Query psy12308
Match_columns 251
No_of_seqs 36 out of 38
Neff 2.2
Searched_HMMs 46136
Date Fri Aug 16 15:43:59 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12308.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12308hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 smart00735 ZM ZASP-like motif. 98.9 4E-10 8.6E-15 70.3 1.5 26 139-164 1-26 (26)
2 PF02334 RTP: Replication term 57.7 9.9 0.00021 32.2 2.7 31 157-188 37-67 (122)
3 KOG4137|consensus 25.7 60 0.0013 26.9 2.4 70 115-195 17-91 (102)
4 PF07108 PipA: PipA protein; 24.0 36 0.00079 30.7 0.9 13 237-249 75-87 (200)
5 PF03376 Adeno_E3B: Adenovirus 23.9 26 0.00057 27.2 0.0 7 90-96 48-54 (67)
6 COG1464 NlpA ABC-type metal io 20.1 68 0.0015 30.1 1.9 44 140-187 103-152 (268)
7 PRK09861 cytoplasmic membrane 19.2 59 0.0013 29.2 1.3 41 143-186 109-154 (272)
8 KOG1648|consensus 19.1 50 0.0011 34.6 0.9 21 17-37 371-396 (813)
9 PRK11063 metQ DL-methionine tr 15.0 98 0.0021 27.7 1.6 45 140-187 105-154 (271)
10 PF00439 Bromodomain: Bromodom 12.3 1E+02 0.0022 21.7 0.7 22 163-184 63-84 (84)
No 1
>smart00735 ZM ZASP-like motif. Short motif (26 amino acids) present in an alpha-actinin-binding protein, ZASP, and similar molecules.
Probab=98.92 E-value=4e-10 Score=70.29 Aligned_cols=26 Identities=46% Similarity=0.944 Sum_probs=24.0
Q ss_pred ceeccccCCCcccccchhHHHHHhhh
Q psy12308 139 HVVNRPYNTPIGLYSEQNIVDSINHH 164 (251)
Q Consensus 139 kvVhkQfNSPIGLYSd~NIaeTl~~Q 164 (251)
++||+|||+||||||++||+|+|.+|
T Consensus 1 ~vv~~qyn~P~glys~~n~~~~l~~~ 26 (26)
T smart00735 1 RVVHKQYNSPIGLYSSENIAETLQGQ 26 (26)
T ss_pred CccccccCCCCCCCCcccHHHhhccC
Confidence 48999999999999999999999875
No 2
>PF02334 RTP: Replication terminator protein; InterPro: IPR003432 The bacterial replication terminator protein (RTP) plays a role in the termination of DNA replication by impeding replication fork movement. Two RTP dimers bind to the two inverted repeat regions at the termination site.; GO: 0003677 DNA binding, 0006274 DNA replication termination; PDB: 2DPU_A 2DPD_A 1F4K_A 1J0R_B 2EFW_F 2DQR_B 1BM9_B.
Probab=57.73 E-value=9.9 Score=32.23 Aligned_cols=31 Identities=29% Similarity=0.479 Sum_probs=22.3
Q ss_pred HHHHHhhhccCceecCCCchHHHHHHHHHHhh
Q psy12308 157 IVDSINHHYKKTVVYDPAKSETFKALQEEELV 188 (251)
Q Consensus 157 IaeTl~~Q~K~~v~YDpanSEtyRaLQEee~~ 188 (251)
+.|.|++-+|+- .|-|.-||+||+|.|-..+
T Consensus 37 ~Ld~lr~EFk~~-Gy~P~hsEvYraLHeL~~d 67 (122)
T PF02334_consen 37 LLDELRSEFKPL-GYRPNHSEVYRALHELVDD 67 (122)
T ss_dssp HHHHHHHHHTTT-T----HHHHHHHHHHHHHT
T ss_pred HHHHHHHHhhhc-CCCCCHHHHHHHHHHHHhh
Confidence 678888887654 4999999999999998874
No 3
>KOG4137|consensus
Probab=25.67 E-value=60 Score=26.94 Aligned_cols=70 Identities=20% Similarity=0.316 Sum_probs=38.1
Q ss_pred HHHHHHHHHHhhhcCCCCCCCCCcceeccccCCCccc-----ccchhHHHHHhhhccCceecCCCchHHHHHHHHHHhhC
Q psy12308 115 SYKQKVADSVLNRVIPDSQSNPNRHVVNRPYNTPIGL-----YSEQNIVDSINHHYKKTVVYDPAKSETFKALQEEELVG 189 (251)
Q Consensus 115 ~mKQKvaetvlqrVvg~~~~~g~rkvVhkQfNSPIGL-----YSd~NIaeTl~~Q~K~~v~YDpanSEtyRaLQEee~~g 189 (251)
-|||+..+..+||.+..... --+-|+|-.+ |+|-+=--+.=.-.+....| .|+|+|+.++|.- .
T Consensus 17 n~rq~~~~e~~q~l~~~k~t-------Yfsi~appSv~PakKycDvTGLpapYtdP~t~Lry--~naeiY~~i~emp--s 85 (102)
T KOG4137|consen 17 NMRQKILKELLQRLIEKKHT-------YFSIEAPPSVKPAKKYCDVTGLPAPYTDPNTGLRY--HNAEIYKLICEMP--S 85 (102)
T ss_pred cHHHHHhhhhhhhcccccCc-------eEEecCCCccccchhhccccCCcccccCCCcccee--ccHHHHHHHHHCC--c
Confidence 59999999999986654321 1122333332 33322111111112222233 5899999999955 4
Q ss_pred CCcccc
Q psy12308 190 GHVQEI 195 (251)
Q Consensus 190 ~~vQEV 195 (251)
|-+||-
T Consensus 86 d~vq~y 91 (102)
T KOG4137|consen 86 DRVQEY 91 (102)
T ss_pred hHhhhH
Confidence 667764
No 4
>PF07108 PipA: PipA protein; InterPro: IPR010777 This family consists of several Salmonella PipA (pathogenicity island-encoded protein A) and related phage sequences. PipA is thought to contribute to enteric but not to systemic salmonellosis [].
Probab=24.02 E-value=36 Score=30.75 Aligned_cols=13 Identities=46% Similarity=0.790 Sum_probs=11.0
Q ss_pred cccchHHHHHHhh
Q psy12308 237 HQSNSFKRLMHMV 249 (251)
Q Consensus 237 hQS~SFKRLM~~V 249 (251)
-||+.|+|||...
T Consensus 75 tqs~TFRRLmNyA 87 (200)
T PF07108_consen 75 TQSETFRRLMNYA 87 (200)
T ss_pred hhhHHHHHHHHHH
Confidence 5899999999754
No 5
>PF03376 Adeno_E3B: Adenovirus E3B protein; InterPro: IPR005041 Adenoviruses are medium-sized, non-enveloped viruses containing double-stranded DNA. They can cause a variety of diseases including pneumonia, cystitis, conjunctivitis and diarrhoea, all of which can be fatal to patients who are immunocompromised []. These viruses have many mechanisms to evade the host immune response, including several proteins which are expressed as part of the early transcription unit 3 (E3) []. One of the regions of E3, known as the E3B region, encodes three proteins known as 10.4K, 14.5K and 14.7K. Two of these proteins, 10.4K and 14.5K, form the RID complex (receptor internalisation and degradation) which protects the infected cell from host-induced lysis by clearing the the TNF and Fas receptors from the cell surface []. Other receptors, such as the epidermal growth factor receptor, are also known to be cleared by RID []. This entry represents the E3B region 10.4K protein, also known as the RID alpha subunit.; GO: 0016020 membrane
Probab=23.94 E-value=26 Score=27.17 Aligned_cols=7 Identities=71% Similarity=1.474 Sum_probs=5.6
Q ss_pred cccccCC
Q psy12308 90 SYLRHHP 96 (251)
Q Consensus 90 sYLrhhp 96 (251)
-|+||||
T Consensus 48 ~Y~RHhP 54 (67)
T PF03376_consen 48 AYRRHHP 54 (67)
T ss_pred HHHHcCc
Confidence 3899987
No 6
>COG1464 NlpA ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]
Probab=20.08 E-value=68 Score=30.09 Aligned_cols=44 Identities=25% Similarity=0.461 Sum_probs=28.3
Q ss_pred eeccccCCCcccccch--hHHHHHhhhccCceec---CCCc-hHHHHHHHHHHh
Q psy12308 140 VVNRPYNTPIGLYSEQ--NIVDSINHHYKKTVVY---DPAK-SETFKALQEEEL 187 (251)
Q Consensus 140 vVhkQfNSPIGLYSd~--NIaeTl~~Q~K~~v~Y---Dpan-SEtyRaLQEee~ 187 (251)
.|-.-|-.|||+||.. +|.|- .++..+- ||+| |-.|++||+.++
T Consensus 103 ~vg~~~i~Pmg~YSkk~ksl~el----~~GatIaiPNDpsN~gRAL~lL~~aGL 152 (268)
T COG1464 103 AVGNTHIEPMGLYSKKYKSLAEL----KDGATIAIPNDPTNEGRALLLLQKAGL 152 (268)
T ss_pred EEeeEEeccceecchhcCcHhhC----CCCCEEECCCCCCchhHHHHHHHHCCc
Confidence 4556788999999953 33322 3233322 7765 678999998875
No 7
>PRK09861 cytoplasmic membrane lipoprotein-28; Provisional
Probab=19.24 E-value=59 Score=29.23 Aligned_cols=41 Identities=27% Similarity=0.489 Sum_probs=25.4
Q ss_pred cccCCCcccccc--hhHHHHHhhhccCceec--CCCc-hHHHHHHHHHH
Q psy12308 143 RPYNTPIGLYSE--QNIVDSINHHYKKTVVY--DPAK-SETFKALQEEE 186 (251)
Q Consensus 143 kQfNSPIGLYSd--~NIaeTl~~Q~K~~v~Y--Dpan-SEtyRaLQEee 186 (251)
.-|-.|+|+||+ .+|+| |.. ...+.+ |+.| +..|++||+.+
T Consensus 109 ~~~~~P~~~Ys~~iksl~D-L~~--Ga~IAipnd~~n~~ral~lL~~ag 154 (272)
T PRK09861 109 NTFVFPMAGYSKKIKTVAQ-IKE--GATVAIPNDPTNLGRALLLLQKEK 154 (272)
T ss_pred EEEEEeeeccccCCCCHHH-cCC--CCEEEEeCCCccHHHHHHHHHHCC
Confidence 446789999998 45555 221 223333 6554 57788888865
No 8
>KOG1648|consensus
Probab=19.14 E-value=50 Score=34.55 Aligned_cols=21 Identities=43% Similarity=1.066 Sum_probs=17.2
Q ss_pred cCCCCCCccccccc-----cccccCC
Q psy12308 17 YGLTEPPLWSSQGR-----RLRKKTP 37 (251)
Q Consensus 17 ~~~~~~~~~~~~~~-----~~~~~~~ 37 (251)
-|.-+||||+.+|. +|||..+
T Consensus 371 ~gqLdPPLW~q~gKgKvfPkLRKRS~ 396 (813)
T KOG1648|consen 371 LGQLDPPLWVQTGKGKVFPKLRKRST 396 (813)
T ss_pred ccccCCccccccCCcccchhhhhcCc
Confidence 47789999999996 6888765
No 9
>PRK11063 metQ DL-methionine transporter substrate-binding subunit; Provisional
Probab=14.98 E-value=98 Score=27.71 Aligned_cols=45 Identities=24% Similarity=0.431 Sum_probs=26.9
Q ss_pred eeccccCCCcccccc--hhHHHHHhhhccCcee--cCCCc-hHHHHHHHHHHh
Q psy12308 140 VVNRPYNTPIGLYSE--QNIVDSINHHYKKTVV--YDPAK-SETFKALQEEEL 187 (251)
Q Consensus 140 vVhkQfNSPIGLYSd--~NIaeTl~~Q~K~~v~--YDpan-SEtyRaLQEee~ 187 (251)
++-.-|-.|+|+||+ .+|+| |.. .+.+. -|+.| +..+++||+.++
T Consensus 105 ~~~~~~vvp~~~ys~~i~si~D-L~~--Gk~IAip~d~~n~~r~L~lL~~~Gl 154 (271)
T PRK11063 105 AVGNTFVYPIAGYSKKIKSLDE-LQD--GSQVAVPNDPTNLGRSLLLLQKVGL 154 (271)
T ss_pred EEeEEEEEEeeccccCCCCHHH-hcC--CCEEEecCCCccHHHHHHHHHHCCC
Confidence 344446689999998 23333 221 23333 35655 677888888665
No 10
>PF00439 Bromodomain: Bromodomain; InterPro: IPR001487 Bromodomains are found in a variety of mammalian, invertebrate and yeast DNA-binding proteins []. Bromodomains can interact with acetylated lysine []. In some proteins, the classical bromodomain has diverged to such an extent that parts of the region are either missing or contain an insertion (e.g., mammalian protein HRX, Caenorhabditis elegans hypothetical protein ZK783.4, yeast protein YTA7). The bromodomain may occur as a single copy, or in duplicate. The precise function of the domain is unclear, but it may be involved in protein-protein interactions and may play a role in assembly or activity of multi-component complexes involved in transcriptional activation [].; GO: 0005515 protein binding; PDB: 3P1C_A 4A9K_B 3SVH_A 3P1E_B 3P1F_A 1JSP_B 2L85_A 3P1D_B 3DWY_B 2D82_A ....
Probab=12.34 E-value=1e+02 Score=21.71 Aligned_cols=22 Identities=23% Similarity=0.483 Sum_probs=18.8
Q ss_pred hhccCceecCCCchHHHHHHHH
Q psy12308 163 HHYKKTVVYDPAKSETFKALQE 184 (251)
Q Consensus 163 ~Q~K~~v~YDpanSEtyRaLQE 184 (251)
.-..|...|++.+|..+++-+|
T Consensus 63 ~i~~Na~~yn~~~s~~~~~A~~ 84 (84)
T PF00439_consen 63 LIFQNARRYNPPDSPIYKAAEK 84 (84)
T ss_dssp HHHHHHHHHSCTTSHHHHHHHH
T ss_pred HHHHHHHHHCCCcCHHHHHhcC
Confidence 3478999999999999998775
Done!