~~~~~ 208 (214)
T PF00078_consen 155 DISYLRYADDILII---SKSKE----ELQKILEKISQWLEELGLKLNPEKTKILH-------------------PSDSVK 208 (214)
T ss_dssp TSEEEEETTEEEEE---ESSHH----HHHHHHHHHHHHHHHTTSBCSSTTTSCS---------------------ESSEE
T ss_pred cccceEeccccEEE---ECCHH----HHHHHHHHHHHHHHHCCCEEChHHEEEEe-------------------CCCCEE
Confidence 45578999999984 33344 79999999999999999999999999875 457789
Q ss_pred eeccee
Q psy13898 160 YLGSII 165 (185)
Q Consensus 160 YLGs~I 165 (185)
|||-.|
T Consensus 209 ~lG~~i 214 (214)
T PF00078_consen 209 FLGYVI 214 (214)
T ss_dssp ETTEEE
T ss_pred EEeEEC
Confidence 999765
No 5
>cd01646 RT_Bac_retron_I RT_Bac_retron_I: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.
Probab=97.98 E-value=1.7e-06 Score=68.20 Aligned_cols=98 Identities=11% Similarity=0.093 Sum_probs=68.3
Q ss_pred ceEEEEeccCC-CCCcccchhhHHHHHHHHHHHHHhhhhhhhHHHHHHHHhhhhcCCCCCCCCCCCCCchhhhhHHHHHH
Q psy13898 37 KCLHVTIQKTN-AGPLTQAKFIFDDHIRCMAAKQRLNRGRTQARLAKMQQIAKLLDLPSSVQPCPSPPLYTLRGQINEWV 115 (185)
Q Consensus 37 r~l~i~i~~~~-~~~~~~a~f~F~d~i~c~~akq~l~~gr~~~r~~k~~~~a~~l~i~~~~s~~~~s~~~~Lq~~l~~L~ 115 (185)
......++||. .+|++...|++ ++.-.. ++. .+...+.+||||+.+.. .++ ..+++.++.+.
T Consensus 48 ~~~~~GlpqG~~lS~~L~~~~l~--~~d~~i-~~~-------~~~~~~~RY~DD~~i~~---~~~----~~~~~~~~~i~ 110 (158)
T cd01646 48 YGQTNGLPIGPLTSRFLANIYLN--DVDHEL-KSK-------LKGVDYVRYVDDIRIFA---DSK----EEAEEILEELK 110 (158)
T ss_pred CCCCceEccCcchHHHHHHHHHH--HHHHHH-Hhc-------cCCceEEEecCcEEEEc---CCH----HHHHHHHHHHH
Confidence 33445566653 56666666552 233221 111 34677899999999853 222 37899999999
Q ss_pred HHHhhhCCccCcccceeeeccccccccceEEECCeeccccceeEeecceecC
Q psy13898 116 TVANEYGLKFSAEKSEVVVLKCEEQVEGAIVMNGTTLKQVDHFKYLGSIISE 167 (185)
Q Consensus 116 ~~s~~~GL~IN~~KTKvM~~~~~~~~~~~i~I~g~~le~Ve~FkYLGs~Is~ 167 (185)
+++++.||.+|++||+++.+.... .+|.+||..+..
T Consensus 111 ~~l~~~gL~ln~~Kt~~~~~~~~~----------------~~~~flg~~~~~ 146 (158)
T cd01646 111 EFLAELGLSLNLSKTEILPLPEGT----------------ASKDFLGYRFSP 146 (158)
T ss_pred HHHHHCCCEEChhhceeeecCCCC----------------ccccccceEeeh
Confidence 999999999999999998865421 679999998874
No 6
>cd01651 RT_G2_intron RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).
Probab=97.92 E-value=4.5e-06 Score=67.73 Aligned_cols=94 Identities=14% Similarity=0.186 Sum_probs=62.8
Q ss_pred CCCCCcccchhhHHHHHHHHH--HHHHhhh----hhhhHHHHHHHHhhhhcCCCCCCCCCCCCCchhhhhHHHHHHHHHh
Q psy13898 46 TNAGPLTQAKFIFDDHIRCMA--AKQRLNR----GRTQARLAKMQQIAKLLDLPSSVQPCPSPPLYTLRGQINEWVTVAN 119 (185)
Q Consensus 46 ~~~~~~~~a~f~F~d~i~c~~--akq~l~~----gr~~~r~~k~~~~a~~l~i~~~~s~~~~s~~~~Lq~~l~~L~~~s~ 119 (185)
|.++....++++|.-.+..+- ..+.+.. +..........+||||+.+..+ +++ .++..++.+.+|++
T Consensus 126 GlpqG~~lSp~L~~~~l~~ld~~l~~~~~~~~~~~~~~~~~~~~~rY~DD~~i~~~---~~~----~~~~~~~~i~~~~~ 198 (226)
T cd01651 126 GTPQGGVISPLLANIYLHELDKFVEEKLKEYYDTSDPKFRRLRYVRYADDFVIGVR---GPK----EAEEIKELIREFLE 198 (226)
T ss_pred CcCCCccHHHHHHHHHHHHHHHHHHHhhhhcccccccccCceEEEEecCceEEecC---CHH----HHHHHHHHHHHHHH
Confidence 444555556666666656551 1111111 0112234667899999999542 223 58999999999999
Q ss_pred hhCCccCcccceeeeccccccccceEEECCeeccccceeEeecce
Q psy13898 120 EYGLKFSAEKSEVVVLKCEEQVEGAIVMNGTTLKQVDHFKYLGSI 164 (185)
Q Consensus 120 ~~GL~IN~~KTKvM~~~~~~~~~~~i~I~g~~le~Ve~FkYLGs~ 164 (185)
+.||.+|.+||+++.++ .+.|.|||-.
T Consensus 199 ~~gl~ln~~Kt~i~~~~------------------~~~~~fLG~~ 225 (226)
T cd01651 199 ELGLELNPEKTRITHFK------------------SEGFDFLGFT 225 (226)
T ss_pred HcCCeechhhcceeecC------------------CCCCeeCCeE
Confidence 99999999999998764 3568888854
No 7
>cd01648 TERT TERT: Telomerase reverse transcriptase (TERT). Telomerase is a ribonucleoprotein (RNP) that synthesizes telomeric DNA repeats. The telomerase RNA subunit provides the template for synthesis of these repeats. The catalytic subunit of RNP is known as telomerase reverse transcriptase (TERT). The reverse transcriptase (RT) domain is located in the C-terminal region of the TERT polypeptide. Single amino acid substitutions in this region lead to telomere shortening and senescence. Telomerase is an enzyme that, in certain cells, maintains the physical ends of chromosomes (telomeres) during replication. In somatic cells, replication of the lagging strand requires the continual presence of an RNA primer approximately 200 nucleotides upstream, which is complementary to the template strand. Since there is a region of DNA less than 200 base pairs from the end of the chromosome where this is not possible, the chromosome is continually shortened. However, a surplus of repetitive DNA at
Probab=97.77 E-value=8.7e-06 Score=61.67 Aligned_cols=99 Identities=10% Similarity=0.020 Sum_probs=59.8
Q ss_pred CCCCCcccchhhHHHHHHHHHHHHHhhhhhhhHHHHHHHHhhhhcCCCCCCCCCCCCCchhhhhHHHHHHHHH-hhhCCc
Q psy13898 46 TNAGPLTQAKFIFDDHIRCMAAKQRLNRGRTQARLAKMQQIAKLLDLPSSVQPCPSPPLYTLRGQINEWVTVA-NEYGLK 124 (185)
Q Consensus 46 ~~~~~~~~a~f~F~d~i~c~~akq~l~~gr~~~r~~k~~~~a~~l~i~~~~s~~~~s~~~~Lq~~l~~L~~~s-~~~GL~ 124 (185)
|.+++...++++|.-.+.-+- +...+............+||||+.+. ++++. +.++.++.+.++. +++||+
T Consensus 19 GlpQG~~lSp~L~nl~l~~l~-~~~~~~~~~~~~~~~~~rYaDD~li~---~~~~~----~~~~~~~~l~~~l~~~~gl~ 90 (119)
T cd01648 19 GIPQGSPLSSLLCSLYYADLE-NKYLSFLDVIDKDSLLLRLVDDFLLI---TTSLD----KAIKFLNLLLRGFINQYKTF 90 (119)
T ss_pred cccCCcchHHHHHHHHHHHHH-HHHHhhcccCCCCceEEEEeCcEEEE---eCCHH----HHHHHHHHHHHhhHHhhCeE
Confidence 444444445555555555442 12112111112234468999998774 23333 7899999999997 999999
Q ss_pred cCcccceeeeccccccccceEEECCeeccccceeEeeccee
Q psy13898 125 FSAEKSEVVVLKCEEQVEGAIVMNGTTLKQVDHFKYLGSII 165 (185)
Q Consensus 125 IN~~KTKvM~~~~~~~~~~~i~I~g~~le~Ve~FkYLGs~I 165 (185)
+|.+||++-.... ....-+.|.|||-.|
T Consensus 91 iN~~Kt~~~~~~~-------------~~~~~~~~~flG~~i 118 (119)
T cd01648 91 VNFDKTQINFSFA-------------QLDSSDLIPWCGLLI 118 (119)
T ss_pred ECcccceeecccc-------------ccCCCCccCceeEee
Confidence 9999999753211 011124589999765
No 8
>cd00304 RT_like RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. 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.
Probab=97.39 E-value=0.0001 Score=52.60 Aligned_cols=46 Identities=15% Similarity=0.105 Sum_probs=38.4
Q ss_pred HHHHHHhhhhcCCCCCCCCCCCCCchhhhhHHHHHHHHHhhhCCccCcccceee
Q psy13898 80 LAKMQQIAKLLDLPSSVQPCPSPPLYTLRGQINEWVTVANEYGLKFSAEKSEVV 133 (185)
Q Consensus 80 ~~k~~~~a~~l~i~~~~s~~~~s~~~~Lq~~l~~L~~~s~~~GL~IN~~KTKvM 133 (185)
.....+++||+.+... +. +++..+..+.+++++.||++|.+||+..
T Consensus 40 ~~~~~~Y~DD~~i~~~---~~-----~~~~~~~~l~~~l~~~gl~ln~~Kt~~~ 85 (98)
T cd00304 40 DITLIRYVDDLVVIAK---SE-----QQAVKKRELEEFLARLGLNLSDEKTQFT 85 (98)
T ss_pred CceEEEeeCcEEEEeC---cH-----HHHHHHHHHHHHHHHcCcEEChheeEEe
Confidence 4668899999988532 11 6889999999999999999999999975
No 9
>cd03714 RT_DIRS1 RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members of the subfamily include the Dictyostelium DIRS-1, Volvox carteri kangaroo, and Panagrellus redivivus PAT elements. These elements differ from LTR and conventional non-LTR retrotransposons. They contain split direct repeat (SDR) termini, and have been proposed to integrate via double-stranded closed-circle DNA intermediates assisted by an encoded recombinase which is similar to gamma-site-specific integrase.
Probab=96.18 E-value=0.0062 Score=45.51 Aligned_cols=71 Identities=15% Similarity=0.143 Sum_probs=44.6
Q ss_pred CCCcccchhhHHHHHHHHHHHHHhhhhhhhHHHHHHHHhhhhcCCCCCCCCCCCCCchhhhhHHHHHHH-HHhhhCCccC
Q psy13898 48 AGPLTQAKFIFDDHIRCMAAKQRLNRGRTQARLAKMQQIAKLLDLPSSVQPCPSPPLYTLRGQINEWVT-VANEYGLKFS 126 (185)
Q Consensus 48 ~~~~~~a~f~F~d~i~c~~akq~l~~gr~~~r~~k~~~~a~~l~i~~~~s~~~~s~~~~Lq~~l~~L~~-~s~~~GL~IN 126 (185)
+..+-.|+.+|...++-+... +. ........++||+-+.. .+++ ..+..+..+.+ .++++||.+|
T Consensus 35 p~Gl~~sp~~f~~~~~~i~~~--~~-----~~~~~v~~Y~DDili~~---~~~~----~~~~~~~~l~~~~l~~~gl~ln 100 (119)
T cd03714 35 PFGLSLAPRVFTKVVEALLAP--LR-----LLGVRIFSYLDDLLIIA---SSIK----TSEAVLRHLRATLLANLGFTLN 100 (119)
T ss_pred CCcccchHHHHHHHHHHHHHH--hh-----cCCeEEEEEecCeEEEe---CcHH----HHHHHHHHHHHHHHHHcCCccC
Confidence 445556666665444433211 11 11234678999988843 2333 56667777766 5999999999
Q ss_pred ccccee
Q psy13898 127 AEKSEV 132 (185)
Q Consensus 127 ~~KTKv 132 (185)
++||++
T Consensus 101 ~~K~~~ 106 (119)
T cd03714 101 LEKSKL 106 (119)
T ss_pred hhhcEe
Confidence 999996
No 10
>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=96.00 E-value=0.0044 Score=51.15 Aligned_cols=72 Identities=13% Similarity=0.098 Sum_probs=50.6
Q ss_pred CCCcccchhhHHHHHHHHHHHHHhhhhhhhHHHHHHHHhhhhcCCCCCCCCCCCCCchhhhhHHHHHHHHHhhhCCccCc
Q psy13898 48 AGPLTQAKFIFDDHIRCMAAKQRLNRGRTQARLAKMQQIAKLLDLPSSVQPCPSPPLYTLRGQINEWVTVANEYGLKFSA 127 (185)
Q Consensus 48 ~~~~~~a~f~F~d~i~c~~akq~l~~gr~~~r~~k~~~~a~~l~i~~~~s~~~~s~~~~Lq~~l~~L~~~s~~~GL~IN~ 127 (185)
++.+-.|+.+|.-+++......+ .+ .....+..+.||+-|. +++.+ +..+.++.+.+.++++||.+|.
T Consensus 130 P~Gl~~SP~~f~~~m~~~l~~~~-~~----~~~~~~~~Y~DDili~---s~~~~----~~~~~l~~v~~~l~~~gl~ln~ 197 (213)
T cd01645 130 PQGMKNSPTICQSFVAQALEPFR-KQ----YPDIVIYHYMDDILIA---SDLEG----QLREIYEELRQTLLRWGLTIPP 197 (213)
T ss_pred CCCCcChHHHHHHHHHHHHHHHH-HH----CCCeEEEEEcCCEEEE---cCCHH----HHHHHHHHHHHHHHHCCCEeCH
Confidence 56677788888776665543221 10 0112356899998773 33333 8899999999999999999999
Q ss_pred ccce
Q psy13898 128 EKSE 131 (185)
Q Consensus 128 ~KTK 131 (185)
+||+
T Consensus 198 ~K~~ 201 (213)
T cd01645 198 EKVQ 201 (213)
T ss_pred HHEe
Confidence 9987
No 11
>cd01709 RT_like_1 RT_like_1: A subfamily of reverse transcriptases (RTs). 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.
Probab=95.36 E-value=0.0036 Score=56.11 Aligned_cols=78 Identities=17% Similarity=0.130 Sum_probs=57.5
Q ss_pred EEeccC-CCCCcccchhhHHHHHHHH--HHHHHhhhhhhhHHHHHHHHhhhhcCCCCCCCCCCCCCchhhhhHHHHHHHH
Q psy13898 41 VTIQKT-NAGPLTQAKFIFDDHIRCM--AAKQRLNRGRTQARLAKMQQIAKLLDLPSSVQPCPSPPLYTLRGQINEWVTV 117 (185)
Q Consensus 41 i~i~~~-~~~~~~~a~f~F~d~i~c~--~akq~l~~gr~~~r~~k~~~~a~~l~i~~~~s~~~~s~~~~Lq~~l~~L~~~ 117 (185)
..+++| .-+|+|...|+ .|+ +.+|. .+...+.++|||+.+-. +++ +.....+.+.+.
T Consensus 82 rGtPqGgviSplLaNiyL-----~~lD~~v~~~-------~~g~~l~RYaDD~vi~~----~~~----~a~~aw~~i~~f 141 (346)
T cd01709 82 RGTPMSHALSDVFGELVL-----FCLDFAVNQA-------TDGGLLYRLHDDLWFWG----QPE----TCAKAWKAIQEF 141 (346)
T ss_pred CccCCCchhhHHHHHHHH-----HHHHHHHHhc-------CCCceEEEEcCeEEEEc----CHH----HHHHHHHHHHHH
Confidence 456665 47888888888 466 23332 22467899999998842 123 677788899999
Q ss_pred HhhhCCccCcccceeeecccc
Q psy13898 118 ANEYGLKFSAEKSEVVVLKCE 138 (185)
Q Consensus 118 s~~~GL~IN~~KTKvM~~~~~ 138 (185)
++..||++|++||++..+...
T Consensus 142 l~~lGLelN~eKT~iV~~~~~ 162 (346)
T cd01709 142 AKVMGLELNKEKTGSVYLSDD 162 (346)
T ss_pred HHHcCceeccccceEEEeccC
Confidence 999999999999999976543
No 12
>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=94.74 E-value=0.029 Score=45.91 Aligned_cols=74 Identities=16% Similarity=0.113 Sum_probs=49.3
Q ss_pred CCCcccchhhHHHHHHHHHHHHHhhhhhhhHHHHHHHHhhhhcCCCCCCCCCCCCCchhhhhHHHHHHHHHhhhCCccCc
Q psy13898 48 AGPLTQAKFIFDDHIRCMAAKQRLNRGRTQARLAKMQQIAKLLDLPSSVQPCPSPPLYTLRGQINEWVTVANEYGLKFSA 127 (185)
Q Consensus 48 ~~~~~~a~f~F~d~i~c~~akq~l~~gr~~~r~~k~~~~a~~l~i~~~~s~~~~s~~~~Lq~~l~~L~~~s~~~GL~IN~ 127 (185)
+.++-.|+.+|..+++.+...-... .-...+..|.||+-|. +. +..+..+.++.+...++++|+.+|.
T Consensus 126 p~Gl~~sp~~f~~~~~~~l~~~~~~-----~~~~~~~~Y~DDili~---s~----~~~e~~~~l~~v~~~l~~~gl~l~~ 193 (210)
T cd03715 126 PQGFKNSPTLFHEALARDLAPFPLE-----HEGTILLQYVDDLLLA---AD----SEEDCLKGTDALLTHLGELGYKVSP 193 (210)
T ss_pred eccccCcHHHHHHHHHHHHHHHHhh-----CCCeEEEEECCcEEEe---cC----CHHHHHHHHHHHHHHHHHCCCCcCH
Confidence 5566667777766666543221100 0012345688888873 32 3347889999999999999999999
Q ss_pred ccceee
Q psy13898 128 EKSEVV 133 (185)
Q Consensus 128 ~KTKvM 133 (185)
+||+..
T Consensus 194 ~K~~~~ 199 (210)
T cd03715 194 KKAQIC 199 (210)
T ss_pred HHeeCC
Confidence 999964
No 13
>cd01647 RT_LTR RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long terminal repeats (LTRs) in their DNA copies but not in their RNA template. RT catalyzes DNA replication from an RNA template, and is responsible for the replication of retroelements. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs are present in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and Caulimoviruses.
Probab=90.60 E-value=0.18 Score=38.16 Aligned_cols=70 Identities=17% Similarity=0.042 Sum_probs=45.8
Q ss_pred CCCcccchhhHHHHHHHHHHHHHhhhhhhhHHHHHHHHhhhhcCCCCCCCCCCCCCchhhhhHHHHHHHHHhhhCCccCc
Q psy13898 48 AGPLTQAKFIFDDHIRCMAAKQRLNRGRTQARLAKMQQIAKLLDLPSSVQPCPSPPLYTLRGQINEWVTVANEYGLKFSA 127 (185)
Q Consensus 48 ~~~~~~a~f~F~d~i~c~~akq~l~~gr~~~r~~k~~~~a~~l~i~~~~s~~~~s~~~~Lq~~l~~L~~~s~~~GL~IN~ 127 (185)
+..+-.++.+|.-.++...... ....+..|.||+-+.. . +..+....++.+....+++|+.+|.
T Consensus 97 p~G~~~s~~~~~~~~~~~l~~~---------~~~~~~~y~DDi~i~~---~----~~~~~~~~~~~~~~~l~~~~~~~~~ 160 (177)
T cd01647 97 PFGLKNAPATFQRLMNKILGDL---------LGDFVEVYLDDILVYS---K----TEEEHLEHLREVLERLREAGLKLNP 160 (177)
T ss_pred cCCCccHHHHHHHHHHhhhccc---------cccccEEEecCccccC---C----CHHHHHHHHHHHHHHHHHcCCEeCH
Confidence 3445556666655554442111 1234567888877732 2 2346778888888899999999999
Q ss_pred ccceee
Q psy13898 128 EKSEVV 133 (185)
Q Consensus 128 ~KTKvM 133 (185)
+||+..
T Consensus 161 ~K~~~~ 166 (177)
T cd01647 161 EKCEFG 166 (177)
T ss_pred HHceec
Confidence 999854
No 14
>cd01644 RT_pepA17 RT_pepA17: Reverse transcriptase (RTs) in retrotransposons. This subfamily represents the RT domain of a multifunctional enzyme. C-terminal to the RT domain is a domain homologous to aspartic proteinases (corresponding to Merops family A17) encoded by retrotransposons and retroviruses. RT catalyzes DNA replication from an RNA template and is responsible for the replication of retroelements.
Probab=52.44 E-value=43 Score=27.72 Aligned_cols=108 Identities=15% Similarity=0.129 Sum_probs=64.6
Q ss_pred CCCCCCcccceeeeeeceeceeeE-----EecccCCCceEEEEecc-------C------CCCCcccchhhHHHHHHHHH
Q psy13898 5 QGSYKTSSLNIQDDRSTGFLQDIE-----VTGDKDDSKCLHVTIQK-------T------NAGPLTQAKFIFDDHIRCMA 66 (185)
Q Consensus 5 ~~~~~~~~~gw~~~~~~~~lqd~~-----~~~d~~dsr~l~i~i~~-------~------~~~~~~~a~f~F~d~i~c~~ 66 (185)
+-+++.-.+.|+-.++..-+ |++ |.-.++|.....+.... + .+.++-+|+++|...++
T Consensus 45 ~~~l~~iL~~~R~~~~~~~~-Di~~af~qI~i~~~d~~~~~F~w~~~~~~~~~~~Y~~~~~pFG~~~AP~~~~~~~~--- 120 (213)
T cd01644 45 LNSLFGVLLRFRQGKIAVSA-DIEKMFHQVKVRPEDRDVLRFLWRKDGDEPKPIEYRMTVVPFGAASAPFLANRALK--- 120 (213)
T ss_pred ccchhhhheeeecCceeEeh-hHHHhhhheecCcccCceEEEEEeCCCCCCcceEEEEEEEccCCccchHHHHHHHH---
Confidence 33455555556555554333 443 44455555555554322 1 25667788888665444
Q ss_pred HHHHhhhhhh--hHHHHHHHHhhhhcCCCCCCCCCCCCCchhhhhHHHHHHHHHhhhCCcc
Q psy13898 67 AKQRLNRGRT--QARLAKMQQIAKLLDLPSSVQPCPSPPLYTLRGQINEWVTVANEYGLKF 125 (185)
Q Consensus 67 akq~l~~gr~--~~r~~k~~~~a~~l~i~~~~s~~~~s~~~~Lq~~l~~L~~~s~~~GL~I 125 (185)
+.+..-+. -+.......+-||+-+. +.+ ..+.+..++++.+..++.|+.+
T Consensus 121 --~~~~~~~~~~~~~~i~~~~YvDDili~---~~s----~~e~~~~~~~v~~~L~~~Gf~l 172 (213)
T cd01644 121 --QHAEDHPHEAAAKIIKRNFYVDDILVS---TDT----LNEAVNVAKRLIALLKKGGFNL 172 (213)
T ss_pred --HHHhhcchhhHHHHHHHeeecccceec---CCC----HHHHHHHHHHHHHHHHhCCccc
Confidence 33333332 24455567888888774 333 3388999999999999999977
No 15
>PF10865 DUF2703: Domain of unknown function (DUF2703); InterPro: IPR021219 This family of protein has no known function.
Probab=47.32 E-value=19 Score=27.63 Aligned_cols=52 Identities=23% Similarity=0.272 Sum_probs=40.5
Q ss_pred CchhhhhHHHHHHHHHhhhCCccCcccceeeecccccc--ccceEEECCeeccc
Q psy13898 103 PLYTLRGQINEWVTVANEYGLKFSAEKSEVVVLKCEEQ--VEGAIVMNGTTLKQ 154 (185)
Q Consensus 103 ~~~~Lq~~l~~L~~~s~~~GL~IN~~KTKvM~~~~~~~--~~~~i~I~g~~le~ 154 (185)
+-..|++.++.|.......|..+...|+.+=.-.+... ..+.|.|||.+||.
T Consensus 21 Tg~~L~~av~~l~~~L~~~Giev~l~~~~l~~~~~~~~~~~S~~I~inG~piE~ 74 (120)
T PF10865_consen 21 TGETLREAVKELAPVLAPLGIEVRLEEIELDEEEFARQPLESPTIRINGRPIED 74 (120)
T ss_pred HHHHHHHHHHHHHHHHHhCCcEEEEEEEECChHHHhhcccCCCeeeECCEehhH
Confidence 44589999999999999999999999986533222211 36889999999964
No 16
>KOG4768|consensus
Probab=45.82 E-value=11 Score=36.94 Aligned_cols=46 Identities=11% Similarity=0.109 Sum_probs=37.3
Q ss_pred HHHhhhhcCCCCCCCCCCCCCchhhhhHHHHHHHHHhhhCCccCcccceeee
Q psy13898 83 MQQIAKLLDLPSSVQPCPSPPLYTLRGQINEWVTVANEYGLKFSAEKSEVVV 134 (185)
Q Consensus 83 ~~~~a~~l~i~~~~s~~~~s~~~~Lq~~l~~L~~~s~~~GL~IN~~KTKvM~ 134 (185)
-.++|||+.+.+.. +..+..+-++.+.-.+...||.+|++||++-.
T Consensus 503 yVRyadd~ii~v~G------S~nd~K~ilr~In~f~sslGls~n~~kt~it~ 548 (796)
T KOG4768|consen 503 YVRYADDIIIGVWG------SVNDCKQILRDINNFLSSLGLSNNSSKTQITV 548 (796)
T ss_pred EEEecCCEEEEEec------cHHHHHHHHHHHHHHHHhhCcccCcccceEEe
Confidence 37899998876543 23368888999999999999999999999854
No 17
>PF05043 Mga: Mga helix-turn-helix domain; InterPro: IPR007737 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions []. The family also contains VirR like proteins which match only at the C terminus of the alignment.; PDB: 3SQN_A.
Probab=39.53 E-value=29 Score=24.06 Aligned_cols=37 Identities=24% Similarity=0.388 Sum_probs=29.6
Q ss_pred HHHHHHHhhhhcCCCCCCCCCCCCCchhhhhHHHHHHHHHhhhCCcc
Q psy13898 79 RLAKMQQIAKLLDLPSSVQPCPSPPLYTLRGQINEWVTVANEYGLKF 125 (185)
Q Consensus 79 r~~k~~~~a~~l~i~~~~s~~~~s~~~~Lq~~l~~L~~~s~~~GL~I 125 (185)
+..++..+|+.+.+..+ .+.+.+.++.++.+++||+|
T Consensus 29 ~~~s~~~la~~~~iS~s----------ti~~~i~~l~~~l~~~~l~i 65 (87)
T PF05043_consen 29 EYVSIEDLAEELFISRS----------TIYRDIKKLNKYLKKYGLKI 65 (87)
T ss_dssp SEEEHHHHHHHHT--HH----------HHHHHHHHHHHHHHCCT-EE
T ss_pred CCcCHHHHHHHHCCCHH----------HHHHHHHHHHHHHHHcCeEE
Confidence 35568899999999542 79999999999999999999
No 18
>KOG2337|consensus
Probab=37.73 E-value=45 Score=32.24 Aligned_cols=88 Identities=20% Similarity=0.323 Sum_probs=47.6
Q ss_pred cccceeeeeeceeceeeEEecccCCCceEEEEeccCCCCCcccchhhHHHHH-----HHHHHHHHhhhhhhhHHHHHHHH
Q psy13898 11 SSLNIQDDRSTGFLQDIEVTGDKDDSKCLHVTIQKTNAGPLTQAKFIFDDHI-----RCMAAKQRLNRGRTQARLAKMQQ 85 (185)
Q Consensus 11 ~~~gw~~~~~~~~lqd~~~~~d~~dsr~l~i~i~~~~~~~~~~a~f~F~d~i-----~c~~akq~l~~gr~~~r~~k~~~ 85 (185)
..+|||| |++-|+ |+.. |.-.. |+=.++|.|+|.. ..-+|-|+|++=-. .|..
T Consensus 358 ~Ll~WGv-RhITFv----------Dn~k--VsySN----PVRQsLy~FEDc~~~g~~KAe~Aa~rLk~IfP-----~m~a 415 (669)
T KOG2337|consen 358 NLLGWGV-RHITFV----------DNGK--VSYSN----PVRQSLYTFEDCLGGGRPKAETAAQRLKEIFP-----SMEA 415 (669)
T ss_pred HHHhhcc-ceEEEE----------ecCe--eeccc----hhhhhhhhhhhhhccCCcchHHHHHHHHHhCc-----cccc
Confidence 3578985 666666 2222 22233 5556778999988 24566777764111 1122
Q ss_pred hhhhcCCCCCCCCCCCCCchhhhhHHHHHHHHHhh
Q psy13898 86 IAKLLDLPSSVQPCPSPPLYTLRGQINEWVTVANE 120 (185)
Q Consensus 86 ~a~~l~i~~~~s~~~~s~~~~Lq~~l~~L~~~s~~ 120 (185)
=+--|.||++.-+--++.+....+.+++|++--+.
T Consensus 416 tG~~lsIPMpGH~I~e~~~e~~~~D~~~Le~LI~~ 450 (669)
T KOG2337|consen 416 TGYVLSIPMPGHPIGESLLEQTKKDLKRLEQLIKD 450 (669)
T ss_pred cceEEeccCCCCccchhhHHHHHHHHHHHHHHHhh
Confidence 22235667654333333445566677777654443
No 19
>COG0013 AlaS Alanyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=36.62 E-value=9.5 Score=38.47 Aligned_cols=61 Identities=23% Similarity=0.285 Sum_probs=42.0
Q ss_pred CCCCCCCCcccceeeeeeceeceeeEEecccCCCceEEEEecc--CC-----CCCcccchhhHHHHHHHHH
Q psy13898 3 VPQGSYKTSSLNIQDDRSTGFLQDIEVTGDKDDSKCLHVTIQK--TN-----AGPLTQAKFIFDDHIRCMA 66 (185)
Q Consensus 3 ~~~~~~~~~~~gw~~~~~~~~lqd~~~~~d~~dsr~l~i~i~~--~~-----~~~~~~a~f~F~d~i~c~~ 66 (185)
+|+-++|+ |+|+-|++.-||++....|.+--+.|--.+.+ |. ...+-.+.++--|||||++
T Consensus 220 Lp~k~IDT---GmGLERi~~vlQ~~~tnyd~dlf~~ii~~~e~~~g~~~~~~~~~~~~s~rVIADH~Rs~~ 287 (879)
T COG0013 220 LPKKNIDT---GMGLERIAAVLQGVPTNYDTDLFRPIIKAIEKLTGKKYGEDEEDPDVSFRVIADHIRSLA 287 (879)
T ss_pred CCCCCccc---CccHHHHHHHHcCCCcchhhhhhHHHHHHHHHHhCCcCCccccccceeEEEehhHHHHHH
Confidence 57777776 89999999999999877776544443322222 21 2222557788899999984
No 20
>PF12633 Adenyl_cycl_N: Adenylate cyclase NT domain; InterPro: IPR024685 Adenylate cyclase is the enzyme responsible for the synthesis of cAMP from ATP. On the basis of sequence similarity, it has been proposed that there are three different classes of adenylate cyclases [, ]. Class I cyclases are found in enterobacteria and related Gram-negative bacteria. This entry represents the N-terminal domain of class-I adenylate cyclases.
Probab=34.04 E-value=29 Score=29.09 Aligned_cols=24 Identities=13% Similarity=0.105 Sum_probs=21.1
Q ss_pred chhhhhHHHHHHHHHhhhCCccCc
Q psy13898 104 LYTLRGQINEWVTVANEYGLKFSA 127 (185)
Q Consensus 104 ~~~Lq~~l~~L~~~s~~~GL~IN~ 127 (185)
...||..++.+++|+.++|+++|-
T Consensus 132 ~~~Lq~K~~~i~~WA~~~gvEv~F 155 (204)
T PF12633_consen 132 RQLLQQKCDLIEQWAASFGVEVHF 155 (204)
T ss_pred HHHHHHHHHHHHHHHHHcCCEEEE
Confidence 445999999999999999999884
No 21
>PRK00252 alaS alanyl-tRNA synthetase; Reviewed
Probab=33.13 E-value=8.1 Score=38.82 Aligned_cols=61 Identities=21% Similarity=0.242 Sum_probs=34.7
Q ss_pred CCCCCCCCcccceeeeeeceeceeeEEecccCCCceEEEEeccCCCCC--cccchhhHHHHHHHHH
Q psy13898 3 VPQGSYKTSSLNIQDDRSTGFLQDIEVTGDKDDSKCLHVTIQKTNAGP--LTQAKFIFDDHIRCMA 66 (185)
Q Consensus 3 ~~~~~~~~~~~gw~~~~~~~~lqd~~~~~d~~dsr~l~i~i~~~~~~~--~~~a~f~F~d~i~c~~ 66 (185)
+|+-.+|+ |+|.-|++..||.+....|.+-=..|--.+.+-.+.+ .-.|.++--|||||++
T Consensus 216 Lp~~~iDT---G~GlER~~~ilq~~~snydtd~f~~~i~~i~~~~~~~y~~~~a~rviaDH~R~~~ 278 (865)
T PRK00252 216 LPKKNIDT---GMGLERIAAVLQGVHSNYETDLFRPLIKAIEELTGVKYEDDVSFRVIADHIRAVA 278 (865)
T ss_pred CCCCeeec---CcCHHHHHHHHcCCCCcchhhhHHHHHHHHHHHhCCCCCCCceEEEEcchHHHHH
Confidence 45666664 7888888888888776655421111100111101111 1367888999999983
No 22
>PF11273 DUF3073: Protein of unknown function (DUF3073); InterPro: IPR021426 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=29.79 E-value=65 Score=22.28 Aligned_cols=32 Identities=31% Similarity=0.558 Sum_probs=19.3
Q ss_pred hhhhhHHHHHHHHhhhhcCCCCCCCCCCCCCchhhhhHHH
Q psy13898 73 RGRTQARLAKMQQIAKLLDLPSSVQPCPSPPLYTLRGQIN 112 (185)
Q Consensus 73 ~gr~~~r~~k~~~~a~~l~i~~~~s~~~~s~~~~Lq~~l~ 112 (185)
+||.+|+|.|. |..|-- .+|+.+...||+.|.
T Consensus 2 RGRaKAKQTKV---AReLKY-----~sp~tDl~~LqrEL~ 33 (65)
T PF11273_consen 2 RGRAKAKQTKV---ARELKY-----SSPDTDLDALQRELS 33 (65)
T ss_pred cchhHHHHHHH---HHHhcc-----CCCcCCHHHHHHHHc
Confidence 68888888764 555554 345555555555443
No 23
>PF03755 YicC_N: YicC-like family, N-terminal region ; InterPro: IPR013527 Proteins in this entry are homologues of YicC (P23839 from SWISSPROT) from Escherichia coli. Although it is relatively poorly characterised YicC has been shown to be important for cells in the stationary phase, and essential for growth at high temperatures []. This domain is found at the N-terminal region of these proteins.
Probab=28.81 E-value=1e+02 Score=24.19 Aligned_cols=100 Identities=15% Similarity=0.188 Sum_probs=59.8
Q ss_pred ceeeeeeceeceeeEEecccCCCceEEEEeccCCCCCcccchhhHHHHHHHHHHHHHhhhhhhhHHHHHHHHhhhhcCCC
Q psy13898 14 NIQDDRSTGFLQDIEVTGDKDDSKCLHVTIQKTNAGPLTQAKFIFDDHIRCMAAKQRLNRGRTQARLAKMQQIAKLLDLP 93 (185)
Q Consensus 14 gw~~~~~~~~lqd~~~~~d~~dsr~l~i~i~~~~~~~~~~a~f~F~d~i~c~~akq~l~~gr~~~r~~k~~~~a~~l~i~ 93 (185)
|||-..+...--.+.|+--+-.+|-|.|.++= |-.... |+..||=. .++.+.+||+...-. +-. .
T Consensus 6 Gfgr~~~~~~~~~~~vEikSvN~R~Ldi~~rl----P~~l~~--lE~~ir~~-i~~~l~RGkV~v~i~----~~~----~ 70 (159)
T PF03755_consen 6 GFGRAEAETDGGSISVEIKSVNHRFLDISIRL----PRELSS--LEPEIRKL-IRKKLSRGKVEVSIR----VER----S 70 (159)
T ss_pred CCceeEEecCCeEEEEEEEecccCceeeEEeC----CHHHHH--HHHHHHHH-HHHhcccceEEEEEE----EEE----C
Confidence 66666555555567788888899999998876 544444 78999988 588999997653210 000 0
Q ss_pred CCCCCCCCCCchhhhhHHHHHHHHHhhhCCccCcc
Q psy13898 94 SSVQPCPSPPLYTLRGQINEWVTVANEYGLKFSAE 128 (185)
Q Consensus 94 ~~~s~~~~s~~~~Lq~~l~~L~~~s~~~GL~IN~~ 128 (185)
......+.-+..-++...+.|.......|+.-+++
T Consensus 71 ~~~~~~~~in~~l~~~y~~~l~~l~~~~~~~~~~~ 105 (159)
T PF03755_consen 71 SESAVELRINEELAKAYYEALKELAEELGLAGPIS 105 (159)
T ss_pred cccCCCcccCHHHHHHHHHHHHHHHHHcCCCCCCC
Confidence 00000011123356666666666677766644443
No 24
>cd03113 CTGs CTP synthetase (CTPs) is a two-domain protein, which consists of an N-terminal synthetase domain and C-terminal glutaminase domain. The enzymes hydrolyze the amide bond of glutamine to ammonia and glutamate at the glutaminase domains and transfer nascent ammonia to the acceptor substrate at the synthetase domain to form an aminated product. Glutaminase domains have evolved from the same ancestor, whereas the synthetase domains are evolutionarily unrelated and have different functions. This protein family is classified based on the N-terminal synthetase domain.
Probab=28.20 E-value=43 Score=29.08 Aligned_cols=33 Identities=24% Similarity=0.361 Sum_probs=26.4
Q ss_pred eccccceeEeecceecCCCCCHHHHHHHHHhhh
Q psy13898 151 TLKQVDHFKYLGSIISEDGTIDKEINRRIQQGS 183 (185)
Q Consensus 151 ~le~Ve~FkYLGs~Is~d~~~~~eI~~RI~~A~ 183 (185)
.|++=..=.|||.+++-=--.++||++||..+.
T Consensus 96 vi~kER~G~ylG~TVQviPHit~eIk~~i~~~~ 128 (255)
T cd03113 96 VIEKERRGDYLGKTVQVIPHITDEIKERIRRVA 128 (255)
T ss_pred HHHHhhccCccCceEEECcCccHHHHHHHHHhh
Confidence 344445556999999988889999999998864
No 25
>PF13382 Adenine_deam_C: Adenine deaminase C-terminal domain; PDB: 3T8L_B 3T81_A 3NQB_A.
Probab=26.75 E-value=96 Score=25.12 Aligned_cols=65 Identities=20% Similarity=0.296 Sum_probs=44.4
Q ss_pred cCCCCCCCCCCCCCchhhhhHHHHHHHHHhhhCCccCcccceeeeccccc-cccceEEECCeeccccceeEe
Q psy13898 90 LDLPSSVQPCPSPPLYTLRGQINEWVTVANEYGLKFSAEKSEVVVLKCEE-QVEGAIVMNGTTLKQVDHFKY 160 (185)
Q Consensus 90 l~i~~~~s~~~~s~~~~Lq~~l~~L~~~s~~~GL~IN~~KTKvM~~~~~~-~~~~~i~I~g~~le~Ve~FkY 160 (185)
|-+.+.+| +.|..++-+.+++|.++.++.|...+ --+|.+++-. ..-|.++|-+.-+=.|++|++
T Consensus 106 Lpi~GlmS---~~~~eev~~~~~~l~~~~~~lG~~~~---~p~~tlsflsl~viP~lriTd~Gl~Dv~~~~f 171 (171)
T PF13382_consen 106 LPIAGLMS---DLPAEEVARQLEELEEALRELGCPFD---DPFMTLSFLSLPVIPELRITDRGLVDVKKFKF 171 (171)
T ss_dssp -TBTTTBB---SS-HHHHHHHHHHHHHHHHTTS-BTT---TBSGGGGGTT-TTSSSEEEETTSEEETTTTE-
T ss_pred ccccceec---CCCHHHHHHHHHHHHHHHHHcCCCCC---CHHHHHHHhhcccCCCcccCCCcCEecccccC
Confidence 33445565 23455889999999999999997765 5678888764 346788887777777776653
No 26
>PRK01584 alanyl-tRNA synthetase; Provisional
Probab=24.23 E-value=15 Score=35.52 Aligned_cols=61 Identities=21% Similarity=0.232 Sum_probs=35.8
Q ss_pred CCCCCCCCcccceeeeeeceeceeeEEecccCCCceEEEEecc------CCCCCcccchhhHHHHHHHHH
Q psy13898 3 VPQGSYKTSSLNIQDDRSTGFLQDIEVTGDKDDSKCLHVTIQK------TNAGPLTQAKFIFDDHIRCMA 66 (185)
Q Consensus 3 ~~~~~~~~~~~gw~~~~~~~~lqd~~~~~d~~dsr~l~i~i~~------~~~~~~~~a~f~F~d~i~c~~ 66 (185)
.|+-++|+ |+|.-|++.-||.+....|.+--..+--.|.+ +.....-.|..+..|||||++
T Consensus 221 Lp~k~IDT---GmGLERl~~vlqg~~s~ydtdlf~pii~~i~~~~~~~y~~~~~~~~a~rvIaDH~R~~~ 287 (594)
T PRK01584 221 LKRKCVDT---GMGIERTIAFLQGKSSVYDTEAFTPIIKRIEKISGKIYGQNEEDDRSIRIIADHIRAAC 287 (594)
T ss_pred CCCCceeC---CcCHHHHHHHHcCCCCccchhhhHHHHHHHHHHhCCCcCCCCCCceeEEEEecHHHHHH
Confidence 56666665 88999999999988876665211111000000 000111257788899999883
No 27
>PF06418 CTP_synth_N: CTP synthase N-terminus; InterPro: IPR017456 CTP synthase is involved in pyrimidine ribonucleotide/ribonucleoside metabolism, catalysing the synthesis of CTP from UTP by amination of the pyrimidine ring at the 4-position []. The enzyme exists as a dimer of identical chains that aggregates as a tetramer. This gene has been found roughly 500 bp upstream of enolase in both beta (Nitrosomonas europaea) and gamma (Escherichia coli) subdivisions of Proteobacterium [].; GO: 0003883 CTP synthase activity, 0006221 pyrimidine nucleotide biosynthetic process; PDB: 2VO1_A 3NVA_B 1VCN_A 1VCO_A 1VCM_A 3IHL_B 2AD5_A 1S1M_B.
Probab=23.23 E-value=37 Score=29.82 Aligned_cols=34 Identities=24% Similarity=0.346 Sum_probs=23.9
Q ss_pred eccccceeEeecceecCCCCCHHHHHHHHHhhhc
Q psy13898 151 TLKQVDHFKYLGSIISEDGTIDKEINRRIQQGSA 184 (185)
Q Consensus 151 ~le~Ve~FkYLGs~Is~d~~~~~eI~~RI~~A~~ 184 (185)
.|++=..=.|||.+++----.++||++||..+..
T Consensus 97 vi~kER~G~ylG~TVQviPHitdeIk~~I~~~a~ 130 (276)
T PF06418_consen 97 VIEKERRGDYLGKTVQVIPHITDEIKERIRRVAK 130 (276)
T ss_dssp HHHHHHTTTTTTS---CCCHHHHHHHHHHHHHHC
T ss_pred HHHHHhcCcccCceeeecchHHHHHHHHHHHhcC
Confidence 3444445569999999888899999999998753
No 28
>COG0504 PyrG CTP synthase (UTP-ammonia lyase) [Nucleotide transport and metabolism]
Probab=22.24 E-value=60 Score=30.99 Aligned_cols=33 Identities=24% Similarity=0.394 Sum_probs=27.2
Q ss_pred eccccceeEeecceecCCCCCHHHHHHHHHhhh
Q psy13898 151 TLKQVDHFKYLGSIISEDGTIDKEINRRIQQGS 183 (185)
Q Consensus 151 ~le~Ve~FkYLGs~Is~d~~~~~eI~~RI~~A~ 183 (185)
.|++=..=.|||.+++-=--.+.||++||..+.
T Consensus 97 Vi~kER~GdYLG~TVQvIPHiT~eIk~~I~~~a 129 (533)
T COG0504 97 VIEKERRGDYLGKTVQVIPHITDEIKDRIREAA 129 (533)
T ss_pred HHHHHhcCCccCceeEECCCcchHHHHHHHHhc
Confidence 455555667999999988889999999999875
No 29
>PF12944 DUF3840: Protein of unknown function (DUF3840)
Probab=20.60 E-value=64 Score=23.79 Aligned_cols=29 Identities=28% Similarity=0.595 Sum_probs=17.3
Q ss_pred CCcccchhhHHHHHHHHHHHH--Hhhhhhhh
Q psy13898 49 GPLTQAKFIFDDHIRCMAAKQ--RLNRGRTQ 77 (185)
Q Consensus 49 ~~~~~a~f~F~d~i~c~~akq--~l~~gr~~ 77 (185)
+|-..----|+-||+|..-.. ||+-|+..
T Consensus 48 DPrSe~d~rfeSHIEc~kpykELRlev~k~R 78 (104)
T PF12944_consen 48 DPRSEEDRRFESHIECRKPYKELRLEVGKQR 78 (104)
T ss_pred CcccccccchHHHHHhcCchHHHhHHHHHHH
Confidence 343333334899999995443 66665443
No 30
>KOG4044|consensus
Probab=20.38 E-value=54 Score=27.12 Aligned_cols=50 Identities=18% Similarity=0.286 Sum_probs=31.6
Q ss_pred HHHHHHHhhhhcCCCCCCCCCCCCCchhhhhHHHHHHHHHhhhCCccCcccceeeec
Q psy13898 79 RLAKMQQIAKLLDLPSSVQPCPSPPLYTLRGQINEWVTVANEYGLKFSAEKSEVVVL 135 (185)
Q Consensus 79 r~~k~~~~a~~l~i~~~~s~~~~s~~~~Lq~~l~~L~~~s~~~GL~IN~~KTKvM~~ 135 (185)
.-.+|.+-|+.|+||.-.. + .+-+-+-.-......-|++.|.+||++=.+
T Consensus 40 ~~~rLl~aaril~vP~ivT---E----qYP~gLG~TV~eLd~~g~~~~~~KT~FSM~ 89 (201)
T KOG4044|consen 40 VTTRLLAAARILQVPVIVT---E----QYPEGLGKTVPELDIEGLKLNLSKTKFSMV 89 (201)
T ss_pred HHHHHHHhhhhhCCcEEee---c----cccccccccchhhchhhhcccccccceeee
Confidence 3557889999999986322 1 122233333333445689999999998443
Done!