Query psy3977
Match_columns 99
No_of_seqs 95 out of 97
Neff 4.8
Searched_HMMs 46136
Date Fri Aug 16 22:07:31 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3977.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3977hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF15228 DAP: Death-associated 100.0 2.4E-41 5.2E-46 230.8 7.1 92 8-99 1-97 (97)
2 TIGR01764 excise DNA binding d 28.8 27 0.00058 18.8 0.6 19 7-25 22-40 (49)
3 PRK10693 response regulator of 19.9 56 0.0012 25.3 1.1 15 8-22 245-259 (303)
4 PF15488 DUF4645: Domain of un 19.3 49 0.0011 26.8 0.7 21 8-28 132-152 (294)
5 PRK09417 mogA molybdenum cofac 16.1 1.3E+02 0.0028 22.5 2.3 27 58-84 74-100 (193)
6 PF15442 DUF4629: Domain of un 14.3 76 0.0017 23.5 0.6 8 70-77 138-145 (150)
7 PRK13744 conjugal transfer pro 13.9 94 0.002 20.4 0.9 17 12-28 32-48 (83)
8 PHA00692 hypothetical protein 12.5 1.1E+02 0.0024 19.7 0.9 15 11-25 37-51 (74)
9 PF14693 Ribosomal_TL5_C: Ribo 12.4 75 0.0016 20.6 0.1 19 9-27 12-30 (88)
10 PF12415 rpo132: Poxvirus DNA 9.7 1.7E+02 0.0037 16.4 1.0 14 62-75 6-19 (33)
No 1
>PF15228 DAP: Death-associated protein
Probab=100.00 E-value=2.4e-41 Score=230.78 Aligned_cols=92 Identities=51% Similarity=0.802 Sum_probs=70.0
Q ss_pred ccCCCcccccCceeeccccCCCCCCCCCCCCccccccccC--CCCCcc-ceee-cccccCCCCCChHHHHhhhcCCCCCc
Q psy3977 8 KGGHAPAVKAGGMRITQHKDPHNKSSTTSDEPTNQALKVS--TSPPKT-TAIA-GAPIRGNADYPPEAVQSFHEKPVPSV 83 (99)
Q Consensus 8 KaGHpPAvKAGGmRI~~k~~~~~~~~~~~ek~~~~~~~~s--~s~~~~-~~~i-g~~~K~~~dFP~~AvqvaH~KP~P~v 83 (99)
|||||||||||||||+||+.....+....+++.+++.|++ ++++++ .++| |+++|+|+|||++|||+||+||+|+|
T Consensus 1 KaGHpPAvKAGGmRI~qk~~~~~~e~~~~~~~~~~~~~~~~~~~~p~~~~~~isg~~~k~~~dfP~~AvqvaHqKP~P~~ 80 (97)
T PF15228_consen 1 KAGHPPAVKAGGMRIVQKKEKGTPEKERKKKDDSEEEVESISNSPPKQTSVIISGAPAKGNHDFPPEAVQVAHQKPRPAV 80 (97)
T ss_pred CCCCCcccccCCCEeeccccCCCCccccccccccccccccccccCCcccceeeccccccccccCcHHHHHHhhcCCCccc
Confidence 7999999999999999999543321111011122333333 333433 5677 99999999999999999999999999
Q ss_pred ccc-CCCCCCcccCCCC
Q psy3977 84 EKS-HHNKPNMIQQPRK 99 (99)
Q Consensus 84 ek~-~~~~~~~IqQPRK 99 (99)
++. +++++++||||||
T Consensus 81 ek~~~~~~~~~IqQPRK 97 (97)
T PF15228_consen 81 EKPPPPRRINIIQQPRK 97 (97)
T ss_pred cCcCCCCCCccccCCCC
Confidence 999 8878899999998
No 2
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=28.79 E-value=27 Score=18.82 Aligned_cols=19 Identities=21% Similarity=0.352 Sum_probs=14.4
Q ss_pred cccCCCcccccCceeeccc
Q psy3977 7 LKGGHAPAVKAGGMRITQH 25 (99)
Q Consensus 7 lKaGHpPAvKAGGmRI~~k 25 (99)
++.|..|+++.||.+...+
T Consensus 22 ~~~g~i~~~~~g~~~~~~~ 40 (49)
T TIGR01764 22 IHEGELPAYRVGRHYRIPR 40 (49)
T ss_pred HHcCCCCeEEeCCeEEEeH
Confidence 4678999999988766543
No 3
>PRK10693 response regulator of RpoS; Provisional
Probab=19.94 E-value=56 Score=25.25 Aligned_cols=15 Identities=13% Similarity=0.406 Sum_probs=11.8
Q ss_pred ccCCCcccccCceee
Q psy3977 8 KGGHAPAVKAGGMRI 22 (99)
Q Consensus 8 KaGHpPAvKAGGmRI 22 (99)
-|||||++..++-++
T Consensus 245 ~AGhp~~~~~~~~~~ 259 (303)
T PRK10693 245 SAGLNATLNTGEHQV 259 (303)
T ss_pred eCCCCCEEecCCeEE
Confidence 499999997666666
No 4
>PF15488 DUF4645: Domain of unknown function (DUF4645)
Probab=19.35 E-value=49 Score=26.78 Aligned_cols=21 Identities=29% Similarity=0.525 Sum_probs=17.5
Q ss_pred ccCCCcccccCceeeccccCC
Q psy3977 8 KGGHAPAVKAGGMRITQHKDP 28 (99)
Q Consensus 8 KaGHpPAvKAGGmRI~~k~~~ 28 (99)
.-|-|||+.+||-||..--.+
T Consensus 132 ~sG~PpalMigGtRVs~gg~e 152 (294)
T PF15488_consen 132 FSGSPPALMIGGTRVSNGGTE 152 (294)
T ss_pred cCCCCceeeeccccccCCCCc
Confidence 468899999999999876554
No 5
>PRK09417 mogA molybdenum cofactor biosynthesis protein MogA; Provisional
Probab=16.15 E-value=1.3e+02 Score=22.55 Aligned_cols=27 Identities=26% Similarity=0.401 Sum_probs=24.9
Q ss_pred cccccCCCCCChHHHHhhhcCCCCCcc
Q psy3977 58 GAPIRGNADYPPEAVQSFHEKPVPSVE 84 (99)
Q Consensus 58 g~~~K~~~dFP~~AvqvaH~KP~P~ve 84 (99)
|-..-+..||.++|+.-+=+|..|.+.
T Consensus 74 GGtg~g~rDvTpeAv~~l~~keipG~~ 100 (193)
T PRK09417 74 GGTGPARRDVTPEATLAVADKEMPGFG 100 (193)
T ss_pred CCCCCCCCCcHHHHHHHHhCCcCCcHH
Confidence 888889999999999999999999876
No 6
>PF15442 DUF4629: Domain of unknown function (DUF4629)
Probab=14.31 E-value=76 Score=23.48 Aligned_cols=8 Identities=63% Similarity=0.929 Sum_probs=6.6
Q ss_pred HHHHhhhc
Q psy3977 70 EAVQSFHE 77 (99)
Q Consensus 70 ~AvqvaH~ 77 (99)
|.|||||-
T Consensus 138 eSVQVFH~ 145 (150)
T PF15442_consen 138 ESVQVFHP 145 (150)
T ss_pred HhHHhhhh
Confidence 68999994
No 7
>PRK13744 conjugal transfer protein TrbG; Provisional
Probab=13.86 E-value=94 Score=20.41 Aligned_cols=17 Identities=41% Similarity=0.473 Sum_probs=11.8
Q ss_pred CcccccCceeeccccCC
Q psy3977 12 APAVKAGGMRITQHKDP 28 (99)
Q Consensus 12 pPAvKAGGmRI~~k~~~ 28 (99)
.|---|||.||+----.
T Consensus 32 apepdaggkrivayvyk 48 (83)
T PRK13744 32 APEPDAGGKRIVAYVYK 48 (83)
T ss_pred CCCCCCCCcEEEEEEee
Confidence 34556899999875443
No 8
>PHA00692 hypothetical protein
Probab=12.54 E-value=1.1e+02 Score=19.69 Aligned_cols=15 Identities=27% Similarity=0.631 Sum_probs=13.0
Q ss_pred CCcccccCceeeccc
Q psy3977 11 HAPAVKAGGMRITQH 25 (99)
Q Consensus 11 HpPAvKAGGmRI~~k 25 (99)
-||....||-||++-
T Consensus 37 yppgfrfggcrvskg 51 (74)
T PHA00692 37 YPPGFRFGGCRVSKG 51 (74)
T ss_pred cCCCccccceeeccc
Confidence 489999999999864
No 9
>PF14693 Ribosomal_TL5_C: Ribosomal protein TL5, C-terminal domain; PDB: 1FEU_D 2HGQ_Y 2HGJ_Y 2Y19_Z 2WRL_Z 3KIT_Z 2WH2_Z 2WDN_Z 3V25_Z 3HUZ_Z ....
Probab=12.41 E-value=75 Score=20.65 Aligned_cols=19 Identities=32% Similarity=0.574 Sum_probs=13.8
Q ss_pred cCCCcccccCceeeccccC
Q psy3977 9 GGHAPAVKAGGMRITQHKD 27 (99)
Q Consensus 9 aGHpPAvKAGGmRI~~k~~ 27 (99)
-|.++.+|.||+--...+.
T Consensus 12 ~G~~~gvk~Gg~l~~~~~~ 30 (88)
T PF14693_consen 12 VGESPGVKKGGILQQVLRE 30 (88)
T ss_dssp ESSSHHHCTTSEEEESTSE
T ss_pred EcccccCcCCcEEEEEEeE
Confidence 3679999999876555543
No 10
>PF12415 rpo132: Poxvirus DNA dependent RNA polymerase; InterPro: IPR024390 All three classes of poxvirus genes - early, intermediate and late - are transcribed by the viral RNA polymerase compex []. This complex is composed of nine distinct subunits which total more than 500kDa in mass. The two largest subunits (147 and 136kDa) are homologous to the largest subunits of eukaryotic and prokaryotic RNA polymerases and, like them, are thought to form a claw-shaped structure whose cleft is the site of template interaction and phosphodiester bond formation. While the smaller subunits of poxvirus RNA polymerase show much less similarity, if any, to the smaller subunits of the eukaryotic and prokaryotic enzymes, it is thought that they may play a similar role in interacting with transcription factors. The 132kDa subunit is the second largest subunit of the poxvirus DNA dependent RNA polymerase and shows structural similarity to the second-largest RNA polymerase subunits of eubacteria, archaebacteria, and eukaryotes.
Probab=9.74 E-value=1.7e+02 Score=16.40 Aligned_cols=14 Identities=29% Similarity=0.382 Sum_probs=10.3
Q ss_pred cCCCCCChHHHHhh
Q psy3977 62 RGNADYPPEAVQSF 75 (99)
Q Consensus 62 K~~~dFP~~Avqva 75 (99)
.+.-|||+|++-.+
T Consensus 6 ~Lsydmp~ei~ylv 19 (33)
T PF12415_consen 6 SLSYDMPPEIIYLV 19 (33)
T ss_pred hhccCCCHHHHHHH
Confidence 36789999987543
Done!