Query psy13868
Match_columns 128
No_of_seqs 114 out of 395
Neff 6.4
Searched_HMMs 46136
Date Fri Aug 16 22:27:19 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13868.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13868hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK13907 rnhA ribonuclease H; 99.5 1.5E-13 3.2E-18 97.2 10.5 80 33-115 1-84 (128)
2 PF00075 RNase_H: RNase H; In 99.5 4.2E-13 9E-18 93.9 10.0 72 32-110 2-75 (132)
3 COG0328 RnhA Ribonuclease HI [ 99.5 4.9E-13 1.1E-17 99.0 9.4 75 32-109 2-80 (154)
4 PRK08719 ribonuclease H; Revie 99.5 4.8E-13 1E-17 98.1 9.1 71 32-108 3-82 (147)
5 PRK06548 ribonuclease H; Provi 99.4 1.7E-12 3.6E-17 96.8 10.6 74 31-109 3-78 (161)
6 PRK00203 rnhA ribonuclease H; 99.4 1.7E-12 3.7E-17 94.7 9.0 73 33-110 3-79 (150)
7 cd06222 RnaseH RNase H (RNase 99.3 2.9E-11 6.2E-16 81.1 10.5 77 35-113 1-82 (130)
8 KOG3752|consensus 99.3 1.9E-11 4E-16 100.9 8.6 79 29-109 208-293 (371)
9 PRK07708 hypothetical protein; 99.3 9.3E-11 2E-15 91.2 11.5 85 30-114 70-162 (219)
10 PRK07238 bifunctional RNase H/ 99.2 1.6E-10 3.6E-15 94.8 11.5 87 33-122 2-96 (372)
11 PF13456 RVT_3: Reverse transc 98.4 1.1E-06 2.5E-11 56.7 6.0 52 70-123 1-52 (87)
12 PF05380 Peptidase_A17: Pao re 94.6 0.25 5.5E-06 36.1 7.5 67 31-99 79-159 (159)
13 PF00336 DNA_pol_viral_C: DNA 85.5 1 2.2E-05 35.4 3.3 64 29-105 90-153 (245)
14 PF05830 NodZ: Nodulation prot 56.8 51 0.0011 27.4 6.6 35 79-113 200-235 (321)
15 KOG1812|consensus 49.7 20 0.00044 30.2 3.4 37 68-106 47-83 (384)
16 PRK08298 cytidine deaminase; V 36.2 1.6E+02 0.0036 21.1 6.1 58 37-101 19-78 (136)
17 COG4631 XdhB Xanthine dehydrog 31.6 22 0.00047 32.0 0.9 24 30-53 465-492 (781)
18 COG3341 Predicted double-stran 28.0 52 0.0011 26.0 2.3 81 30-112 62-153 (225)
19 cd01285 nucleoside_deaminase N 23.8 2.3E+02 0.005 18.9 6.0 34 68-103 43-76 (109)
20 cd01467 vWA_BatA_type VWA BatA 23.6 1.2E+02 0.0025 21.5 3.4 26 77-102 88-113 (180)
21 cd01462 VWA_YIEM_type VWA YIEM 22.7 1.3E+02 0.0027 20.8 3.4 26 77-102 80-105 (152)
22 cd01454 vWA_norD_type norD typ 22.5 1.2E+02 0.0026 21.6 3.3 29 75-103 87-115 (174)
23 PF07057 TraI: DNA helicase Tr 21.7 31 0.00066 24.9 0.0 12 30-41 6-17 (126)
24 PRK10860 tRNA-specific adenosi 21.3 2.4E+02 0.0052 21.0 4.8 14 71-84 61-74 (172)
25 PF13519 VWA_2: von Willebrand 21.0 96 0.0021 21.1 2.5 28 75-102 83-110 (172)
No 1
>PRK13907 rnhA ribonuclease H; Provisional
Probab=99.52 E-value=1.5e-13 Score=97.18 Aligned_cols=80 Identities=25% Similarity=0.257 Sum_probs=63.9
Q ss_pred cEEEEeeCCccC--CCcceEEEEecCce--eEEeecCCCCcchHHHHHHHHHHHHHHHhcCCCCceEEEEeCcHHHHHHh
Q psy13868 33 AVVWYTDGSKTE--AGSGAGIHCVKPRV--NISLPLGTYTGVYQAEVLAIRNCAEENINMGLSKREIYIFSDSQAALRAI 108 (128)
Q Consensus 33 ~i~IyTDGS~~~--~~~G~gv~~~~~~~--~~~~~L~~~~sv~~AEl~AI~~AL~~~~~~~~~~~~i~I~SDS~sai~ai 108 (128)
+++||||||+.. +..|+|+++.+... ..+..+ ...+++.||+.|++.||+++.+.+..+ +.|+|||+.+++.+
T Consensus 1 ~~~iy~DGa~~~~~g~~G~G~vi~~~~~~~~~~~~~-~~~tn~~AE~~All~aL~~a~~~g~~~--v~i~sDS~~vi~~~ 77 (128)
T PRK13907 1 MIEVYIDGASKGNPGPSGAGVFIKGVQPAVQLSLPL-GTMSNHEAEYHALLAALKYCTEHNYNI--VSFRTDSQLVERAV 77 (128)
T ss_pred CEEEEEeeCCCCCCCccEEEEEEEECCeeEEEEecc-cccCCcHHHHHHHHHHHHHHHhCCCCE--EEEEechHHHHHHH
Confidence 478999999974 34999999866532 233333 357999999999999999999887654 99999999999999
Q ss_pred hCCCCCc
Q psy13868 109 GNFQTKS 115 (128)
Q Consensus 109 ~~~~~~s 115 (128)
++...++
T Consensus 78 ~~~~~~~ 84 (128)
T PRK13907 78 EKEYAKN 84 (128)
T ss_pred hHHHhcC
Confidence 9866544
No 2
>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=99.48 E-value=4.2e-13 Score=93.94 Aligned_cols=72 Identities=33% Similarity=0.436 Sum_probs=56.2
Q ss_pred CcEEEEeeCCccC--CCcceEEEEecCceeEEeecCCCCcchHHHHHHHHHHHHHHHhcCCCCceEEEEeCcHHHHHHhh
Q psy13868 32 GAVVWYTDGSKTE--AGSGAGIHCVKPRVNISLPLGTYTGVYQAEVLAIRNCAEENINMGLSKREIYIFSDSQAALRAIG 109 (128)
Q Consensus 32 ~~i~IyTDGS~~~--~~~G~gv~~~~~~~~~~~~L~~~~sv~~AEl~AI~~AL~~~~~~~~~~~~i~I~SDS~sai~ai~ 109 (128)
+.+.||||||+.. +..|+|+++... ...+..++ ..+++.|||.||..||+ +.. . +.+.|+|||+++++.|.
T Consensus 2 ~~~~iytDgS~~~~~~~~~~g~v~~~~-~~~~~~~~-~~s~~~aEl~Ai~~AL~-~~~-~---~~v~I~tDS~~v~~~l~ 74 (132)
T PF00075_consen 2 KAIIIYTDGSCRPNPGKGGAGYVVWGG-RNFSFRLG-GQSNNRAELQAIIEALK-ALE-H---RKVTIYTDSQYVLNALN 74 (132)
T ss_dssp TSEEEEEEEEECTTTTEEEEEEEEETT-EEEEEEEE-SECHHHHHHHHHHHHHH-THS-T---SEEEEEES-HHHHHHHH
T ss_pred CcEEEEEeCCccCCCCceEEEEEEECC-eEEEeccc-ccchhhhheehHHHHHH-Hhh-c---ccccccccHHHHHHHHH
Confidence 5789999999863 336777766544 46666677 88999999999999999 442 2 56999999999999888
Q ss_pred C
Q psy13868 110 N 110 (128)
Q Consensus 110 ~ 110 (128)
+
T Consensus 75 ~ 75 (132)
T PF00075_consen 75 K 75 (132)
T ss_dssp T
T ss_pred H
Confidence 7
No 3
>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]
Probab=99.46 E-value=4.9e-13 Score=99.05 Aligned_cols=75 Identities=24% Similarity=0.244 Sum_probs=61.1
Q ss_pred CcEEEEeeCCccC--CCcceEEEEecC--ceeEEeecCCCCcchHHHHHHHHHHHHHHHhcCCCCceEEEEeCcHHHHHH
Q psy13868 32 GAVVWYTDGSKTE--AGSGAGIHCVKP--RVNISLPLGTYTGVYQAEVLAIRNCAEENINMGLSKREIYIFSDSQAALRA 107 (128)
Q Consensus 32 ~~i~IyTDGS~~~--~~~G~gv~~~~~--~~~~~~~L~~~~sv~~AEl~AI~~AL~~~~~~~~~~~~i~I~SDS~sai~a 107 (128)
..+.||||||+.. |..|+|+|.... ....+..+. .+|++.||+.|++.||+++.+.+.. .|.|+|||+++++.
T Consensus 2 ~~v~if~DGa~~gNpG~gG~g~vl~~~~~~~~~s~~~~-~tTNNraEl~A~i~AL~~l~~~~~~--~v~l~tDS~yv~~~ 78 (154)
T COG0328 2 KKVEIFTDGACLGNPGPGGWGAVLRYGDGEKELSGGEG-RTTNNRAELRALIEALEALKELGAC--EVTLYTDSKYVVEG 78 (154)
T ss_pred CceEEEecCccCCCCCCceEEEEEEcCCceEEEeeeee-cccChHHHHHHHHHHHHHHHhcCCc--eEEEEecHHHHHHH
Confidence 4689999999974 338888887532 233555566 8999999999999999999886554 49999999999999
Q ss_pred hh
Q psy13868 108 IG 109 (128)
Q Consensus 108 i~ 109 (128)
|.
T Consensus 79 i~ 80 (154)
T COG0328 79 IT 80 (154)
T ss_pred HH
Confidence 98
No 4
>PRK08719 ribonuclease H; Reviewed
Probab=99.45 E-value=4.8e-13 Score=98.06 Aligned_cols=71 Identities=24% Similarity=0.353 Sum_probs=56.1
Q ss_pred CcEEEEeeCCccCCC-----cceEEEEecC--ce--eEEeecCCCCcchHHHHHHHHHHHHHHHhcCCCCceEEEEeCcH
Q psy13868 32 GAVVWYTDGSKTEAG-----SGAGIHCVKP--RV--NISLPLGTYTGVYQAEVLAIRNCAEENINMGLSKREIYIFSDSQ 102 (128)
Q Consensus 32 ~~i~IyTDGS~~~~~-----~G~gv~~~~~--~~--~~~~~L~~~~sv~~AEl~AI~~AL~~~~~~~~~~~~i~I~SDS~ 102 (128)
..++||||||+..++ .|+|+++..+ .. ..+..+....|+++|||.|+..||+.+.+. ..|+|||+
T Consensus 3 ~~~~iYtDGs~~~n~~~~~~~G~G~vv~~~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~aL~~~~~~------~~i~tDS~ 76 (147)
T PRK08719 3 ASYSIYIDGAAPNNQHGCVRGGIGLVVYDEAGEIVDEQSITVNRYTDNAELELLALIEALEYARDG------DVIYSDSD 76 (147)
T ss_pred ceEEEEEecccCCCCCCCCCcEEEEEEEeCCCCeeEEEEecCCCCccHHHHHHHHHHHHHHHcCCC------CEEEechH
Confidence 468999999997533 5889887443 22 355556667899999999999999988542 37999999
Q ss_pred HHHHHh
Q psy13868 103 AALRAI 108 (128)
Q Consensus 103 sai~ai 108 (128)
++++.|
T Consensus 77 yvi~~i 82 (147)
T PRK08719 77 YCVRGF 82 (147)
T ss_pred HHHHHH
Confidence 999999
No 5
>PRK06548 ribonuclease H; Provisional
Probab=99.43 E-value=1.7e-12 Score=96.77 Aligned_cols=74 Identities=23% Similarity=0.139 Sum_probs=56.0
Q ss_pred CCcEEEEeeCCccCC--CcceEEEEecCceeEEeecCCCCcchHHHHHHHHHHHHHHHhcCCCCceEEEEeCcHHHHHHh
Q psy13868 31 KGAVVWYTDGSKTEA--GSGAGIHCVKPRVNISLPLGTYTGVYQAEVLAIRNCAEENINMGLSKREIYIFSDSQAALRAI 108 (128)
Q Consensus 31 ~~~i~IyTDGS~~~~--~~G~gv~~~~~~~~~~~~L~~~~sv~~AEl~AI~~AL~~~~~~~~~~~~i~I~SDS~sai~ai 108 (128)
+..+.||||||+..+ ..|.|+|+.+. ...+... ...|++.|||.|++.||+.+... . ..+.|+|||++++++|
T Consensus 3 ~~~~~IytDGa~~gnpg~~G~g~~~~~~-~~~~g~~-~~~TNnraEl~Aii~aL~~~~~~-~--~~v~I~TDS~yvi~~i 77 (161)
T PRK06548 3 NNEIIAATDGSSLANPGPSGWAWYVDEN-TWDSGGW-DIATNNIAELTAVRELLIATRHT-D--RPILILSDSKYVINSL 77 (161)
T ss_pred CCEEEEEEeeccCCCCCceEEEEEEeCC-cEEccCC-CCCCHHHHHHHHHHHHHHhhhcC-C--ceEEEEeChHHHHHHH
Confidence 456999999999753 38899888643 2222222 35799999999999999866432 2 3499999999999999
Q ss_pred h
Q psy13868 109 G 109 (128)
Q Consensus 109 ~ 109 (128)
.
T Consensus 78 ~ 78 (161)
T PRK06548 78 T 78 (161)
T ss_pred H
Confidence 9
No 6
>PRK00203 rnhA ribonuclease H; Reviewed
Probab=99.40 E-value=1.7e-12 Score=94.71 Aligned_cols=73 Identities=23% Similarity=0.172 Sum_probs=56.0
Q ss_pred cEEEEeeCCccCC--CcceEEEEecCce--eEEeecCCCCcchHHHHHHHHHHHHHHHhcCCCCceEEEEeCcHHHHHHh
Q psy13868 33 AVVWYTDGSKTEA--GSGAGIHCVKPRV--NISLPLGTYTGVYQAEVLAIRNCAEENINMGLSKREIYIFSDSQAALRAI 108 (128)
Q Consensus 33 ~i~IyTDGS~~~~--~~G~gv~~~~~~~--~~~~~L~~~~sv~~AEl~AI~~AL~~~~~~~~~~~~i~I~SDS~sai~ai 108 (128)
++.||||||+..+ ..|+|+++..... ..+... ...|+++|||.|+..||+.+.+. ..+.|+|||+++++.|
T Consensus 3 ~v~iytDGs~~~n~~~~g~g~v~~~~~~~~~~~~~~-~~~TN~~aEL~Ai~~AL~~~~~~----~~v~I~tDS~yvi~~i 77 (150)
T PRK00203 3 QVEIYTDGACLGNPGPGGWGAILRYKGHEKELSGGE-ALTTNNRMELMAAIEALEALKEP----CEVTLYTDSQYVRQGI 77 (150)
T ss_pred eEEEEEEecccCCCCceEEEEEEEECCeeEEEecCC-CCCcHHHHHHHHHHHHHHHcCCC----CeEEEEECHHHHHHHH
Confidence 5899999999743 3888888753322 233333 46789999999999999988542 3599999999999999
Q ss_pred hC
Q psy13868 109 GN 110 (128)
Q Consensus 109 ~~ 110 (128)
..
T Consensus 78 ~~ 79 (150)
T PRK00203 78 TE 79 (150)
T ss_pred HH
Confidence 85
No 7
>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=99.32 E-value=2.9e-11 Score=81.12 Aligned_cols=77 Identities=31% Similarity=0.423 Sum_probs=60.0
Q ss_pred EEEeeCCccCC--CcceEEEEecCceeEE---eecCCCCcchHHHHHHHHHHHHHHHhcCCCCceEEEEeCcHHHHHHhh
Q psy13868 35 VWYTDGSKTEA--GSGAGIHCVKPRVNIS---LPLGTYTGVYQAEVLAIRNCAEENINMGLSKREIYIFSDSQAALRAIG 109 (128)
Q Consensus 35 ~IyTDGS~~~~--~~G~gv~~~~~~~~~~---~~L~~~~sv~~AEl~AI~~AL~~~~~~~~~~~~i~I~SDS~sai~ai~ 109 (128)
++|||||...+ ++|+|++..+...... .......+++.+|+.|++.||+++...+. +++.|++||+.+++.+.
T Consensus 1 ~~~~Dgs~~~~~~~~g~g~v~~~~~~~~~~~~~~~~~~~s~~~aEl~al~~al~~~~~~~~--~~i~i~~Ds~~~~~~~~ 78 (130)
T cd06222 1 VIYTDGSCRGNPGPAGAGVVLRDPGGEVLLSGGLLGGNTTNNRAELLALIEALELALELGG--KKVNIYTDSQYVINALT 78 (130)
T ss_pred CEEecccCCCCCCceEEEEEEEeCCCeEEEeccccCCCCcHHHHHHHHHHHHHHHHHhCCC--ceEEEEECHHHHHHHhh
Confidence 48999999754 5999999866432221 22225789999999999999999986554 45999999999999999
Q ss_pred CCCC
Q psy13868 110 NFQT 113 (128)
Q Consensus 110 ~~~~ 113 (128)
+...
T Consensus 79 ~~~~ 82 (130)
T cd06222 79 GWYE 82 (130)
T ss_pred cccc
Confidence 8754
No 8
>KOG3752|consensus
Probab=99.27 E-value=1.9e-11 Score=100.88 Aligned_cols=79 Identities=25% Similarity=0.320 Sum_probs=67.5
Q ss_pred ccCCcEEEEeeCCccCCC-----cceEEEEec-CceeEEeecC-CCCcchHHHHHHHHHHHHHHHhcCCCCceEEEEeCc
Q psy13868 29 LKKGAVVWYTDGSKTEAG-----SGAGIHCVK-PRVNISLPLG-TYTGVYQAEVLAIRNCAEENINMGLSKREIYIFSDS 101 (128)
Q Consensus 29 ~~~~~i~IyTDGS~~~~~-----~G~gv~~~~-~~~~~~~~L~-~~~sv~~AEl~AI~~AL~~~~~~~~~~~~i~I~SDS 101 (128)
...+...+|||||+..+| +|+|||.++ +....+.++. ...|+|.|||.||..||+-+.+....+ ++|.|||
T Consensus 208 e~~~~~vvytDGS~~~ng~~~~~AGyGvywg~~~e~N~s~pv~~g~qtNnrAEl~Av~~ALkka~~~~~~k--v~I~TDS 285 (371)
T KOG3752|consen 208 EEIEIQVVYTDGSSSGNGRKSSRAGYGVYWGPGHELNVSGPLAGGRQTNNRAELIAAIEALKKARSKNINK--VVIRTDS 285 (371)
T ss_pred ccccceEEEecCccccCCCCCCcceeEEeeCCCCcccccccCCCCcccccHHHHHHHHHHHHHHHhcCCCc--EEEEech
Confidence 345669999999998633 999999954 4577788886 789999999999999999998876655 9999999
Q ss_pred HHHHHHhh
Q psy13868 102 QAALRAIG 109 (128)
Q Consensus 102 ~sai~ai~ 109 (128)
+.++++|+
T Consensus 286 ~~~i~~l~ 293 (371)
T KOG3752|consen 286 EYFINSLT 293 (371)
T ss_pred HHHHHHHH
Confidence 99999997
No 9
>PRK07708 hypothetical protein; Validated
Probab=99.26 E-value=9.3e-11 Score=91.18 Aligned_cols=85 Identities=18% Similarity=0.148 Sum_probs=67.2
Q ss_pred cCCcEEEEeeCCcc--CCCcceEEEEecCc--ee----EEeecCCCCcchHHHHHHHHHHHHHHHhcCCCCceEEEEeCc
Q psy13868 30 KKGAVVWYTDGSKT--EAGSGAGIHCVKPR--VN----ISLPLGTYTGVYQAEVLAIRNCAEENINMGLSKREIYIFSDS 101 (128)
Q Consensus 30 ~~~~i~IyTDGS~~--~~~~G~gv~~~~~~--~~----~~~~L~~~~sv~~AEl~AI~~AL~~~~~~~~~~~~i~I~SDS 101 (128)
.++.+.+|+|||.. ++++|+|+++..+. .. ....++...|++.||+.|++.||+.+.+.+.....|.|++||
T Consensus 70 ep~~~~vY~DGs~~~n~g~aG~GvVI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~Ali~aL~~A~e~g~~~~~V~I~~DS 149 (219)
T PRK07708 70 EPHEILVYFDGGFDKETKLAGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQELEELGVKHEPVTFRGDS 149 (219)
T ss_pred CCCcEEEEEeeccCCCCCCcEEEEEEEECCCCEEEEEEeeccccccccCcHHHHHHHHHHHHHHHHcCCCcceEEEEecc
Confidence 35679999999985 34589999885432 22 223566678999999999999999999987655568999999
Q ss_pred HHHHHHhhCCCCC
Q psy13868 102 QAALRAIGNFQTK 114 (128)
Q Consensus 102 ~sai~ai~~~~~~ 114 (128)
+.+++.+......
T Consensus 150 qlVi~qi~g~wk~ 162 (219)
T PRK07708 150 QVVLNQLAGEWPC 162 (219)
T ss_pred HHHHHHhCCCcee
Confidence 9999999987644
No 10
>PRK07238 bifunctional RNase H/acid phosphatase; Provisional
Probab=99.21 E-value=1.6e-10 Score=94.84 Aligned_cols=87 Identities=17% Similarity=0.125 Sum_probs=66.9
Q ss_pred cEEEEeeCCccCC--CcceEEEEecCc-----eeEEeecCCCCcchHHHHHHHHHHHHHHHhcCCCCceEEEEeCcHHHH
Q psy13868 33 AVVWYTDGSKTEA--GSGAGIHCVKPR-----VNISLPLGTYTGVYQAEVLAIRNCAEENINMGLSKREIYIFSDSQAAL 105 (128)
Q Consensus 33 ~i~IyTDGS~~~~--~~G~gv~~~~~~-----~~~~~~L~~~~sv~~AEl~AI~~AL~~~~~~~~~~~~i~I~SDS~sai 105 (128)
.+.||||||+..+ ..|+|+++.++. ...+..++ ..|++.||+.|++.||+++.+.+.. .+.|++||+.++
T Consensus 2 ~~~i~~DGa~~~n~g~aG~G~vi~~~~~~~~~~~~~~~~~-~~tnn~AE~~All~gL~~a~~~g~~--~v~i~~DS~lvi 78 (372)
T PRK07238 2 KVVVEADGGSRGNPGPAGYGAVVWDADRGEVLAERAEAIG-RATNNVAEYRGLIAGLEAAAELGAT--EVEVRMDSKLVV 78 (372)
T ss_pred eEEEEecCCCCCCCCceEEEEEEEeCCCCcEEEEeecccC-CCCchHHHHHHHHHHHHHHHhCCCC--eEEEEeCcHHHH
Confidence 4789999999853 489999987642 12344455 6788999999999999999887765 499999999999
Q ss_pred HHhhCCCC-CchhhHHHH
Q psy13868 106 RAIGNFQT-KSKITWEST 122 (128)
Q Consensus 106 ~ai~~~~~-~s~~~~~~~ 122 (128)
+.+.+... +++--+.+.
T Consensus 79 ~~i~~~~~~~~~~l~~~~ 96 (372)
T PRK07238 79 EQMSGRWKVKHPDMKPLA 96 (372)
T ss_pred HHhCCCCccCChHHHHHH
Confidence 99998764 444334433
No 11
>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B.
Probab=98.38 E-value=1.1e-06 Score=56.71 Aligned_cols=52 Identities=27% Similarity=0.261 Sum_probs=38.7
Q ss_pred chHHHHHHHHHHHHHHHhcCCCCceEEEEeCcHHHHHHhhCCCCCchhhHHHHH
Q psy13868 70 VYQAEVLAIRNCAEENINMGLSKREIYIFSDSQAALRAIGNFQTKSKITWESTQ 123 (128)
Q Consensus 70 v~~AEl~AI~~AL~~~~~~~~~~~~i~I~SDS~sai~ai~~~~~~s~~~~~~~~ 123 (128)
+..||+.|++.||+++.+.+..+ +.|+|||+.+++.|++..........+.+
T Consensus 1 ~~~aE~~al~~al~~a~~~g~~~--i~v~sDs~~vv~~i~~~~~~~~~~~~~~~ 52 (87)
T PF13456_consen 1 PLEAEALALLEALQLAWELGIRK--IIVESDSQLVVDAINGRSSSRSELRPLIQ 52 (87)
T ss_dssp HHHHHHHHHHHHHHHHHCCT-SC--EEEEES-HHHHHHHTTSS---SCCHHHHH
T ss_pred CcHHHHHHHHHHHHHHHHCCCCE--EEEEecCccccccccccccccccccccch
Confidence 36899999999999999888765 99999999999999998544333333333
No 12
>PF05380 Peptidase_A17: Pao retrotransposon peptidase ; InterPro: IPR008042 This signature identifies members of the Pao retrotransposon family.
Probab=94.56 E-value=0.25 Score=36.15 Aligned_cols=67 Identities=12% Similarity=0.117 Sum_probs=42.7
Q ss_pred CCcEEEEeeCCccCCCcceEEEEecC---ceeE-----EeecC--CCCcchHHHHHHHHHHHHHHHh----cCCCCceEE
Q psy13868 31 KGAVVWYTDGSKTEAGSGAGIHCVKP---RVNI-----SLPLG--TYTGVYQAEVLAIRNCAEENIN----MGLSKREIY 96 (128)
Q Consensus 31 ~~~i~IyTDGS~~~~~~G~gv~~~~~---~~~~-----~~~L~--~~~sv~~AEl~AI~~AL~~~~~----~~~~~~~i~ 96 (128)
...+++|+|+|. .+.|+.+|.... .... +.++. ...||=+-||+|+..|.+++.. .......++
T Consensus 79 ~~~L~~F~DAS~--~aygavvYlr~~~~~~~~~~ll~aKsrv~P~k~~tIPRlEL~a~~l~~~l~~~~~~~l~~~~~~~~ 156 (159)
T PF05380_consen 79 SVELHVFCDASE--SAYGAVVYLRSYSDGSVQVRLLFAKSRVAPLKTVTIPRLELLAALLGVRLANTVKKELDIEISQVV 156 (159)
T ss_pred ceeeeEeecccc--cceeeEeEeeeccCCceeeeeeeecccccCCCCCcHHHHHHHHHHHHHHHHHHHHHHcCCCcceeE
Confidence 457999999994 567777776431 1111 11222 2459999999999999999742 233334455
Q ss_pred EEe
Q psy13868 97 IFS 99 (128)
Q Consensus 97 I~S 99 (128)
++|
T Consensus 157 ~wt 159 (159)
T PF05380_consen 157 FWT 159 (159)
T ss_pred EeC
Confidence 543
No 13
>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=85.51 E-value=1 Score=35.40 Aligned_cols=64 Identities=20% Similarity=0.191 Sum_probs=39.9
Q ss_pred ccCCcEEEEeeCCccCCCcceEEEEecCceeEEeecCCCCcchHHHHHHHHHHHHHHHhcCCCCceEEEEeCcHHHH
Q psy13868 29 LKKGAVVWYTDGSKTEAGSGAGIHCVKPRVNISLPLGTYTGVYQAEVLAIRNCAEENINMGLSKREIYIFSDSQAAL 105 (128)
Q Consensus 29 ~~~~~i~IyTDGS~~~~~~G~gv~~~~~~~~~~~~L~~~~sv~~AEl~AI~~AL~~~~~~~~~~~~i~I~SDS~sai 105 (128)
....--+||+|+.-. |.|+.+........+.. .-.|++|||+|...|.-+... + .|.|||..++
T Consensus 90 qr~~lc~VfaDATpT----gwgi~i~~~~~~~Tfs~--~l~IhtaELlaaClAr~~~~~----r---~l~tDnt~Vl 153 (245)
T PF00336_consen 90 QRPGLCQVFADATPT----GWGISITGQRMRGTFSK--PLPIHTAELLAACLARLMSGA----R---CLGTDNTVVL 153 (245)
T ss_pred CCCCCCceeccCCCC----cceeeecCceeeeeecc--cccchHHHHHHHHHHHhccCC----c---EEeecCcEEE
Confidence 345667899998654 44444544333333322 346899999999777665521 2 4888987664
No 14
>PF05830 NodZ: Nodulation protein Z (NodZ); InterPro: IPR008716 The nodulation genes of Rhizobia are regulated by the nodD gene product in response to host-produced flavonoids and appear to encode enzymes involved in the production of a lipo-chitose signal molecule required for infection and nodule formation. NodZ is required for the addition of a 2-O-methylfucose residue to the terminal reducing N-acetylglucosamine of the nodulation signal. This substitution is essential for the biological activity of this molecule. Mutations in nodZ result in defective nodulation. nodZ represents a unique nodulation gene that is not under the control of NodD and yet is essential for the synthesis of an active nodulation signal [].; GO: 0016758 transferase activity, transferring hexosyl groups, 0009312 oligosaccharide biosynthetic process, 0009877 nodulation; PDB: 3SIX_A 2HLH_A 2HHC_A 3SIW_A 2OCX_A.
Probab=56.77 E-value=51 Score=27.39 Aligned_cols=35 Identities=9% Similarity=0.129 Sum_probs=21.9
Q ss_pred HHHHHHHHhcC-CCCceEEEEeCcHHHHHHhhCCCC
Q psy13868 79 RNCAEENINMG-LSKREIYIFSDSQAALRAIGNFQT 113 (128)
Q Consensus 79 ~~AL~~~~~~~-~~~~~i~I~SDS~sai~ai~~~~~ 113 (128)
..+++-++... ..+..|.++|||+.++..++....
T Consensus 200 ~~ai~~ak~~~~~k~~~IFLATDSaeVid~fr~~FP 235 (321)
T PF05830_consen 200 CTAIDKAKALAPPKPVRIFLATDSAEVIDQFRKKFP 235 (321)
T ss_dssp HHHHHHHHTS--SS-EEEEEEES-HHHHHHHHHHST
T ss_pred HHHHHHHHhccCCCCeeEEEecCcHHHHHHHHHHCC
Confidence 34555444432 223469999999999999887654
No 15
>KOG1812|consensus
Probab=49.66 E-value=20 Score=30.17 Aligned_cols=37 Identities=24% Similarity=0.478 Sum_probs=30.6
Q ss_pred CcchHHHHHHHHHHHHHHHhcCCCCceEEEEeCcHHHHH
Q psy13868 68 TGVYQAEVLAIRNCAEENINMGLSKREIYIFSDSQAALR 106 (128)
Q Consensus 68 ~sv~~AEl~AI~~AL~~~~~~~~~~~~i~I~SDS~sai~ 106 (128)
.+...||++|+..+|..+.+.+... +.+++|+..-..
T Consensus 47 ~~~~~ae~~al~~~l~ea~~~~~~~--~~~~~d~~~~~~ 83 (384)
T KOG1812|consen 47 ITPLEAELMALKRGLTEALELGLNH--IVIYCDDELIYE 83 (384)
T ss_pred cchhhHHHHHHhhccHHHHhhcccc--ceEecccHHHHH
Confidence 6678899999999999999988776 999999544433
No 16
>PRK08298 cytidine deaminase; Validated
Probab=36.19 E-value=1.6e+02 Score=21.13 Aligned_cols=58 Identities=16% Similarity=0.139 Sum_probs=34.6
Q ss_pred EeeCCccCCCcceEEEEecCceeEEeecC--CCCcchHHHHHHHHHHHHHHHhcCCCCceEEEEeCc
Q psy13868 37 YTDGSKTEAGSGAGIHCVKPRVNISLPLG--TYTGVYQAEVLAIRNCAEENINMGLSKREIYIFSDS 101 (128)
Q Consensus 37 yTDGS~~~~~~G~gv~~~~~~~~~~~~L~--~~~sv~~AEl~AI~~AL~~~~~~~~~~~~i~I~SDS 101 (128)
|...| ++|+++...+.++..-..+. .+..=.-||..||..|+.. .....+.|.|.+|.
T Consensus 19 Y~PYS----~VgAAllt~dG~i~tG~NvEnas~~~t~CAEr~Ai~~av~~---G~~~~~~i~v~~~~ 78 (136)
T PRK08298 19 YPNGW----GGAAAMRVEDGTILTSVAPEVINASTELCMETGAICEAHKL---QKRVTHSICVAREN 78 (136)
T ss_pred cCCCC----ceeEEEEeCCCCEEEEEeecCCCCCcchhHHHHHHHHHHHC---CCceEEEEEEEcCC
Confidence 55555 79999988765544333331 1222357999999988743 11223457777765
No 17
>COG4631 XdhB Xanthine dehydrogenase, molybdopterin-binding subunit B [Nucleotide transport and metabolism]
Probab=31.64 E-value=22 Score=32.04 Aligned_cols=24 Identities=38% Similarity=0.518 Sum_probs=17.5
Q ss_pred cCCcEEEEeeCCcc--CCC--cceEEEE
Q psy13868 30 KKGAVVWYTDGSKT--EAG--SGAGIHC 53 (128)
Q Consensus 30 ~~~~i~IyTDGS~~--~~~--~G~gv~~ 53 (128)
...-++||||||.. .|| +|=|.+-
T Consensus 465 AGALVHvY~DGSi~lNHGGTEMGQGL~t 492 (781)
T COG4631 465 AGALVHVYTDGSIHLNHGGTEMGQGLYT 492 (781)
T ss_pred CceEEEEeccCeEEEcCCCcccccchhH
Confidence 34568999999995 455 7777764
No 18
>COG3341 Predicted double-stranded RNA/RNA-DNA hybrid binding protein [General function prediction only]
Probab=27.99 E-value=52 Score=26.00 Aligned_cols=81 Identities=12% Similarity=0.063 Sum_probs=49.3
Q ss_pred cCCcEEEEeeCCccC-CC-cceEEEEecCc-----eeEEeecCCCCcchHHHHHHHHHHHHHHHhcCCCCceEEEE----
Q psy13868 30 KKGAVVWYTDGSKTE-AG-SGAGIHCVKPR-----VNISLPLGTYTGVYQAEVLAIRNCAEENINMGLSKREIYIF---- 98 (128)
Q Consensus 30 ~~~~i~IyTDGS~~~-~~-~G~gv~~~~~~-----~~~~~~L~~~~sv~~AEl~AI~~AL~~~~~~~~~~~~i~I~---- 98 (128)
+.+.+.-+.+|+-.. .+ .++=++.+... ...+...+ ..++-.+|.+|++.+|+.+...+.. +.++++
T Consensus 62 ~~e~~i~~~~G~y~~~p~t~~~k~yr~k~~~~~~~lt~~~~~~-~~~n~s~d~la~ly~~~~~~~~~nr-k~~i~y~~~~ 139 (225)
T COG3341 62 DFEYIISWAKGDYDAKPGTQEFKEYRGKCTIEYSWLTESSEFS-IKSNDSGDVLAKLYGLRYEVPLDNR-KSVINYLTPG 139 (225)
T ss_pred chhccceeccCCccccCCCcceeEEeccccccceeeeeecccc-cccCchHHHHHHhccccccccccCc-cceeeccCCc
Confidence 455666677775532 22 44444443211 12222222 3466789999999999998776543 345668
Q ss_pred eCcHHHHHHhhCCC
Q psy13868 99 SDSQAALRAIGNFQ 112 (128)
Q Consensus 99 SDS~sai~ai~~~~ 112 (128)
.||++.++-...-.
T Consensus 140 ~ds~a~~k~~k~~~ 153 (225)
T COG3341 140 NDSWAYFKYVKDKC 153 (225)
T ss_pred chhHHHHHHHhhhh
Confidence 89999987766543
No 19
>cd01285 nucleoside_deaminase Nucleoside deaminases include adenosine, guanine and cytosine deaminases. These enzymes are Zn dependent and catalyze the deamination of nucleosides. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion that performs a nucleophilic attack on the substrate. The functional enzyme is a homodimer. Cytosine deaminase catalyzes the deamination of cytosine to uracil and ammonia and is a member of the pyrimidine salvage pathway. Cytosine deaminase is found in bacteria and fungi but is not present in mammals; for this reason, the enzyme is currently of interest for antimicrobial drug design and gene therapy applications against tumors. Some members of this family are tRNA-specific adenosine deaminases that generate inosine at the first position of their anticodon (position 34) of specific tRNAs; this modification is thought to enlarge the codon recognition capacity during protei
Probab=23.77 E-value=2.3e+02 Score=18.90 Aligned_cols=34 Identities=26% Similarity=0.270 Sum_probs=20.5
Q ss_pred CcchHHHHHHHHHHHHHHHhcCCCCceEEEEeCcHH
Q psy13868 68 TGVYQAEVLAIRNCAEENINMGLSKREIYIFSDSQA 103 (128)
Q Consensus 68 ~sv~~AEl~AI~~AL~~~~~~~~~~~~i~I~SDS~s 103 (128)
.....||..||..+.+........ ...+|+--..
T Consensus 43 ~~~~HAE~~ai~~~~~~~~~~~~~--~~~ly~t~EP 76 (109)
T cd01285 43 DPTAHAEIVAIRNAARRLGSYLLS--GCTLYTTLEP 76 (109)
T ss_pred CCcccHHHHHHHHHHHHhCCCccC--CeEEEEeCCC
Confidence 346679999999988764221122 2556655433
No 20
>cd01467 vWA_BatA_type VWA BatA type: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses. In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if
Probab=23.59 E-value=1.2e+02 Score=21.47 Aligned_cols=26 Identities=23% Similarity=0.247 Sum_probs=16.5
Q ss_pred HHHHHHHHHHhcCCCCceEEEEeCcH
Q psy13868 77 AIRNCAEENINMGLSKREIYIFSDSQ 102 (128)
Q Consensus 77 AI~~AL~~~~~~~~~~~~i~I~SDS~ 102 (128)
|+..|++.+.......+.++++||-.
T Consensus 88 al~~a~~~l~~~~~~~~~iiliTDG~ 113 (180)
T cd01467 88 AIGLAIKRLKNSEAKERVIVLLTDGE 113 (180)
T ss_pred HHHHHHHHHHhcCCCCCEEEEEeCCC
Confidence 45556666544333346799999975
No 21
>cd01462 VWA_YIEM_type VWA YIEM type: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if
Probab=22.70 E-value=1.3e+02 Score=20.80 Aligned_cols=26 Identities=23% Similarity=0.210 Sum_probs=15.6
Q ss_pred HHHHHHHHHHhcCCCCceEEEEeCcH
Q psy13868 77 AIRNCAEENINMGLSKREIYIFSDSQ 102 (128)
Q Consensus 77 AI~~AL~~~~~~~~~~~~i~I~SDS~ 102 (128)
|+..+++.+......+..|+|+||-.
T Consensus 80 al~~a~~~l~~~~~~~~~ivliTDG~ 105 (152)
T cd01462 80 ALRYALELIERRDPRKADIVLITDGY 105 (152)
T ss_pred HHHHHHHHHHhcCCCCceEEEECCCC
Confidence 44555555544333345799999974
No 22
>cd01454 vWA_norD_type norD type: Denitrifying bacteria contain both membrane bound and periplasmic nitrate reductases. Denitrification plays a major role in completing the nitrogen cycle by converting nitrate or nitrite to nitrogen gas. The pathway for microbial denitrification has been established as NO3- ------ NO2- ------ NO ------- N2O --------- N2. This reaction generally occurs under oxygen limiting conditions. Genetic and biochemical studies have shown that the first srep of the biochemical pathway is catalyzed by periplasmic nitrate reductases. This family is widely present in proteobacteria and firmicutes. This version of the domain is also present in some archaeal members. The function of the vWA domain in this sub-group is not known. Members of this subgroup have a conserved MIDAS motif.
Probab=22.45 E-value=1.2e+02 Score=21.61 Aligned_cols=29 Identities=24% Similarity=0.313 Sum_probs=19.7
Q ss_pred HHHHHHHHHHHHhcCCCCceEEEEeCcHH
Q psy13868 75 VLAIRNCAEENINMGLSKREIYIFSDSQA 103 (128)
Q Consensus 75 l~AI~~AL~~~~~~~~~~~~i~I~SDS~s 103 (128)
..|+..|++.+......++.++++||-..
T Consensus 87 ~~al~~a~~~l~~~~~~~~~iiliTDG~~ 115 (174)
T cd01454 87 GAAIRHAAERLLARPEKRKILLVISDGEP 115 (174)
T ss_pred HHHHHHHHHHHhcCCCcCcEEEEEeCCCc
Confidence 45666777766554444567899999865
No 23
>PF07057 TraI: DNA helicase TraI; InterPro: IPR009767 This entry represents a conserved region approximately 130 residues long within the bacterial DNA helicase TraI. TraI is a bifunctional protein that catalyses the unwinding of duplex DNA as well as acts as a sequence-specific DNA trans-esterase, providing the site- and strand-specific nick required to initiate DNA transfer [].; GO: 0003677 DNA binding, 0003678 DNA helicase activity, 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0000746 conjugation; PDB: 3FLD_B.
Probab=21.69 E-value=31 Score=24.93 Aligned_cols=12 Identities=42% Similarity=0.385 Sum_probs=0.0
Q ss_pred cCCcEEEEeeCC
Q psy13868 30 KKGAVVWYTDGS 41 (128)
Q Consensus 30 ~~~~i~IyTDGS 41 (128)
-.++++||||+=
T Consensus 6 aKeHVQvYTDn~ 17 (126)
T PF07057_consen 6 AKEHVQVYTDNL 17 (126)
T ss_dssp ------------
T ss_pred hhheeeeEeCCH
Confidence 467899999984
No 24
>PRK10860 tRNA-specific adenosine deaminase; Provisional
Probab=21.34 E-value=2.4e+02 Score=20.95 Aligned_cols=14 Identities=29% Similarity=0.366 Sum_probs=11.3
Q ss_pred hHHHHHHHHHHHHH
Q psy13868 71 YQAEVLAIRNCAEE 84 (128)
Q Consensus 71 ~~AEl~AI~~AL~~ 84 (128)
--||..||..|.+.
T Consensus 61 ~HAEi~Ai~~a~~~ 74 (172)
T PRK10860 61 AHAEIMALRQGGLV 74 (172)
T ss_pred cCHHHHHHHHHHHh
Confidence 46999999988763
No 25
>PF13519 VWA_2: von Willebrand factor type A domain; PDB: 3IBS_B 3RAG_B 2X5N_A.
Probab=21.03 E-value=96 Score=21.14 Aligned_cols=28 Identities=18% Similarity=0.235 Sum_probs=17.7
Q ss_pred HHHHHHHHHHHHhcCCCCceEEEEeCcH
Q psy13868 75 VLAIRNCAEENINMGLSKREIYIFSDSQ 102 (128)
Q Consensus 75 l~AI~~AL~~~~~~~~~~~~i~I~SDS~ 102 (128)
..|+..|++++......++.++++||-.
T Consensus 83 ~~al~~a~~~~~~~~~~~~~iv~iTDG~ 110 (172)
T PF13519_consen 83 YDALQEAAKMLASSDNRRRAIVLITDGE 110 (172)
T ss_dssp HHHHHHHHHHHHC-SSEEEEEEEEES-T
T ss_pred HHHHHHHHHHHHhCCCCceEEEEecCCC
Confidence 3566677776654433456799999965
Done!