Query psy13892
Match_columns 628
No_of_seqs 170 out of 1417
Neff 8.6
Searched_HMMs 46136
Date Fri Aug 16 23:05:35 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13892.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13892hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05380 Peptidase_A17: Pao re 100.0 2E-32 4.2E-37 254.1 14.0 159 172-336 1-159 (159)
2 cd01644 RT_pepA17 RT_pepA17: R 100.0 5.3E-32 1.2E-36 262.3 12.6 150 2-157 58-213 (213)
3 cd03714 RT_DIRS1 RT_DIRS1: Rev 99.8 3.5E-21 7.7E-26 170.5 8.5 98 8-119 1-99 (119)
4 cd03715 RT_ZFREV_like RT_ZFREV 99.8 3E-21 6.5E-26 188.7 8.2 106 2-119 86-191 (210)
5 cd01645 RT_Rtv RT_Rtv: Reverse 99.8 1.8E-20 3.9E-25 183.2 8.8 114 2-120 83-196 (213)
6 cd01647 RT_LTR RT_LTR: Reverse 99.7 6.1E-17 1.3E-21 153.2 7.7 102 2-119 57-158 (177)
7 PF09337 zf-H2C2: His(2)-Cys(2 99.4 2E-13 4.4E-18 92.9 2.6 39 573-612 1-39 (39)
8 PF00078 RVT_1: Reverse transc 99.0 3.4E-10 7.4E-15 110.6 6.2 117 2-120 63-194 (214)
9 cd00304 RT_like RT_like: Rever 98.9 1.4E-09 3E-14 92.5 6.0 98 8-152 1-98 (98)
10 PF00336 DNA_pol_viral_C: DNA 98.7 2.9E-08 6.2E-13 91.0 6.3 165 173-389 25-195 (245)
11 cd06222 RnaseH RNase H (RNase 98.6 1.6E-07 3.6E-12 82.9 7.5 112 260-387 2-128 (130)
12 PF00075 RNase_H: RNase H; In 98.2 1.9E-06 4.1E-11 77.4 5.9 100 257-380 3-116 (132)
13 PRK13907 rnhA ribonuclease H; 98.1 1E-05 2.3E-10 72.3 8.2 112 258-387 2-123 (128)
14 PRK07708 hypothetical protein; 98.1 1.8E-05 4E-10 77.0 10.2 121 257-388 73-205 (219)
15 cd01648 TERT TERT: Telomerase 98.0 8.2E-06 1.8E-10 71.9 6.1 115 8-153 1-119 (119)
16 COG0328 RnhA Ribonuclease HI [ 97.8 0.00014 3.1E-09 66.0 9.2 113 257-387 3-141 (154)
17 PRK00203 rnhA ribonuclease H; 97.7 7E-05 1.5E-09 68.9 6.0 111 257-387 3-138 (150)
18 cd01650 RT_nLTR_like RT_nLTR: 97.7 5.9E-05 1.3E-09 74.1 5.4 95 2-120 81-181 (220)
19 PRK07238 bifunctional RNase H/ 97.6 0.00013 2.8E-09 77.8 8.1 116 257-387 2-128 (372)
20 PRK08719 ribonuclease H; Revie 97.5 0.00016 3.5E-09 66.0 6.1 111 257-386 4-142 (147)
21 PF13456 RVT_3: Reverse transc 97.5 3.3E-05 7.1E-10 63.7 1.4 77 305-387 3-83 (87)
22 PRK06548 ribonuclease H; Provi 97.5 0.00025 5.3E-09 65.5 6.8 110 256-387 4-138 (161)
23 cd01651 RT_G2_intron RT_G2_int 97.3 0.00036 7.9E-09 68.7 6.5 72 49-120 124-205 (226)
24 PF07727 RVT_2: Reverse transc 97.2 4.7E-05 1E-09 75.9 -1.6 125 6-163 80-220 (246)
25 cd03487 RT_Bac_retron_II RT_Ba 97.0 0.0015 3.3E-08 63.9 6.5 139 2-155 56-198 (214)
26 cd01646 RT_Bac_retron_I RT_Bac 96.8 0.0019 4.1E-08 59.9 5.6 73 47-120 49-121 (158)
27 KOG3752|consensus 95.3 0.047 1E-06 56.1 7.1 115 258-387 213-361 (371)
28 cd01709 RT_like_1 RT_like_1: A 86.1 1.1 2.3E-05 46.4 4.8 72 48-121 80-151 (346)
29 PF02022 Integrase_Zn: Integra 71.6 2.7 5.7E-05 29.0 1.5 36 571-613 3-38 (40)
30 KOG0860|consensus 65.6 2.6 5.7E-05 36.1 0.7 41 560-600 55-95 (116)
31 PF13976 gag_pre-integrs: GAG- 65.2 3.7 8E-05 31.6 1.4 43 569-615 24-66 (67)
32 PF14948 RESP18: RESP18 domain 23.1 98 0.0021 26.3 3.2 36 185-220 11-46 (105)
33 KOG1005|consensus 21.3 1.4E+02 0.0031 34.7 5.1 78 46-128 629-708 (888)
34 smart00111 C4 C-terminal tande 20.8 41 0.0009 29.1 0.6 14 600-613 100-113 (114)
No 1
>PF05380 Peptidase_A17: Pao retrotransposon peptidase ; InterPro: IPR008042 This signature identifies members of the Pao retrotransposon family.
Probab=99.98 E-value=2e-32 Score=254.10 Aligned_cols=159 Identities=40% Similarity=0.681 Sum_probs=149.0
Q ss_pred hhHHHHHHhHhhhcccCCCchhHHHHHHHHHHHHHhcCCCCCccCChhhHHHHHHHHHhccccCccccceeecCCCCCCC
Q psy13892 172 ICKRLLLSVLASFFDILGLWTPIIMSLKLLVQSAWIQKKEWDDELDSKDKEKFLEIVDSMNFVSNIPVARYFDVPNNHDD 251 (628)
Q Consensus 172 ~tkR~~~s~~~~~~dplG~~~p~~~~~k~ll~~l~~~~~~Wd~~i~~e~~~~~~~~~~~l~~~~~~~~pr~~~~~~~~~~ 251 (628)
+|||+++|.++++|||+|+++|+++++|.++|.+|+.+.+||++++++....|..|.+.+.....+.+||++.. .
T Consensus 1 pTKR~ils~ia~~yDPlGl~~p~~i~~K~llq~lw~~~l~WD~~lp~el~~~w~~~~~~l~~~~~i~iPR~i~~-----~ 75 (159)
T PF05380_consen 1 PTKRQILSFIASIYDPLGLLAPIIIRAKLLLQKLWQSKLDWDDPLPDELRKEWKKWLKELESLSPIRIPRCIPI-----S 75 (159)
T ss_pred CChHHHHHHHHHHcCcchhhHHHHHHHHHHHHhhhccccchhhhhhHHHHHHHHHHHHHHhhcccccCCccccc-----c
Confidence 48999999999999999999999999999999999999999999999999999999999998778899997653 2
Q ss_pred CCcceeEEEeeccccccceeeEEEEEeecCCCeeeeEeecccccCCCCCCccchhhHHHHHHHHHHHHHHHhhcccccee
Q psy13892 252 QSVRYELHAFSDACSYSYASVVYLRSVSHSGDIRTNIVFAKSRVAPTNKPTLPRLELLGALIAYRSLKFVKNSLHINIDK 331 (628)
Q Consensus 252 ~~~~~~l~vftDAS~~g~Gavl~~~~~~~~g~~~~~~~~sks~~~~~~~~si~~~ELlAi~~a~~~~~~~~~~~~~~~~~ 331 (628)
.....++++|||||..|||||+|.+. ..||...+.+++||+|++|.+..||||+||+|+++|++++..+..++++.+.+
T Consensus 76 ~~~~~~L~~F~DAS~~aygavvYlr~-~~~~~~~~~ll~aKsrv~P~k~~tIPRlEL~a~~l~~~l~~~~~~~l~~~~~~ 154 (159)
T PF05380_consen 76 DYRSVELHVFCDASESAYGAVVYLRS-YSDGSVQVRLLFAKSRVAPLKTVTIPRLELLAALLGVRLANTVKKELDIEISQ 154 (159)
T ss_pred cccceeeeEeecccccceeeEeEeee-ccCCceeeeeeeecccccCCCCCcHHHHHHHHHHHHHHHHHHHHHHcCCCcce
Confidence 34567999999999999999999998 67888889999999999999988999999999999999999999999999999
Q ss_pred EEEEe
Q psy13892 332 CYLWI 336 (628)
Q Consensus 332 ~~i~t 336 (628)
+++||
T Consensus 155 ~~~wt 159 (159)
T PF05380_consen 155 VVFWT 159 (159)
T ss_pred eEEeC
Confidence 99986
No 2
>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=99.97 E-value=5.3e-32 Score=262.34 Aligned_cols=150 Identities=32% Similarity=0.550 Sum_probs=133.7
Q ss_pred cceEeehhHHhhccccccCcCCcCeEEEEEecCCCCCCCCCC-ceEEEEeeccccCcCchHHHHHHHHHHHhhhcch-hh
Q psy13892 2 YRCALIGDIEKAFLNVGLNEGERDYTRILWVKDVAKPLDSDN-VVVLRHTRLPFGVVSSPFLLSCVIRTHLDKYSGD-YI 79 (628)
Q Consensus 2 ~~~~~~~Dl~~af~qi~l~~~d~~~~~F~~~~~~~~~~~~~~-~~~y~~~rmpFGl~~aP~~~~~~i~~~l~~~~~~-~~ 79 (628)
++|++++||++|||||+|+|+|+++|+|+|++++ +++ ++.|+|+|||||+++||++||++|++++.++.+. .+
T Consensus 58 ~~~~~~~Di~~af~qI~i~~~d~~~~~F~w~~~~-----~~~~~~~Y~~~~~pFG~~~AP~~~~~~~~~~~~~~~~~~~~ 132 (213)
T cd01644 58 GKIAVSADIEKMFHQVKVRPEDRDVLRFLWRKDG-----DEPKPIEYRMTVVPFGAASAPFLANRALKQHAEDHPHEAAA 132 (213)
T ss_pred CceeEehhHHHhhhheecCcccCceEEEEEeCCC-----CCCcceEEEEEEEccCCccchHHHHHHHHHHHhhcchhhHH
Confidence 6899999999999999999999999999999873 344 4899999999999999999999999999998865 35
Q ss_pred hhhhhceeecccccccCChHHHHHHHHhHHHHHhhhccccccccccCccccccCCCccc----cccccccceeeeeeccC
Q psy13892 80 DQLKNNIYMDNILCGVNNEEEIENFVGTARKVFSDASLNLREWASNYPSVLIGTLSPEL----VNTSRVQNTLGMLWDTQ 155 (628)
Q Consensus 80 ~~i~~~~YvDDili~s~t~ee~~~~~~~v~~~l~~~g~~l~~~~~~~~~~lg~~i~~~~----~~~~~~~k~LG~~w~~~ 155 (628)
+.+...+|||||+++++|.+||.+.+++|.++|+++||++++|.+|+.+++ +.++++. ...+...|.||+.|++.
T Consensus 133 ~~i~~~~YvDDili~~~s~~e~~~~~~~v~~~L~~~Gf~l~kw~sn~~~~l-~~~~~~~~~~~~~~~~~~k~LGl~W~~~ 211 (213)
T cd01644 133 KIIKRNFYVDDILVSTDTLNEAVNVAKRLIALLKKGGFNLRKWASNSQEVL-DDLPEERVLLDRDSDVTEKTLGLRWNPK 211 (213)
T ss_pred HHHHHeeecccceecCCCHHHHHHHHHHHHHHHHhCCccchhcccCchhhh-hcccccccccccccccchhcccceeecc
Confidence 566678999999999999999999999999999999999999999999999 5665432 23556799999999987
Q ss_pred CC
Q psy13892 156 ED 157 (628)
Q Consensus 156 ~d 157 (628)
.|
T Consensus 212 ~D 213 (213)
T cd01644 212 TD 213 (213)
T ss_pred CC
Confidence 65
No 3
>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=99.84 E-value=3.5e-21 Score=170.46 Aligned_cols=98 Identities=18% Similarity=0.353 Sum_probs=83.9
Q ss_pred hhHHhhccccccCcCCcCeEEEEEecCCCCCCCCCCceEEEEeeccccCcCchHHHHHHHHHHHhhhcchhhhhhhhcee
Q psy13892 8 GDIEKAFLNVGLNEGERDYTRILWVKDVAKPLDSDNVVVLRHTRLPFGVVSSPFLLSCVIRTHLDKYSGDYIDQLKNNIY 87 (628)
Q Consensus 8 ~Dl~~af~qi~l~~~d~~~~~F~~~~~~~~~~~~~~~~~y~~~rmpFGl~~aP~~~~~~i~~~l~~~~~~~~~~i~~~~Y 87 (628)
+|+.+|||||+|+|+|+++|+|.++.+ .|+|+|||||+++||++||+.|+.++..+... ......|
T Consensus 1 lD~~~ay~~i~l~~~~~~~~af~~~~~-----------~~~~~~mp~Gl~~sp~~f~~~~~~i~~~~~~~---~~~v~~Y 66 (119)
T cd03714 1 VDLKDAYFHIPILPRSRDLLGFAWQGE-----------TYQFKALPFGLSLAPRVFTKVVEALLAPLRLL---GVRIFSY 66 (119)
T ss_pred CchhhceEEEecCCCCcceeeEEECCC-----------cEEEEecCCcccchHHHHHHHHHHHHHHhhcC---CeEEEEE
Confidence 599999999999999999999988876 89999999999999999999999999876421 1223679
Q ss_pred ecccccccCChHHHHHHHHhHHH-HHhhhcccc
Q psy13892 88 MDNILCGVNNEEEIENFVGTARK-VFSDASLNL 119 (628)
Q Consensus 88 vDDili~s~t~ee~~~~~~~v~~-~l~~~g~~l 119 (628)
+|||++.++|.+++.+..+.+.+ +++++||.+
T Consensus 67 ~DDili~~~~~~~~~~~~~~l~~~~l~~~gl~l 99 (119)
T cd03714 67 LDDLLIIASSIKTSEAVLRHLRATLLANLGFTL 99 (119)
T ss_pred ecCeEEEeCcHHHHHHHHHHHHHHHHHHcCCcc
Confidence 99999999986666666666655 699999998
No 4
>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=99.84 E-value=3e-21 Score=188.66 Aligned_cols=106 Identities=18% Similarity=0.264 Sum_probs=95.4
Q ss_pred cceEeehhHHhhccccccCcCCcCeEEEEEecCCCCCCCCCCceEEEEeeccccCcCchHHHHHHHHHHHhhhcchhhhh
Q psy13892 2 YRCALIGDIEKAFLNVGLNEGERDYTRILWVKDVAKPLDSDNVVVLRHTRLPFGVVSSPFLLSCVIRTHLDKYSGDYIDQ 81 (628)
Q Consensus 2 ~~~~~~~Dl~~af~qi~l~~~d~~~~~F~~~~~~~~~~~~~~~~~y~~~rmpFGl~~aP~~~~~~i~~~l~~~~~~~~~~ 81 (628)
.+|+.++|+++||+||+|+|+++++|+|.|.++ .|+|+|||||+++||++|++.|+.++..+.... ..
T Consensus 86 ~~~~s~lDl~~af~~i~l~~~~~~~taf~~~~~-----------~y~~~~lp~Gl~~sp~~f~~~~~~~l~~~~~~~-~~ 153 (210)
T cd03715 86 HQWYTVLDLANAFFSLPLAPDSQPLFAFEWEGQ-----------QYTFTRLPQGFKNSPTLFHEALARDLAPFPLEH-EG 153 (210)
T ss_pred CeEEEEeeccCeEEEEEcccccEEeEEEEECCe-----------eEEEEEEeccccCcHHHHHHHHHHHHHHHHhhC-CC
Confidence 579999999999999999999999999988765 999999999999999999999999998874321 11
Q ss_pred hhhceeecccccccCChHHHHHHHHhHHHHHhhhcccc
Q psy13892 82 LKNNIYMDNILCGVNNEEEIENFVGTARKVFSDASLNL 119 (628)
Q Consensus 82 i~~~~YvDDili~s~t~ee~~~~~~~v~~~l~~~g~~l 119 (628)
....+|+|||+++++|.+||.++++.|+++|+++||.+
T Consensus 154 ~~~~~Y~DDili~s~~~~e~~~~l~~v~~~l~~~gl~l 191 (210)
T cd03715 154 TILLQYVDDLLLAADSEEDCLKGTDALLTHLGELGYKV 191 (210)
T ss_pred eEEEEECCcEEEecCCHHHHHHHHHHHHHHHHHCCCCc
Confidence 22368999999999999999999999999999999998
No 5
>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=99.82 E-value=1.8e-20 Score=183.24 Aligned_cols=114 Identities=17% Similarity=0.259 Sum_probs=98.1
Q ss_pred cceEeehhHHhhccccccCcCCcCeEEEEEecCCCCCCCCCCceEEEEeeccccCcCchHHHHHHHHHHHhhhcchhhhh
Q psy13892 2 YRCALIGDIEKAFLNVGLNEGERDYTRILWVKDVAKPLDSDNVVVLRHTRLPFGVVSSPFLLSCVIRTHLDKYSGDYIDQ 81 (628)
Q Consensus 2 ~~~~~~~Dl~~af~qi~l~~~d~~~~~F~~~~~~~~~~~~~~~~~y~~~rmpFGl~~aP~~~~~~i~~~l~~~~~~~~~~ 81 (628)
.+|++++|+++||+||+|+|+|+.+|+|.|...+ .+++.+.|+|+|||||+++||++||++|+.++..+.+.+. .
T Consensus 83 ~~~~s~lDl~~af~~i~l~~~~~~~taf~~~~~~----~~~~~~~~~~~~lP~Gl~~SP~~f~~~m~~~l~~~~~~~~-~ 157 (213)
T cd01645 83 GWPLIVLDLKDCFFSIPLHPDDRERFAFTVPSIN----NKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRKQYP-D 157 (213)
T ss_pred CceEEEEEccCcEEEeeeccCCcceeEEEecccc----CCCCCceEEEEEeCCCCcChHHHHHHHHHHHHHHHHHHCC-C
Confidence 3689999999999999999999999999986321 1234569999999999999999999999999988764321 1
Q ss_pred hhhceeecccccccCChHHHHHHHHhHHHHHhhhccccc
Q psy13892 82 LKNNIYMDNILCGVNNEEEIENFVGTARKVFSDASLNLR 120 (628)
Q Consensus 82 i~~~~YvDDili~s~t~ee~~~~~~~v~~~l~~~g~~l~ 120 (628)
+....|+|||+++++|.++|.++++.|+++|+++||.+.
T Consensus 158 ~~~~~Y~DDili~s~~~~~~~~~l~~v~~~l~~~gl~ln 196 (213)
T cd01645 158 IVIYHYMDDILIASDLEGQLREIYEELRQTLLRWGLTIP 196 (213)
T ss_pred eEEEEEcCCEEEEcCCHHHHHHHHHHHHHHHHHCCCEeC
Confidence 223689999999999999999999999999999999983
No 6
>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=99.68 E-value=6.1e-17 Score=153.18 Aligned_cols=102 Identities=24% Similarity=0.351 Sum_probs=94.0
Q ss_pred cceEeehhHHhhccccccCcCCcCeEEEEEecCCCCCCCCCCceEEEEeeccccCcCchHHHHHHHHHHHhhhcchhhhh
Q psy13892 2 YRCALIGDIEKAFLNVGLNEGERDYTRILWVKDVAKPLDSDNVVVLRHTRLPFGVVSSPFLLSCVIRTHLDKYSGDYIDQ 81 (628)
Q Consensus 2 ~~~~~~~Dl~~af~qi~l~~~d~~~~~F~~~~~~~~~~~~~~~~~y~~~rmpFGl~~aP~~~~~~i~~~l~~~~~~~~~~ 81 (628)
+++++.+|+.+||+||+++++++.+++|.|..+ .|++++||||+++||..|+..|+.++....+..
T Consensus 57 ~~~~~~~D~~~~~~~i~l~~~~~~~~~~~~~~~-----------~~~~~~~p~G~~~s~~~~~~~~~~~l~~~~~~~--- 122 (177)
T cd01647 57 AKVFSKLDLRSGYHQIPLAEESRPKTAFRTPFG-----------LYEYTRMPFGLKNAPATFQRLMNKILGDLLGDF--- 122 (177)
T ss_pred CcEEEecccccCcceeeeccCChhhceeecCCC-----------ccEEEEecCCCccHHHHHHHHHHhhhccccccc---
Confidence 578999999999999999999999999988766 899999999999999999999999998874433
Q ss_pred hhhceeecccccccCChHHHHHHHHhHHHHHhhhcccc
Q psy13892 82 LKNNIYMDNILCGVNNEEEIENFVGTARKVFSDASLNL 119 (628)
Q Consensus 82 i~~~~YvDDili~s~t~ee~~~~~~~v~~~l~~~g~~l 119 (628)
...|+||+++.+++.++|...++.+.+.|+++||.+
T Consensus 123 --~~~y~DDi~i~~~~~~~~~~~~~~~~~~l~~~~~~~ 158 (177)
T cd01647 123 --VEVYLDDILVYSKTEEEHLEHLREVLERLREAGLKL 158 (177)
T ss_pred --cEEEecCccccCCCHHHHHHHHHHHHHHHHHcCCEe
Confidence 268999999999999999999999999999999987
No 7
>PF09337 zf-H2C2: His(2)-Cys(2) zinc finger; InterPro: IPR015416 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents an H2C2-type zinc finger that binds to histone upstream activating sequence (UAS) elements found in histone gene promoters []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].
Probab=99.38 E-value=2e-13 Score=92.87 Aligned_cols=39 Identities=26% Similarity=0.526 Sum_probs=36.8
Q ss_pred HHhccCCChhHHHHHHHhhcccccchhHHHHHhccCcccc
Q psy13892 573 HRACFHNGASQTLATLRLDYWITQGRSAVKQILKSCVNCK 612 (628)
Q Consensus 573 H~~~gH~G~~~t~~~ir~~yww~~~~~~Vr~~v~~C~~Cq 612 (628)
|. .+|+|+++|+++|+++||||+|+++|+++|++|..||
T Consensus 1 H~-~~H~Gi~kT~~~i~~~y~W~gm~~~V~~~ir~C~~Cq 39 (39)
T PF09337_consen 1 HN-QGHPGINKTTAKISQRYHWPGMKKDVRRVIRSCPQCQ 39 (39)
T ss_pred CC-ccCCCHHHHHHHHHHhheecCHHHHHHHHHhcCcccC
Confidence 45 4599999999999999999999999999999999998
No 8
>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=99.02 E-value=3.4e-10 Score=110.62 Aligned_cols=117 Identities=21% Similarity=0.220 Sum_probs=94.9
Q ss_pred cceEeehhHHhhccccccCcCCcCeEEEEEecC---------------CCCCCCCCCceEEEEeeccccCcCchHHHHHH
Q psy13892 2 YRCALIGDIEKAFLNVGLNEGERDYTRILWVKD---------------VAKPLDSDNVVVLRHTRLPFGVVSSPFLLSCV 66 (628)
Q Consensus 2 ~~~~~~~Dl~~af~qi~l~~~d~~~~~F~~~~~---------------~~~~~~~~~~~~y~~~rmpFGl~~aP~~~~~~ 66 (628)
+.|++.+|+++||.+|+.++-.+.+.+|.+.+. .... ... ...+..+.+|+|...||.+++..
T Consensus 63 ~~~~~~~Di~~~f~sI~~~~l~~~l~~~~~~~~~~~~i~~~~~~~~~~~~~~-~~~-~~~~~~~glpqG~~~S~~l~~~~ 140 (214)
T PF00078_consen 63 YLYFLKLDISKAFDSIPHHRLLRKLKRFGVPKKLIRLIQNLLSDRTAKVYLD-GDL-SPYFQKRGLPQGSPLSPLLFNIY 140 (214)
T ss_dssp SSEEEEEECCCCGGGSBBHTTTGGGGEEEEECCSCHHHHHHHHHHHH-EECG-CSS-SEEEEESBS-TTSTCHHHHHHHH
T ss_pred ccccceeccccccccceeeecccccccccccccccccccccccccccccccc-ccc-ccccccccccccccccchhhccc
Confidence 468999999999999999999999999977632 0000 011 55899999999999999999999
Q ss_pred HHHHHhhhcchhhhhhhhceeecccccccCChHHHHHHHHhHHHHHhhhccccc
Q psy13892 67 IRTHLDKYSGDYIDQLKNNIYMDNILCGVNNEEEIENFVGTARKVFSDASLNLR 120 (628)
Q Consensus 67 i~~~l~~~~~~~~~~i~~~~YvDDili~s~t~ee~~~~~~~v~~~l~~~g~~l~ 120 (628)
|..+...+.......+....|+||+++++++.+++.+.++.+.+.+++.|+.+.
T Consensus 141 l~~l~~~~~~~~~~~~~~~rY~DD~~i~~~~~~~~~~~~~~i~~~~~~~gl~ln 194 (214)
T PF00078_consen 141 LDDLDRELQQELNPDISYLRYADDILIISKSKEELQKILEKISQWLEELGLKLN 194 (214)
T ss_dssp HHHHHHHHHHHS-TTSEEEEETTEEEEEESSHHHHHHHHHHHHHHHHHTTSBCS
T ss_pred cccccccccccccccccceEeccccEEEECCHHHHHHHHHHHHHHHHHCCCEEC
Confidence 999888775532123345789999999999999999999999999999999883
No 9
>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=98.93 E-value=1.4e-09 Score=92.53 Aligned_cols=98 Identities=17% Similarity=0.217 Sum_probs=76.7
Q ss_pred hhHHhhccccccCcCCcCeEEEEEecCCCCCCCCCCceEEEEeeccccCcCchHHHHHHHHHHHhhhcchhhhhhhhcee
Q psy13892 8 GDIEKAFLNVGLNEGERDYTRILWVKDVAKPLDSDNVVVLRHTRLPFGVVSSPFLLSCVIRTHLDKYSGDYIDQLKNNIY 87 (628)
Q Consensus 8 ~Dl~~af~qi~l~~~d~~~~~F~~~~~~~~~~~~~~~~~y~~~rmpFGl~~aP~~~~~~i~~~l~~~~~~~~~~i~~~~Y 87 (628)
+|++++|+||. ||||...||.+++.+|..+...+... ...+....|
T Consensus 1 ~d~~~~~~~~~---------------------------------lPqG~~~Sp~l~~~~~~~l~~~~~~~-~~~~~~~~Y 46 (98)
T cd00304 1 FDVKSFFTSIP---------------------------------LPQGSPLSPALANLYMEKLEAPILKQ-LLDITLIRY 46 (98)
T ss_pred CCHHHcCCCCc---------------------------------cCCCCchHHHHHHHHHHHHHHHHHHh-cCCceEEEe
Confidence 59999999996 89999999999999999988775431 112334789
Q ss_pred ecccccccCChHHHHHHHHhHHHHHhhhccccccccccCccccccCCCccccccccccceeeeee
Q psy13892 88 MDNILCGVNNEEEIENFVGTARKVFSDASLNLREWASNYPSVLIGTLSPELVNTSRVQNTLGMLW 152 (628)
Q Consensus 88 vDDili~s~t~ee~~~~~~~v~~~l~~~g~~l~~~~~~~~~~lg~~i~~~~~~~~~~~k~LG~~w 152 (628)
+||+++.+++. ++...++.+.+.+++.|+.+...++... ......++||+.+
T Consensus 47 ~DD~~i~~~~~-~~~~~~~~l~~~l~~~gl~ln~~Kt~~~------------~~~~~~~flG~~~ 98 (98)
T cd00304 47 VDDLVVIAKSE-QQAVKKRELEEFLARLGLNLSDEKTQFT------------EKEKKFKFLGILV 98 (98)
T ss_pred eCcEEEEeCcH-HHHHHHHHHHHHHHHcCcEEChheeEEe------------cCCCCeeeeceeC
Confidence 99999999998 9999999999999999999854333210 1235677888754
No 10
>PF00336 DNA_pol_viral_C: DNA polymerase (viral) C-terminal domain; InterPro: IPR001462 This domain is at the C terminus of hepatitis B-type viruses P proteins and represents a functional domain that controls the RNase H activities of the protein. The domain is always associated with IPR000201 from INTERPRO and .; GO: 0004523 ribonuclease H activity
Probab=98.69 E-value=2.9e-08 Score=91.04 Aligned_cols=165 Identities=19% Similarity=0.195 Sum_probs=98.6
Q ss_pred hHHHHHHhHhhhcccCCCchhHHHHHHHHHHHHHhc-----CCCCCccCChhhHHHHHHHHHhccccCccccceeecCCC
Q psy13892 173 CKRLLLSVLASFFDILGLWTPIIMSLKLLVQSAWIQ-----KKEWDDELDSKDKEKFLEIVDSMNFVSNIPVARYFDVPN 247 (628)
Q Consensus 173 tkR~~~s~~~~~~dplG~~~p~~~~~k~ll~~l~~~-----~~~Wd~~i~~e~~~~~~~~~~~l~~~~~~~~pr~~~~~~ 247 (628)
++---.+.+.++...+|+++|++..+-..+..++.. .+... .-. +.++-.+... ..++-|.
T Consensus 25 nrpiDwKvcQRivGlLgF~aPFTqcgy~aL~PlY~~iq~k~aF~FS----~~Y----k~~L~kqy~~-l~pvarq----- 90 (245)
T PF00336_consen 25 NRPIDWKVCQRIVGLLGFAAPFTQCGYPALMPLYAAIQSKQAFTFS----PTY----KAFLCKQYMN-LYPVARQ----- 90 (245)
T ss_pred CCCcchHHHHhhhhhhhcccccccCCchhhhhHHHHHhhhheeecC----HHH----HHHHHHhhcc-ccccccC-----
Confidence 333445667778888999999988777766665542 23332 111 2222222211 2333333
Q ss_pred CCCCCCcceeEEEeeccccccceeeEEEEEeecCCCeeeeEeecccccCCCCCCccchhhHHHHHHHHHHHHHHHhhccc
Q psy13892 248 NHDDQSVRYELHAFSDACSYSYASVVYLRSVSHSGDIRTNIVFAKSRVAPTNKPTLPRLELLGALIAYRSLKFVKNSLHI 327 (628)
Q Consensus 248 ~~~~~~~~~~l~vftDAS~~g~Gavl~~~~~~~~g~~~~~~~~sks~~~~~~~~si~~~ELlAi~~a~~~~~~~~~~~~~ 327 (628)
....-.||+||+.+|||.++.. | ..+.-++ .-..|.-.||+|.++|--+
T Consensus 91 ------r~~lc~VfaDATpTgwgi~i~~------~--~~~~Tfs-------~~l~IhtaELlaaClAr~~---------- 139 (245)
T PF00336_consen 91 ------RPGLCQVFADATPTGWGISITG------Q--RMRGTFS-------KPLPIHTAELLAACLARLM---------- 139 (245)
T ss_pred ------CCCCCceeccCCCCcceeeecC------c--eeeeeec-------ccccchHHHHHHHHHHHhc----------
Confidence 2234679999999999987431 1 1122222 2357889999999877441
Q ss_pred cceeEEEEecchhhhHhhhcCCccC-hhHHhHHHHHHHhcCCcceEeecCCCCCCCCCCCCCC
Q psy13892 328 NIDKCYLWIDNQCVIHWLTGNKVLP-TFVNNRVKEIKASVFPIVYKYIPTDSNPADLACRGSS 389 (628)
Q Consensus 328 ~~~~~~i~tDs~~~l~~l~~~~~~~-~~~~~r~~~i~~~~~~~~i~hipg~~N~AD~lSR~~~ 389 (628)
.+.++ +.|||..+++.=-+.=.|. ...+||+ +.+.++.|||++.||||..||+..
T Consensus 140 ~~~r~-l~tDnt~Vlsrkyts~PW~lac~A~wi------Lrgts~~yVPS~~NPAD~PsR~~~ 195 (245)
T PF00336_consen 140 SGARC-LGTDNTVVLSRKYTSFPWLLACAANWI------LRGTSFYYVPSKYNPADDPSRGKL 195 (245)
T ss_pred cCCcE-EeecCcEEEecccccCcHHHHHHHHHh------hcCceEEEeccccCcCCCCCCCcc
Confidence 22333 8899998777321111111 1234443 456899999999999999999964
No 11
>cd06222 RnaseH RNase H (RNase HI) is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a not sequence-specific manner. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H knockout mice lack mitochondrial DNA replication and die as embryos. The retroviral reverse transcriptase contains an RNase H domain that plays an important role in converting a single stranded retroviral genomic RNA into a dsDNA for integration into host chromosomes. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.
Probab=98.56 E-value=1.6e-07 Score=82.88 Aligned_cols=112 Identities=21% Similarity=0.249 Sum_probs=77.4
Q ss_pred Eeeccccc------cceeeEEEEEeecCCCeeeeEeecccccCCCCCCccchhhHHHHHHHHHHHHHHHhhccccceeEE
Q psy13892 260 AFSDACSY------SYASVVYLRSVSHSGDIRTNIVFAKSRVAPTNKPTLPRLELLGALIAYRSLKFVKNSLHINIDKCY 333 (628)
Q Consensus 260 vftDAS~~------g~Gavl~~~~~~~~g~~~~~~~~sks~~~~~~~~si~~~ELlAi~~a~~~~~~~~~~~~~~~~~~~ 333 (628)
+|||||.. |+|+++.. .++.. .+.+.... ...|..+.|+.|++.|++.+. .....++.
T Consensus 2 ~~~Dgs~~~~~~~~g~g~v~~~----~~~~~---~~~~~~~~---~~~s~~~aEl~al~~al~~~~------~~~~~~i~ 65 (130)
T cd06222 2 IYTDGSCRGNPGPAGAGVVLRD----PGGEV---LLSGGLLG---GNTTNNRAELLALIEALELAL------ELGGKKVN 65 (130)
T ss_pred EEecccCCCCCCceEEEEEEEe----CCCeE---EEeccccC---CCCcHHHHHHHHHHHHHHHHH------hCCCceEE
Confidence 68999987 77777763 22211 22211111 567899999999999999665 34578899
Q ss_pred EEecchhhhHhhhcCCc-cChhHHhHHHHHHHhc---CCcceEeecC----CCC-CCCCCCCC
Q psy13892 334 LWIDNQCVIHWLTGNKV-LPTFVNNRVKEIKASV---FPIVYKYIPT----DSN-PADLACRG 387 (628)
Q Consensus 334 i~tDs~~~l~~l~~~~~-~~~~~~~r~~~i~~~~---~~~~i~hipg----~~N-~AD~lSR~ 387 (628)
|+|||..++..+++... ........+..+++.. ..+.+.|+|+ ..| .||.|+|.
T Consensus 66 i~~Ds~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~v~~h~~~~~n~~ad~la~~ 128 (130)
T cd06222 66 IYTDSQYVINALTGWYEGKPVKNVDLWQRLLALLKRFHKVRFEWVPGHSGIEGNERADALAKE 128 (130)
T ss_pred EEECHHHHHHHhhccccCCChhhHHHHHHHHHHHhCCCeEEEEEcCCCCCCcchHHHHHHHHh
Confidence 99999999999988622 2233334444444433 3689999999 888 59998874
No 12
>PF00075 RNase_H: RNase H; InterPro: IPR002156 The RNase H domain is responsible for hydrolysis of the RNA portion of RNA x DNA hybrids, and this activity requires the presence of divalent cations (Mg2+ or Mn2+) that bind its active site. This domain is a part of a large family of homologous RNase H enzymes of which the RNase HI protein from Escherichia coli is the best characterised []. Secondary structure predictions for the enzymes from E. coli, yeast, human liver and diverse retroviruses (such as Rous sarcoma virus and the Foamy viruses) supported, in every case, the five beta-strands (1 to 5) and four or five alpha-helices (A, B/C, D, E) that have been identified by crystallography in the RNase H domain of Human immunodeficiency virus 1 (HIV-1) reverse transcriptase and in E. coli RNase H []. Reverse transcriptase (RT) is a modular enzyme carrying polymerase and ribonuclease H (RNase H) activities in separable domains. Reverse transcriptase (RT) converts the single-stranded RNA genome of a retrovirus into a double-stranded DNA copy for integration into the host genome. This process requires ribonuclease H as well as RNA- and DNA-directed DNA polymerase activities. Retroviral RNase H 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. Bacterial RNase H 3.1.26.4 from EC catalyses endonucleolytic cleavage to 5'-phosphomonoester acting on RNA-DNA hybrids. The 3D structure of the RNase H domain from diverse bacteria and retroviruses has been solved [, , ]. All have four beta strands and four to five alpha helices. The E. coli RNase H1 protein binds a single Mg2+ ion cofactor in the active site of the enzyme. The divalent cation is bound by the carboxyl groups of four acidic residues, Asp-10, Glu-48, Asp-70, and Asp-134 []. The first three acidic residues are highly conserved in all bacterial and retroviral RNase H sequences. ; GO: 0003676 nucleic acid binding, 0004523 ribonuclease H activity; PDB: 3LP3_B 2KW4_A 3P1G_A 1RIL_A 2RPI_A 4EQJ_G 4EP2_B 3OTY_P 3U3G_D 2ZQB_D ....
Probab=98.22 E-value=1.9e-06 Score=77.43 Aligned_cols=100 Identities=21% Similarity=0.330 Sum_probs=63.9
Q ss_pred eEEEeecccc------ccceeeEEEEEeecCCCeeeeEeecccccCCCCCCccchhhHHHHHHHHHHHHHHHhhccccce
Q psy13892 257 ELHAFSDACS------YSYASVVYLRSVSHSGDIRTNIVFAKSRVAPTNKPTLPRLELLGALIAYRSLKFVKNSLHINID 330 (628)
Q Consensus 257 ~l~vftDAS~------~g~Gavl~~~~~~~~g~~~~~~~~sks~~~~~~~~si~~~ELlAi~~a~~~~~~~~~~~~~~~~ 330 (628)
.+.+|||||- .|+|.|++ +| + ..+. .+. ..|..+.||.|+..|++.+ . ..
T Consensus 3 ~~~iytDgS~~~~~~~~~~g~v~~------~~--~---~~~~-~~~---~~s~~~aEl~Ai~~AL~~~---~------~~ 58 (132)
T PF00075_consen 3 AIIIYTDGSCRPNPGKGGAGYVVW------GG--R---NFSF-RLG---GQSNNRAELQAIIEALKAL---E------HR 58 (132)
T ss_dssp SEEEEEEEEECTTTTEEEEEEEEE------TT--E---EEEE-EEE---SECHHHHHHHHHHHHHHTH---S------TS
T ss_pred cEEEEEeCCccCCCCceEEEEEEE------CC--e---EEEe-ccc---ccchhhhheehHHHHHHHh---h------cc
Confidence 5899999993 36666433 22 1 1111 111 5788999999999999943 1 17
Q ss_pred eEEEEecchhhhHhhhc-----C---CccChhHHhHHHHHHHhcCCcceEeecCCCCC
Q psy13892 331 KCYLWIDNQCVIHWLTG-----N---KVLPTFVNNRVKEIKASVFPIVYKYIPTDSNP 380 (628)
Q Consensus 331 ~~~i~tDs~~~l~~l~~-----~---~~~~~~~~~r~~~i~~~~~~~~i~hipg~~N~ 380 (628)
++.|+|||+.++.++.. . +....-+.+++.++......+.|.||||..|.
T Consensus 59 ~v~I~tDS~~v~~~l~~~~~~~~~~~~~~~~~i~~~i~~~~~~~~~v~~~~V~~H~~~ 116 (132)
T PF00075_consen 59 KVTIYTDSQYVLNALNKWLHGNGWKKTSNGRPIKNEIWELLSRGIKVRFRWVPGHSGV 116 (132)
T ss_dssp EEEEEES-HHHHHHHHTHHHHTTSBSCTSSSBHTHHHHHHHHHSSEEEEEESSSSSSS
T ss_pred cccccccHHHHHHHHHHhccccccccccccccchhheeeccccceEEeeeeccCcCCC
Confidence 89999999999998877 3 11111233344433333346899999999764
No 13
>PRK13907 rnhA ribonuclease H; Provisional
Probab=98.11 E-value=1e-05 Score=72.30 Aligned_cols=112 Identities=16% Similarity=0.091 Sum_probs=72.4
Q ss_pred EEEeeccccc------cceeeEEEEEeecCCCeeeeEeecccccCCCCCCccchhhHHHHHHHHHHHHHHHhhcccccee
Q psy13892 258 LHAFSDACSY------SYASVVYLRSVSHSGDIRTNIVFAKSRVAPTNKPTLPRLELLGALIAYRSLKFVKNSLHINIDK 331 (628)
Q Consensus 258 l~vftDAS~~------g~Gavl~~~~~~~~g~~~~~~~~sks~~~~~~~~si~~~ELlAi~~a~~~~~~~~~~~~~~~~~ 331 (628)
++|+||||-. |||+|+. +.+|. +... .+....+-.+.|+.|++.|++.+... ...+
T Consensus 2 ~~iy~DGa~~~~~g~~G~G~vi~----~~~~~---~~~~-----~~~~~~tn~~AE~~All~aL~~a~~~------g~~~ 63 (128)
T PRK13907 2 IEVYIDGASKGNPGPSGAGVFIK----GVQPA---VQLS-----LPLGTMSNHEAEYHALLAALKYCTEH------NYNI 63 (128)
T ss_pred EEEEEeeCCCCCCCccEEEEEEE----ECCee---EEEE-----ecccccCCcHHHHHHHHHHHHHHHhC------CCCE
Confidence 5688998753 6777763 22331 1111 11223567899999999999966543 2457
Q ss_pred EEEEecchhhhHhhhcCCccChhHHhHHHHHHHh---cCCcceEeecCCCCC-CCCCCCC
Q psy13892 332 CYLWIDNQCVIHWLTGNKVLPTFVNNRVKEIKAS---VFPIVYKYIPTDSNP-ADLACRG 387 (628)
Q Consensus 332 ~~i~tDs~~~l~~l~~~~~~~~~~~~r~~~i~~~---~~~~~i~hipg~~N~-AD~lSR~ 387 (628)
+.|+|||+.++.++++.-.........+.++..+ ...+.+.|+|+..|- ||.|.|.
T Consensus 64 v~i~sDS~~vi~~~~~~~~~~~~~~~l~~~~~~l~~~f~~~~~~~v~r~~N~~Ad~LA~~ 123 (128)
T PRK13907 64 VSFRTDSQLVERAVEKEYAKNKMFAPLLEEALQYIKSFDLFFIKWIPSSQNKVADELARK 123 (128)
T ss_pred EEEEechHHHHHHHhHHHhcChhHHHHHHHHHHHHhcCCceEEEEcCchhchhHHHHHHH
Confidence 9999999999999988611111223333344333 235677999999995 9998774
No 14
>PRK07708 hypothetical protein; Validated
Probab=98.10 E-value=1.8e-05 Score=77.00 Aligned_cols=121 Identities=18% Similarity=0.213 Sum_probs=78.2
Q ss_pred eEEEeecccc------ccceeeEEEEEeecCCCeeeeEeecccccCCCCCCccchhhHHHHHHHHHHHHHHHhhccccce
Q psy13892 257 ELHAFSDACS------YSYASVVYLRSVSHSGDIRTNIVFAKSRVAPTNKPTLPRLELLGALIAYRSLKFVKNSLHINID 330 (628)
Q Consensus 257 ~l~vftDAS~------~g~Gavl~~~~~~~~g~~~~~~~~sks~~~~~~~~si~~~ELlAi~~a~~~~~~~~~~~~~~~~ 330 (628)
.+++++|+|. .|+|+|++. .+|.... .+.....+.+ ..+-++.|+.|++.|++.+..+ ++.-.
T Consensus 73 ~~~vY~DGs~~~n~g~aG~GvVI~~----~~g~~~~-~~~~~~~l~~--~~TNN~AEy~Ali~aL~~A~e~----g~~~~ 141 (219)
T PRK07708 73 EILVYFDGGFDKETKLAGLGIVIYY----KQGNKRY-RIRRNAYIEG--IYDNNEAEYAALYYAMQELEEL----GVKHE 141 (219)
T ss_pred cEEEEEeeccCCCCCCcEEEEEEEE----CCCCEEE-EEEeeccccc--cccCcHHHHHHHHHHHHHHHHc----CCCcc
Confidence 5899999976 467777763 2232211 1111112221 2477889999999999966543 33334
Q ss_pred eEEEEecchhhhHhhhcC-CccChhHHhHHHHHHHhcC----CcceEeecCCCCC-CCCCCCCC
Q psy13892 331 KCYLWIDNQCVIHWLTGN-KVLPTFVNNRVKEIKASVF----PIVYKYIPTDSNP-ADLACRGS 388 (628)
Q Consensus 331 ~~~i~tDs~~~l~~l~~~-~~~~~~~~~r~~~i~~~~~----~~~i~hipg~~N~-AD~lSR~~ 388 (628)
.+.|++||+-++.++++. +.........+.++.+... .+.+.|||-+.|- ||.|.+..
T Consensus 142 ~V~I~~DSqlVi~qi~g~wk~~~~~l~~y~~~i~~l~~~~~l~~~~~~VpR~~N~~AD~LAk~A 205 (219)
T PRK07708 142 PVTFRGDSQVVLNQLAGEWPCYDEHLNHWLDRIEQKLKQLKLTPVYEPISRKQNKEADQLATQA 205 (219)
T ss_pred eEEEEeccHHHHHHhCCCceeCChhHHHHHHHHHHHHhhCCceEEEEECCchhhhHHHHHHHHH
Confidence 589999999999999987 3334444444444443322 3677899999995 99998863
No 15
>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=98.04 E-value=8.2e-06 Score=71.91 Aligned_cols=115 Identities=15% Similarity=0.075 Sum_probs=78.3
Q ss_pred hhHHhhccccccCcCCcCeEEEEEecCCCCCCCCCCceEEEEeeccccCcCchHHHHHHHHHHHhhhcchh---hhhhhh
Q psy13892 8 GDIEKAFLNVGLNEGERDYTRILWVKDVAKPLDSDNVVVLRHTRLPFGVVSSPFLLSCVIRTHLDKYSGDY---IDQLKN 84 (628)
Q Consensus 8 ~Dl~~af~qi~l~~~d~~~~~F~~~~~~~~~~~~~~~~~y~~~rmpFGl~~aP~~~~~~i~~~l~~~~~~~---~~~i~~ 84 (628)
.|+++||=.|.. .|.+. +-+|.|...||.++.-.+..+........ ......
T Consensus 1 ~d~~~~~~~~~~--------~~~~~-----------------~GlpQG~~lSp~L~nl~l~~l~~~~~~~~~~~~~~~~~ 55 (119)
T cd01648 1 TDIKKCYDSIPQ--------YYRQK-----------------VGIPQGSPLSSLLCSLYYADLENKYLSFLDVIDKDSLL 55 (119)
T ss_pred CChHHhccchhh--------hhhhc-----------------CcccCCcchHHHHHHHHHHHHHHHHHhhcccCCCCceE
Confidence 488999988876 22222 23799999999999998887776654321 111223
Q ss_pred ceeecccccccCChHHHHHHHHhHHHHH-hhhccccccccccCccccccCCCccccccccccceeeeeec
Q psy13892 85 NIYMDNILCGVNNEEEIENFVGTARKVF-SDASLNLREWASNYPSVLIGTLSPELVNTSRVQNTLGMLWD 153 (628)
Q Consensus 85 ~~YvDDili~s~t~ee~~~~~~~v~~~l-~~~g~~l~~~~~~~~~~lg~~i~~~~~~~~~~~k~LG~~w~ 153 (628)
..|+||+++.+++.+++.+.++.+.+.+ ++.|+.+..=++.-... . .+........+||+.++
T Consensus 56 ~rYaDD~li~~~~~~~~~~~~~~l~~~l~~~~gl~iN~~Kt~~~~~----~--~~~~~~~~~~flG~~i~ 119 (119)
T cd01648 56 LRLVDDFLLITTSLDKAIKFLNLLLRGFINQYKTFVNFDKTQINFS----F--AQLDSSDLIPWCGLLIN 119 (119)
T ss_pred EEEeCcEEEEeCCHHHHHHHHHHHHHhhHHhhCeEECcccceeecc----c--cccCCCCccCceeEeeC
Confidence 5799999999999999999999999998 89999874311111100 0 01123456788888764
No 16
>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]
Probab=97.78 E-value=0.00014 Score=65.97 Aligned_cols=113 Identities=19% Similarity=0.246 Sum_probs=70.4
Q ss_pred eEEEeecccc------ccceeeEEEEEeecCCCeeeeEeecccccCCCCCCccchhhHHHHHHHHHHHHHHHhhccccce
Q psy13892 257 ELHAFSDACS------YSYASVVYLRSVSHSGDIRTNIVFAKSRVAPTNKPTLPRLELLGALIAYRSLKFVKNSLHINID 330 (628)
Q Consensus 257 ~l~vftDAS~------~g~Gavl~~~~~~~~g~~~~~~~~sks~~~~~~~~si~~~ELlAi~~a~~~~~~~~~~~~~~~~ 330 (628)
.+++|||+|. -|||+|+. ..+++.. ...+...-|-++.|++|++.|++.+.. +...
T Consensus 3 ~v~if~DGa~~gNpG~gG~g~vl~----~~~~~~~--------~s~~~~~tTNNraEl~A~i~AL~~l~~------~~~~ 64 (154)
T COG0328 3 KVEIFTDGACLGNPGPGGWGAVLR----YGDGEKE--------LSGGEGRTTNNRAELRALIEALEALKE------LGAC 64 (154)
T ss_pred ceEEEecCccCCCCCCceEEEEEE----cCCceEE--------EeeeeecccChHHHHHHHHHHHHHHHh------cCCc
Confidence 4789999974 57888877 1222220 111222456789999999999996664 3467
Q ss_pred eEEEEecchhhhHhhh----cC--CccCh----hHH--hHHHHHHHh---cCCcceEeecCCCC-C----CCCCCCC
Q psy13892 331 KCYLWIDNQCVIHWLT----GN--KVLPT----FVN--NRVKEIKAS---VFPIVYKYIPTDSN-P----ADLACRG 387 (628)
Q Consensus 331 ~~~i~tDs~~~l~~l~----~~--~~~~~----~~~--~r~~~i~~~---~~~~~i~hipg~~N-~----AD~lSR~ 387 (628)
.+.++|||+-++.-+. +. ..|.+ .+. ..+.++.+. ...+.+++|||.++ | ||.|-|.
T Consensus 65 ~v~l~tDS~yv~~~i~~w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~~~~~~v~~~WVkgH~g~~~NeraD~LA~~ 141 (154)
T COG0328 65 EVTLYTDSKYVVEGITRWIVKWKKNGWKTADKKPVKNKDLWEELDELLKRHELVFWEWVKGHAGHPENERADQLARE 141 (154)
T ss_pred eEEEEecHHHHHHHHHHHHhhccccCccccccCccccHHHHHHHHHHHhhCCeEEEEEeeCCCCChHHHHHHHHHHH
Confidence 8999999998776444 22 22321 111 122333333 33589999998876 3 5776664
No 17
>PRK00203 rnhA ribonuclease H; Reviewed
Probab=97.68 E-value=7e-05 Score=68.90 Aligned_cols=111 Identities=19% Similarity=0.256 Sum_probs=66.0
Q ss_pred eEEEeecccc------ccceeeEEEEEeecCCCeeeeEeecccccCCCCCCccchhhHHHHHHHHHHHHHHHhhccccce
Q psy13892 257 ELHAFSDACS------YSYASVVYLRSVSHSGDIRTNIVFAKSRVAPTNKPTLPRLELLGALIAYRSLKFVKNSLHINID 330 (628)
Q Consensus 257 ~l~vftDAS~------~g~Gavl~~~~~~~~g~~~~~~~~sks~~~~~~~~si~~~ELlAi~~a~~~~~~~~~~~~~~~~ 330 (628)
.+.||||+|- .|||+|+.. .++. ..+. . .....|.++.||.|++.|++.+. ...
T Consensus 3 ~v~iytDGs~~~n~~~~g~g~v~~~----~~~~---~~~~-~----~~~~~TN~~aEL~Ai~~AL~~~~--------~~~ 62 (150)
T PRK00203 3 QVEIYTDGACLGNPGPGGWGAILRY----KGHE---KELS-G----GEALTTNNRMELMAAIEALEALK--------EPC 62 (150)
T ss_pred eEEEEEEecccCCCCceEEEEEEEE----CCee---EEEe-c----CCCCCcHHHHHHHHHHHHHHHcC--------CCC
Confidence 3789999996 467776652 1221 1111 1 12245778999999999988442 135
Q ss_pred eEEEEecchhhhHhhhcC------Ccc----ChhHHhH--HHHHHHhc--CCcceEeecCCC----CC-CCCCCCC
Q psy13892 331 KCYLWIDNQCVIHWLTGN------KVL----PTFVNNR--VKEIKASV--FPIVYKYIPTDS----NP-ADLACRG 387 (628)
Q Consensus 331 ~~~i~tDs~~~l~~l~~~------~~~----~~~~~~r--~~~i~~~~--~~~~i~hipg~~----N~-AD~lSR~ 387 (628)
.+.|+|||+.++.-|+.- +.| ..-+.|+ +.+|.+.. ..+.|.||||.. |- ||.|.|.
T Consensus 63 ~v~I~tDS~yvi~~i~~w~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~~~~~v~~~wV~~H~~~~~N~~AD~lA~~ 138 (150)
T PRK00203 63 EVTLYTDSQYVRQGITEWIHGWKKNGWKTADKKPVKNVDLWQRLDAALKRHQIKWHWVKGHAGHPENERCDELARA 138 (150)
T ss_pred eEEEEECHHHHHHHHHHHHHHHHHcCCcccCCCccccHHHHHHHHHHhccCceEEEEecCCCCCHHHHHHHHHHHH
Confidence 689999998776544320 111 1123322 23333332 258999999888 43 7877764
No 18
>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=97.65 E-value=5.9e-05 Score=74.08 Aligned_cols=95 Identities=17% Similarity=0.185 Sum_probs=73.4
Q ss_pred cceEeehhHHhhccccccCcCCcCeEEEEEecCCCCCCCCCCceEEEEeeccccCcCchHHHHHHHHHHHhhhcch----
Q psy13892 2 YRCALIGDIEKAFLNVGLNEGERDYTRILWVKDVAKPLDSDNVVVLRHTRLPFGVVSSPFLLSCVIRTHLDKYSGD---- 77 (628)
Q Consensus 2 ~~~~~~~Dl~~af~qi~l~~~d~~~~~F~~~~~~~~~~~~~~~~~y~~~rmpFGl~~aP~~~~~~i~~~l~~~~~~---- 77 (628)
..+++.+|+++||..|.-+.= .+-..+|.|...||.+|..+++.+...+...
T Consensus 81 ~~~~l~~Di~~aFdsi~~~~l------------------------~~~lGipQG~~lSp~l~~l~~~~l~~~~~~~~~~~ 136 (220)
T cd01650 81 SLVLVFLDFEKAFDSVDHEFL------------------------LKALGVRQGDPLSPLLFNLALDDLLRLLNKEEEIK 136 (220)
T ss_pred ceEEEEEEHHhhcCcCCHHHH------------------------HHHhCCccCCcccHHHHHHHHHHHHHHHHhhcccc
Confidence 358999999999988853321 1111789999999999999998887766421
Q ss_pred -hhhhhhhceeecccccccCChH-HHHHHHHhHHHHHhhhccccc
Q psy13892 78 -YIDQLKNNIYMDNILCGVNNEE-EIENFVGTARKVFSDASLNLR 120 (628)
Q Consensus 78 -~~~~i~~~~YvDDili~s~t~e-e~~~~~~~v~~~l~~~g~~l~ 120 (628)
....+....|+||+++.+.+.+ ++...++.+.+.+.+.|+.+.
T Consensus 137 ~~~~~~~~~~yaDD~~i~~~~~~~~~~~~~~~~~~~~~~~gl~in 181 (220)
T cd01650 137 LGGPGITHLAYADDIVLFSEGKSRKLQELLQRLQEWSKESGLKIN 181 (220)
T ss_pred CCCCccceEEeccceeeeccCCHHHHHHHHHHHHHHHHHcCCEEC
Confidence 0123444789999999999988 899999999999999999873
No 19
>PRK07238 bifunctional RNase H/acid phosphatase; Provisional
Probab=97.63 E-value=0.00013 Score=77.81 Aligned_cols=116 Identities=16% Similarity=0.218 Sum_probs=75.1
Q ss_pred eEEEeeccccc------cceeeEEEEEeecCCCeeeeEeecccccCCCCCCccchhhHHHHHHHHHHHHHHHhhccccce
Q psy13892 257 ELHAFSDACSY------SYASVVYLRSVSHSGDIRTNIVFAKSRVAPTNKPTLPRLELLGALIAYRSLKFVKNSLHINID 330 (628)
Q Consensus 257 ~l~vftDAS~~------g~Gavl~~~~~~~~g~~~~~~~~sks~~~~~~~~si~~~ELlAi~~a~~~~~~~~~~~~~~~~ 330 (628)
.++|++|+|.. |+|+++. +.+|.. .+........ ..|-+..|+.|++.|++.+..+ .+.
T Consensus 2 ~~~i~~DGa~~~n~g~aG~G~vi~----~~~~~~--~~~~~~~~~~---~~tnn~AE~~All~gL~~a~~~------g~~ 66 (372)
T PRK07238 2 KVVVEADGGSRGNPGPAGYGAVVW----DADRGE--VLAERAEAIG---RATNNVAEYRGLIAGLEAAAEL------GAT 66 (372)
T ss_pred eEEEEecCCCCCCCCceEEEEEEE----eCCCCc--EEEEeecccC---CCCchHHHHHHHHHHHHHHHhC------CCC
Confidence 47899999865 6666655 233311 1111111122 4566789999999999966643 356
Q ss_pred eEEEEecchhhhHhhhcC-CccChhHHhHHHHHHH---hcCCcceEeecCCCCC-CCCCCCC
Q psy13892 331 KCYLWIDNQCVIHWLTGN-KVLPTFVNNRVKEIKA---SVFPIVYKYIPTDSNP-ADLACRG 387 (628)
Q Consensus 331 ~~~i~tDs~~~l~~l~~~-~~~~~~~~~r~~~i~~---~~~~~~i~hipg~~N~-AD~lSR~ 387 (628)
++.|++||+.++..+++. +....-+..-+.++++ ....+.|.|+|.+.|- ||.|.+.
T Consensus 67 ~v~i~~DS~lvi~~i~~~~~~~~~~l~~~~~~i~~l~~~f~~~~i~~v~r~~N~~AD~LA~~ 128 (372)
T PRK07238 67 EVEVRMDSKLVVEQMSGRWKVKHPDMKPLAAQARELASQFGRVTYTWIPRARNAHADRLANE 128 (372)
T ss_pred eEEEEeCcHHHHHHhCCCCccCChHHHHHHHHHHHHHhcCCceEEEECCchhhhHHHHHHHH
Confidence 899999999999998875 2122222222233333 3346899999999995 9999886
No 20
>PRK08719 ribonuclease H; Reviewed
Probab=97.54 E-value=0.00016 Score=66.03 Aligned_cols=111 Identities=18% Similarity=0.174 Sum_probs=63.9
Q ss_pred eEEEeeccccc---------cceeeEEEEEeecCCCeeeeEeecccccCCCCCCccchhhHHHHHHHHHHHHHHHhhccc
Q psy13892 257 ELHAFSDACSY---------SYASVVYLRSVSHSGDIRTNIVFAKSRVAPTNKPTLPRLELLGALIAYRSLKFVKNSLHI 327 (628)
Q Consensus 257 ~l~vftDAS~~---------g~Gavl~~~~~~~~g~~~~~~~~sks~~~~~~~~si~~~ELlAi~~a~~~~~~~~~~~~~ 327 (628)
.+++|||+|.. |||++++. .+|... .-.+.. +. ...|-++.||.|++.|++.+..
T Consensus 4 ~~~iYtDGs~~~n~~~~~~~G~G~vv~~----~~~~~~--~~~~~~-~~--~~~Tnn~aEl~A~~~aL~~~~~------- 67 (147)
T PRK08719 4 SYSIYIDGAAPNNQHGCVRGGIGLVVYD----EAGEIV--DEQSIT-VN--RYTDNAELELLALIEALEYARD------- 67 (147)
T ss_pred eEEEEEecccCCCCCCCCCcEEEEEEEe----CCCCee--EEEEec-CC--CCccHHHHHHHHHHHHHHHcCC-------
Confidence 58899998872 77777662 233211 001111 11 1247889999999999985431
Q ss_pred cceeEEEEecchhhhHhhh--------cC-C-ccChhHHhH--HHHHHHhc--CCcceEeecCCC----CC-CCCCCC
Q psy13892 328 NIDKCYLWIDNQCVIHWLT--------GN-K-VLPTFVNNR--VKEIKASV--FPIVYKYIPTDS----NP-ADLACR 386 (628)
Q Consensus 328 ~~~~~~i~tDs~~~l~~l~--------~~-~-~~~~~~~~r--~~~i~~~~--~~~~i~hipg~~----N~-AD~lSR 386 (628)
..+|+|||+-++.-++ +. + .-...+.|+ +..|.++. ..+.|.||||.. |- ||.|-|
T Consensus 68 ---~~~i~tDS~yvi~~i~~~~~~W~~~~w~~s~g~~v~n~dl~~~i~~l~~~~~i~~~~VkgH~g~~~Ne~aD~lA~ 142 (147)
T PRK08719 68 ---GDVIYSDSDYCVRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDELRARKYVEVEKVTAHSGIEGNEAADMLAQ 142 (147)
T ss_pred ---CCEEEechHHHHHHHHHHHHHHHhCCcccCCCcccccHHHHHHHHHHhCCCcEEEEEecCCCCChhHHHHHHHHH
Confidence 2379999987776553 22 1 111223221 12233222 258999999955 53 776544
No 21
>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B.
Probab=97.53 E-value=3.3e-05 Score=63.66 Aligned_cols=77 Identities=21% Similarity=0.231 Sum_probs=54.8
Q ss_pred hhhHHHHHHHHHHHHHHHhhccccceeEEEEecchhhhHhhhcCCccChhHHhHHHHHHHhc---CCcceEeecCCCCC-
Q psy13892 305 RLELLGALIAYRSLKFVKNSLHINIDKCYLWIDNQCVIHWLTGNKVLPTFVNNRVKEIKASV---FPIVYKYIPTDSNP- 380 (628)
Q Consensus 305 ~~ELlAi~~a~~~~~~~~~~~~~~~~~~~i~tDs~~~l~~l~~~~~~~~~~~~r~~~i~~~~---~~~~i~hipg~~N~- 380 (628)
..|++|+..|++.+.. ....++.+.|||..++..+++...........+..|+... ..+.+.|+|.+.|.
T Consensus 3 ~aE~~al~~al~~a~~------~g~~~i~v~sDs~~vv~~i~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~r~~N~~ 76 (87)
T PF13456_consen 3 EAEALALLEALQLAWE------LGIRKIIVESDSQLVVDAINGRSSSRSELRPLIQDIRSLLDRFWNVSVSHIPREQNKV 76 (87)
T ss_dssp HHHHHHHHHHHHHHHC------CT-SCEEEEES-HHHHHHHTTSS---SCCHHHHHHHHHHHCCCSCEEEEE--GGGSHH
T ss_pred HHHHHHHHHHHHHHHH------CCCCEEEEEecCccccccccccccccccccccchhhhhhhccccceEEEEEChHHhHH
Confidence 5799999999996653 3467999999999999999988323225555566666554 36899999999995
Q ss_pred CCCCCCC
Q psy13892 381 ADLACRG 387 (628)
Q Consensus 381 AD~lSR~ 387 (628)
||.|.|.
T Consensus 77 A~~LA~~ 83 (87)
T PF13456_consen 77 ADALAKF 83 (87)
T ss_dssp HHHHHHH
T ss_pred HHHHHHH
Confidence 9988763
No 22
>PRK06548 ribonuclease H; Provisional
Probab=97.50 E-value=0.00025 Score=65.51 Aligned_cols=110 Identities=22% Similarity=0.136 Sum_probs=66.1
Q ss_pred eeEEEeeccccc------cceeeEEEEEeecCCCeeeeEeecccccCCCCCCccchhhHHHHHHHHHHHHHHHhhccccc
Q psy13892 256 YELHAFSDACSY------SYASVVYLRSVSHSGDIRTNIVFAKSRVAPTNKPTLPRLELLGALIAYRSLKFVKNSLHINI 329 (628)
Q Consensus 256 ~~l~vftDAS~~------g~Gavl~~~~~~~~g~~~~~~~~sks~~~~~~~~si~~~ELlAi~~a~~~~~~~~~~~~~~~ 329 (628)
..++||||+|.. |||+++. .++ ....+...-|-++.||+|++.|++... ...
T Consensus 4 ~~~~IytDGa~~gnpg~~G~g~~~~-----~~~----------~~~g~~~~~TNnraEl~Aii~aL~~~~-------~~~ 61 (161)
T PRK06548 4 NEIIAATDGSSLANPGPSGWAWYVD-----ENT----------WDSGGWDIATNNIAELTAVRELLIATR-------HTD 61 (161)
T ss_pred CEEEEEEeeccCCCCCceEEEEEEe-----CCc----------EEccCCCCCCHHHHHHHHHHHHHHhhh-------cCC
Confidence 358999998765 3444432 111 011222345778999999998876321 123
Q ss_pred eeEEEEecchhhhHhhhc--------C--CccChhHHhH--HHHHHHhc--CCcceEeecCCC----CC-CCCCCCC
Q psy13892 330 DKCYLWIDNQCVIHWLTG--------N--KVLPTFVNNR--VKEIKASV--FPIVYKYIPTDS----NP-ADLACRG 387 (628)
Q Consensus 330 ~~~~i~tDs~~~l~~l~~--------~--~~~~~~~~~r--~~~i~~~~--~~~~i~hipg~~----N~-AD~lSR~ 387 (628)
.++.|+|||+.++.-++. . +.-..-|+|+ +.+|.+.. ..+.|.||+|.. |- ||.|-|.
T Consensus 62 ~~v~I~TDS~yvi~~i~~W~~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~~~v~~~wVkgHsg~~gNe~aD~LA~~ 138 (161)
T PRK06548 62 RPILILSDSKYVINSLTKWVYSWKMRKWRKADGKPVLNQEIIQEIDSLMENRNIRMSWVNAHTGHPLNEAADSLARQ 138 (161)
T ss_pred ceEEEEeChHHHHHHHHHHHHHHHHCCCcccCCCccccHHHHHHHHHHHhcCceEEEEEecCCCCHHHHHHHHHHHH
Confidence 468999999998886663 2 1112234433 12222222 258999999987 53 7888775
No 23
>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=97.35 E-value=0.00036 Score=68.67 Aligned_cols=72 Identities=22% Similarity=0.315 Sum_probs=57.1
Q ss_pred EeeccccCcCchHHHHHHHHHHHhhhcchh----------hhhhhhceeecccccccCChHHHHHHHHhHHHHHhhhccc
Q psy13892 49 HTRLPFGVVSSPFLLSCVIRTHLDKYSGDY----------IDQLKNNIYMDNILCGVNNEEEIENFVGTARKVFSDASLN 118 (628)
Q Consensus 49 ~~rmpFGl~~aP~~~~~~i~~~l~~~~~~~----------~~~i~~~~YvDDili~s~t~ee~~~~~~~v~~~l~~~g~~ 118 (628)
-..+|.|...||.++.-++..+........ ...+....|+||+++.+++.+++.+..+.+.+.+++.|+.
T Consensus 124 ~~GlpqG~~lSp~L~~~~l~~ld~~l~~~~~~~~~~~~~~~~~~~~~rY~DD~~i~~~~~~~~~~~~~~i~~~~~~~gl~ 203 (226)
T cd01651 124 EKGTPQGGVISPLLANIYLHELDKFVEEKLKEYYDTSDPKFRRLRYVRYADDFVIGVRGPKEAEEIKELIREFLEELGLE 203 (226)
T ss_pred CCCcCCCccHHHHHHHHHHHHHHHHHHHhhhhcccccccccCceEEEEecCceEEecCCHHHHHHHHHHHHHHHHHcCCe
Confidence 345999999999999988877655543221 0234456799999999999999999999999999999998
Q ss_pred cc
Q psy13892 119 LR 120 (628)
Q Consensus 119 l~ 120 (628)
+.
T Consensus 204 ln 205 (226)
T cd01651 204 LN 205 (226)
T ss_pred ec
Confidence 74
No 24
>PF07727 RVT_2: Reverse transcriptase (RNA-dependent DNA polymerase); InterPro: IPR013103 A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. This entry includes reverse transcriptases not recognised by IPR000477 from INTERPRO [].
Probab=97.21 E-value=4.7e-05 Score=75.93 Aligned_cols=125 Identities=22% Similarity=0.243 Sum_probs=85.3
Q ss_pred eehhHHhhccccccCcCCcCe---EEEEEecCCCCCCCCCCceEEEEeeccccCcCchHHHHHHHHHHHhhhcch-----
Q psy13892 6 LIGDIEKAFLNVGLNEGERDY---TRILWVKDVAKPLDSDNVVVLRHTRLPFGVVSSPFLLSCVIRTHLDKYSGD----- 77 (628)
Q Consensus 6 ~~~Dl~~af~qi~l~~~d~~~---~~F~~~~~~~~~~~~~~~~~y~~~rmpFGl~~aP~~~~~~i~~~l~~~~~~----- 77 (628)
-.+|+..||++=.|+++ ..+ ..|.-. ..+..+++..+--+||+.||..+...++..|....-.
T Consensus 80 ~q~Dv~tAfL~~~l~e~-iym~~P~g~~~~--------~~~~~v~~L~kaLYGLKQa~r~W~~~l~~~L~~~GF~~~~~D 150 (246)
T PF07727_consen 80 HQMDVKTAFLNGDLDEE-IYMRQPPGFEDP--------GPPGKVCRLKKALYGLKQAPRLWYKTLDKFLKKLGFKQSKAD 150 (246)
T ss_pred ccccccceeeecccccc-hhhccccccccc--------ccccccccccccceecccccchhhhhcccccchhhhhccccc
Confidence 35799999999999875 111 122111 1134589999999999999999999999888776311
Q ss_pred ---h-----hhhhhhceeecccccccCChHHHHHHHHhHHHHHhhhccccccccccCccccccCCCccccccccccceee
Q psy13892 78 ---Y-----IDQLKNNIYMDNILCGVNNEEEIENFVGTARKVFSDASLNLREWASNYPSVLIGTLSPELVNTSRVQNTLG 149 (628)
Q Consensus 78 ---~-----~~~i~~~~YvDDili~s~t~ee~~~~~~~v~~~l~~~g~~l~~~~~~~~~~lg~~i~~~~~~~~~~~k~LG 149 (628)
| ...+...+||||+++.+++.++..+..+.+.+. |.++ - -+....+||
T Consensus 151 ~clfi~~~~~~~~ii~vYVDDili~~~~~~~i~~~~~~l~~~-----F~iK--------d-----------lG~~~~fLG 206 (246)
T PF07727_consen 151 PCLFIKKSGDGFIIILVYVDDILIAGPSEEEIEEFKKELKKK-----FEIK--------D-----------LGELKYFLG 206 (246)
T ss_pred ccccccccccccccccccccccccccccccceeccccccccc-----cccc--------c-----------ccccccccc
Confidence 1 123556889999999999987776655554333 3221 0 124567899
Q ss_pred eeeccCCCeEEEee
Q psy13892 150 MLWDTQEDTLSLKF 163 (628)
Q Consensus 150 ~~w~~~~d~~~~~~ 163 (628)
+......+.+.++.
T Consensus 207 i~i~~~~~~i~lsQ 220 (246)
T PF07727_consen 207 IEIERTKGGIFLSQ 220 (246)
T ss_pred eEEEECCCEEEEcH
Confidence 98777777776654
No 25
>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=96.97 E-value=0.0015 Score=63.88 Aligned_cols=139 Identities=18% Similarity=0.255 Sum_probs=85.4
Q ss_pred cceEeehhHHhhccccccCcCCcCeEEEEEe-cCCCCCCCCCCceEEEEeeccccCcCchHHHHHHHHHHHhhhcchh-h
Q psy13892 2 YRCALIGDIEKAFLNVGLNEGERDYTRILWV-KDVAKPLDSDNVVVLRHTRLPFGVVSSPFLLSCVIRTHLDKYSGDY-I 79 (628)
Q Consensus 2 ~~~~~~~Dl~~af~qi~l~~~d~~~~~F~~~-~~~~~~~~~~~~~~y~~~rmpFGl~~aP~~~~~~i~~~l~~~~~~~-~ 79 (628)
..|++.+|++++|.+|.-+.=-+.+...... .... . --.....+. ..+|.|...||.++.-+|..+-..+.... .
T Consensus 56 ~~~v~~~Di~~fFdsI~~~~L~~~l~~~~~~~~~~~-~-~l~~~~~~~-~GlpQG~~lSp~Lanl~l~~~d~~l~~~~~~ 132 (214)
T cd03487 56 AKYVLKLDIKDFFPSITFERVRGVFRSLGYFSPDVA-T-ILAKLCTYN-GHLPQGAPTSPALSNLVFRKLDERLSKLAKS 132 (214)
T ss_pred CCEEEEeehhhhcccCCHHHHHHHHHHcCCCCHHHH-H-HHHHHHhCC-CCcCCCCcccHHHHHHHHHHHHHHHHHHHHH
Confidence 3689999999999998764311111111000 0000 0 000000111 27999999999999988876544432211 1
Q ss_pred hhhhhceeecccccccCChH--HHHHHHHhHHHHHhhhccccccccccCccccccCCCccccccccccceeeeeeccC
Q psy13892 80 DQLKNNIYMDNILCGVNNEE--EIENFVGTARKVFSDASLNLREWASNYPSVLIGTLSPELVNTSRVQNTLGMLWDTQ 155 (628)
Q Consensus 80 ~~i~~~~YvDDili~s~t~e--e~~~~~~~v~~~l~~~g~~l~~~~~~~~~~lg~~i~~~~~~~~~~~k~LG~~w~~~ 155 (628)
..+....|+||+++.+++.+ +..+.+..+.+.|.+.|+.+.. +++.+ . .......++|+....+
T Consensus 133 ~~~~~~RYaDD~~i~~~~~~~~~~~~~~~~i~~~l~~~gL~ln~----~Kt~i---~-----~~~~~~~~~G~~i~~~ 198 (214)
T cd03487 133 NGLTYTRYADDITFSSNKKLKEALDKLLEIIRSILSEEGFKINK----SKTRI---S-----SKGSRQIVTGLVVNNG 198 (214)
T ss_pred cCCeEEEEeccEEEEccccchhHHHHHHHHHHHHHHHCCceeCC----CceEE---c-----cCCCCcEEEEEEEeCC
Confidence 12344689999999999988 8999999999999999998842 11111 0 1235678999987654
No 26
>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=96.83 E-value=0.0019 Score=59.93 Aligned_cols=73 Identities=19% Similarity=0.326 Sum_probs=58.9
Q ss_pred EEEeeccccCcCchHHHHHHHHHHHhhhcchhhhhhhhceeecccccccCChHHHHHHHHhHHHHHhhhccccc
Q psy13892 47 LRHTRLPFGVVSSPFLLSCVIRTHLDKYSGDYIDQLKNNIYMDNILCGVNNEEEIENFVGTARKVFSDASLNLR 120 (628)
Q Consensus 47 y~~~rmpFGl~~aP~~~~~~i~~~l~~~~~~~~~~i~~~~YvDDili~s~t~ee~~~~~~~v~~~l~~~g~~l~ 120 (628)
.....+|.|...||.+++.+|..+-...... ...+....|+||+++.+++.++..+.++.+.+.+.+.|+.+.
T Consensus 49 ~~~~GlpqG~~lS~~L~~~~l~~~d~~i~~~-~~~~~~~RY~DD~~i~~~~~~~~~~~~~~i~~~l~~~gL~ln 121 (158)
T cd01646 49 GQTNGLPIGPLTSRFLANIYLNDVDHELKSK-LKGVDYVRYVDDIRIFADSKEEAEEILEELKEFLAELGLSLN 121 (158)
T ss_pred CCCceEccCcchHHHHHHHHHHHHHHHHHhc-cCCceEEEecCcEEEEcCCHHHHHHHHHHHHHHHHHCCCEEC
Confidence 3456799999999999999988765444321 123444679999999999999999999999999999999884
No 27
>KOG3752|consensus
Probab=95.28 E-value=0.047 Score=56.14 Aligned_cols=115 Identities=23% Similarity=0.238 Sum_probs=69.2
Q ss_pred EEEeecccccc-------ceeeEEEEEeecCCCeeeeEeecccccCCCCCCccchhhHHHHHHHHHHHHHHHhhccccce
Q psy13892 258 LHAFSDACSYS-------YASVVYLRSVSHSGDIRTNIVFAKSRVAPTNKPTLPRLELLGALIAYRSLKFVKNSLHINID 330 (628)
Q Consensus 258 l~vftDAS~~g-------~Gavl~~~~~~~~g~~~~~~~~sks~~~~~~~~si~~~ELlAi~~a~~~~~~~~~~~~~~~~ 330 (628)
.+|+||+|..| -|..+|.. +|...-. ..++.+ -.-|-++.||.|+..|++-+... .+.
T Consensus 213 ~vvytDGS~~~ng~~~~~AGyGvywg----~~~e~N~----s~pv~~-g~qtNnrAEl~Av~~ALkka~~~------~~~ 277 (371)
T KOG3752|consen 213 QVVYTDGSSSGNGRKSSRAGYGVYWG----PGHELNV----SGPLAG-GRQTNNRAELIAAIEALKKARSK------NIN 277 (371)
T ss_pred eEEEecCccccCCCCCCcceeEEeeC----CCCcccc----cccCCC-CcccccHHHHHHHHHHHHHHHhc------CCC
Confidence 78999998776 34445532 2211100 011111 24577899999999999955432 345
Q ss_pred eEEEEecchhhhHhhhcC------Ccc-----Ch----hHH-----hHHHH-HHHh-cCCcceEeecCCCC-----CCCC
Q psy13892 331 KCYLWIDNQCVIHWLTGN------KVL-----PT----FVN-----NRVKE-IKAS-VFPIVYKYIPTDSN-----PADL 383 (628)
Q Consensus 331 ~~~i~tDs~~~l~~l~~~------~~~-----~~----~~~-----~r~~~-i~~~-~~~~~i~hipg~~N-----~AD~ 383 (628)
+++|.|||.-++.||+.= +.| +. ++. +.+.+ +++. ...+++.||+|... .||+
T Consensus 278 kv~I~TDS~~~i~~l~~wv~~~k~~~~k~~~~~~~i~~~v~n~~~~~e~~~l~q~~~~~~vq~~~V~Gh~gi~gne~Ad~ 357 (371)
T KOG3752|consen 278 KVVIRTDSEYFINSLTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNELDELEQEISNKKVQQEYVGGHSGILGNEMADA 357 (371)
T ss_pred cEEEEechHHHHHHHHHHHhhhccCccccccCCCccceeeecchHHHHHHHHHhhhccCceEEEEecCcCCcchHHHHHH
Confidence 999999999998877631 111 11 111 11222 2331 23599999999874 2899
Q ss_pred CCCC
Q psy13892 384 ACRG 387 (628)
Q Consensus 384 lSR~ 387 (628)
+.|.
T Consensus 358 lARk 361 (371)
T KOG3752|consen 358 LARK 361 (371)
T ss_pred HHhh
Confidence 9886
No 28
>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=86.09 E-value=1.1 Score=46.43 Aligned_cols=72 Identities=15% Similarity=0.020 Sum_probs=52.5
Q ss_pred EEeeccccCcCchHHHHHHHHHHHhhhcchhhhhhhhceeecccccccCChHHHHHHHHhHHHHHhhhcccccc
Q psy13892 48 RHTRLPFGVVSSPFLLSCVIRTHLDKYSGDYIDQLKNNIYMDNILCGVNNEEEIENFVGTARKVFSDASLNLRE 121 (628)
Q Consensus 48 ~~~rmpFGl~~aP~~~~~~i~~~l~~~~~~~~~~i~~~~YvDDili~s~t~ee~~~~~~~v~~~l~~~g~~l~~ 121 (628)
+=+-+|.|-..||.+.+-.|. .|...-+.-.......-|.||+++.++ .+++.+..+.+.++++..|+.+.+
T Consensus 80 r~rGtPqGgviSplLaNiyL~-~lD~~v~~~~~g~~l~RYaDD~vi~~~-~~~a~~aw~~i~~fl~~lGLelN~ 151 (346)
T cd01709 80 RKRGTPMSHALSDVFGELVLF-CLDFAVNQATDGGLLYRLHDDLWFWGQ-PETCAKAWKAIQEFAKVMGLELNK 151 (346)
T ss_pred cCCccCCCchhhHHHHHHHHH-HHHHHHHhcCCCceEEEEcCeEEEEcC-HHHHHHHHHHHHHHHHHcCceecc
Confidence 446789999999988877766 333322211123334679999999944 688888999999999999998854
No 29
>PF02022 Integrase_Zn: Integrase Zinc binding domain The structure of the N-terminal zinc binding domain.; InterPro: IPR003308 Retroviral integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains: an N-terminal zinc binding domain, a central catalytic core and a C-terminal DNA-binding domain [, ]. Often found as part of the POL polyprotein.; GO: 0008270 zinc ion binding; PDB: 1E0E_A 3F9K_F 1E27_C 1K6Y_B 1WJD_A 1WJB_A 1WJF_A 1WJE_B 3HPG_B 3HPH_C ....
Probab=71.56 E-value=2.7 Score=28.99 Aligned_cols=36 Identities=31% Similarity=0.641 Sum_probs=24.7
Q ss_pred HHHHhccCCChhHHHHHHHhhcccccchhHHHHHhccCccccc
Q psy13892 571 DVHRACFHNGASQTLATLRLDYWITQGRSAVKQILKSCVNCKR 613 (628)
Q Consensus 571 ~~H~~~gH~G~~~t~~~ir~~yww~~~~~~Vr~~v~~C~~Cqr 613 (628)
+.|+ ..|.+. ..|+.+|=+|+ ...|.+|++|..||.
T Consensus 3 e~H~-k~H~n~----~~L~~~f~ip~--~vAk~IV~~C~~Cq~ 38 (40)
T PF02022_consen 3 EEHE-KYHSNA----KALRHKFGIPR--LVAKQIVNQCPKCQQ 38 (40)
T ss_dssp HHHH-HHHH-H----HHHHHHHT--H--HHHHHHHHHSCCHHS
T ss_pred hHHH-HHccCH----HHHHHHHccCH--HHHHHHHHHCHHHhh
Confidence 4565 345554 56788899986 467999999999986
No 30
>KOG0860|consensus
Probab=65.56 E-value=2.6 Score=36.14 Aligned_cols=41 Identities=12% Similarity=0.081 Sum_probs=28.0
Q ss_pred CCCchhhHHHHHHHHhccCCChhHHHHHHHhhcccccchhH
Q psy13892 560 RRCHLTNIIVTDVHRACFHNGASQTLATLRLDYWITQGRSA 600 (628)
Q Consensus 560 ~~~~l~~lii~~~H~~~gH~G~~~t~~~ir~~yww~~~~~~ 600 (628)
++.+|..|-=+..-...+-.+..++...|+++|||.+++-.
T Consensus 55 R~ekL~~L~drad~L~~~as~F~~~A~klkrk~wWkn~Km~ 95 (116)
T KOG0860|consen 55 RGEKLDELDDRADQLQAGASQFEKTAVKLKRKMWWKNCKMR 95 (116)
T ss_pred hcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34445544333333345677889999999999999987653
No 31
>PF13976 gag_pre-integrs: GAG-pre-integrase domain
Probab=65.15 E-value=3.7 Score=31.60 Aligned_cols=43 Identities=12% Similarity=-0.008 Sum_probs=31.3
Q ss_pred HHHHHHhccCCChhHHHHHHHhhcccccchhHHHHHhccCccccccc
Q psy13892 569 VTDVHRACFHNGASQTLATLRLDYWITQGRSAVKQILKSCVNCKRFR 615 (628)
Q Consensus 569 i~~~H~~~gH~G~~~t~~~ir~~yww~~~~~~Vr~~v~~C~~Cqr~k 615 (628)
+..-|.+.||++...+...++ +.-.+++.. .-...|..|+..|
T Consensus 24 ~~lWH~RLGH~~~~~l~~l~~-~~~~~~~~~---~~~~~C~~C~~gK 66 (67)
T PF13976_consen 24 TDLWHRRLGHPSFQVLKKLSK-KGLLPGLKI---SKSSVCESCILGK 66 (67)
T ss_pred HHHHHHhcCCCCHHHHHHHhh-ccCcCCCCC---CCCccChhhhhcc
Confidence 466699999999997777666 444666653 2266899999876
No 32
>PF14948 RESP18: RESP18 domain
Probab=23.13 E-value=98 Score=26.27 Aligned_cols=36 Identities=17% Similarity=0.378 Sum_probs=30.0
Q ss_pred cccCCCchhHHHHHHHHHHHHHhcCCCCCccCChhh
Q psy13892 185 FDILGLWTPIIMSLKLLVQSAWIQKKEWDDELDSKD 220 (628)
Q Consensus 185 ~dplG~~~p~~~~~k~ll~~l~~~~~~Wd~~i~~e~ 220 (628)
....|+.+|+..++...||+|....+.|.|.|..++
T Consensus 11 ~~~~~vs~pvlQrLQ~vLqqL~~qGl~WqDDiTQ~v 46 (105)
T PF14948_consen 11 WPLYQVSPPVLQRLQVVLQQLMPQGLFWQDDITQYV 46 (105)
T ss_pred ccccccCHHHHHHHHHHHHHHHhcCCcccchHHHHH
Confidence 345688899999999999999999999998665554
No 33
>KOG1005|consensus
Probab=21.31 E-value=1.4e+02 Score=34.68 Aligned_cols=78 Identities=18% Similarity=0.231 Sum_probs=53.8
Q ss_pred EEEEeeccccCcCchHHHHHHHHHHHhhhcchhhhhh--hhceeecccccccCChHHHHHHHHhHHHHHhhhcccccccc
Q psy13892 46 VLRHTRLPFGVVSSPFLLSCVIRTHLDKYSGDYIDQL--KNNIYMDNILCGVNNEEEIENFVGTARKVFSDASLNLREWA 123 (628)
Q Consensus 46 ~y~~~rmpFGl~~aP~~~~~~i~~~l~~~~~~~~~~i--~~~~YvDDili~s~t~ee~~~~~~~v~~~l~~~g~~l~~~~ 123 (628)
.-+-.-+|.|-.-|..+..-.+..+.+.+-+...+.- ...-|+||.|+-+.+.+++...++.+.. ||+...+.
T Consensus 629 yvq~~GIpQGs~LSslLc~lyy~dle~~y~~~~~~~g~~vLlR~vDDFLfITt~~~~a~kfl~~l~~-----Gf~~yn~~ 703 (888)
T KOG1005|consen 629 YVQKKGIPQGSILSSLLCHLYYGDLEDKYFSFEKEDGSIVLLRYVDDFLFITTENDQAKKFLKLLSR-----GFNKYNFF 703 (888)
T ss_pred EEEecCccCCCchhHHHHHHHHHhHHHHHhhcccCCCcEEEEEeecceEEEecCHHHHHHHHHHHhc-----ccccccee
Confidence 3456679999988888887777777666643322221 3356999999999999999998876544 55444445
Q ss_pred ccCcc
Q psy13892 124 SNYPS 128 (628)
Q Consensus 124 ~~~~~ 128 (628)
+|+.+
T Consensus 704 tn~~K 708 (888)
T KOG1005|consen 704 TNEPK 708 (888)
T ss_pred ccCcc
Confidence 56555
No 34
>smart00111 C4 C-terminal tandem repeated domain in type 4 procollagens. Duplicated domain in C-terminus of type 4 collagens. Mutations in alpha-5 collagen IV are associated with X-linked Alport syndrome.
Probab=20.81 E-value=41 Score=29.07 Aligned_cols=14 Identities=14% Similarity=0.695 Sum_probs=12.9
Q ss_pred HHHHHhccCccccc
Q psy13892 600 AVKQILKSCVNCKR 613 (628)
Q Consensus 600 ~Vr~~v~~C~~Cqr 613 (628)
.++.+|++|.+|.+
T Consensus 100 ~~~~~ISRC~VC~~ 113 (114)
T smart00111 100 DLRPYISRCQVCEK 113 (114)
T ss_pred hhhhhccccceeec
Confidence 78999999999986
Done!