Query psy6677
Match_columns 320
No_of_seqs 1 out of 3
Neff 1.0
Searched_HMMs 46136
Date Sat Aug 17 00:16:10 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6677.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6677hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF14412 AHH: A nuclease famil 28.2 74 0.0016 23.6 3.1 41 277-317 66-107 (109)
2 PF11220 DUF3015: Protein of u 25.3 59 0.0013 27.5 2.3 25 290-314 89-114 (144)
3 COG3098 Uncharacterized protei 23.8 97 0.0021 26.1 3.3 39 275-317 68-106 (109)
4 PRK09928 choline transport pro 23.5 61 0.0013 33.2 2.5 39 281-319 264-302 (679)
5 cd07603 BAR_ACAPs The Bin/Amph 20.7 1.1E+02 0.0025 26.2 3.2 35 284-319 40-74 (200)
6 cd07604 BAR_ASAPs The Bin/Amph 19.0 1.1E+02 0.0024 26.7 2.9 36 284-319 40-76 (215)
7 PF13424 TPR_12: Tetratricopep 18.9 2.3E+02 0.0049 18.7 3.8 31 286-317 28-58 (78)
8 PF07328 VirD1: T-DNA border e 18.0 1.3E+02 0.0029 26.4 3.1 22 298-319 109-130 (147)
9 cd07602 BAR_RhoGAP_OPHN1-like 16.3 1.7E+02 0.0037 25.9 3.4 22 298-319 59-80 (207)
10 PF13512 TPR_18: Tetratricopep 16.1 2.1E+02 0.0046 24.0 3.8 39 277-316 78-127 (142)
No 1
>PF14412 AHH: A nuclease family of the HNH/ENDO VII superfamily with conserved AHH
Probab=28.15 E-value=74 Score=23.57 Aligned_cols=41 Identities=34% Similarity=0.568 Sum_probs=32.6
Q ss_pred CCCCC-cchhhhhhhhhhhhhchhhHHHHHHHHHHHHHHHHH
Q psy6677 277 PNHPD-LNIYLSIALSKFRRSTRDDRQEFGAVLQNFGAVLQN 317 (320)
Q Consensus 277 pnhpd-lniylsialskfrrstrddrqefgavlqnfgavlqn 317 (320)
-+|+. .+-|+.-.|.+..+....++++|-..|+..+.-|+|
T Consensus 66 g~H~~~Y~~~V~~~L~~~~~~~~~~~~~~~~~l~~i~~~l~~ 107 (109)
T PF14412_consen 66 GRHPNEYNKYVRERLDKIENSKKENREEFRKELQKIKNELRN 107 (109)
T ss_pred CCCcHHHHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHc
Confidence 46777 777888888888886778899999999888876654
No 2
>PF11220 DUF3015: Protein of unknown function (DUF3015); InterPro: IPR021383 This bacterial family of proteins has no known function.
Probab=25.32 E-value=59 Score=27.53 Aligned_cols=25 Identities=44% Similarity=0.761 Sum_probs=17.6
Q ss_pred hhhhhhhchhhHHHHHHHHH-HHHHH
Q psy6677 290 LSKFRRSTRDDRQEFGAVLQ-NFGAV 314 (320)
Q Consensus 290 lskfrrstrddrqefgavlq-nfgav 314 (320)
|.....-..+||.+|++++| ||+.+
T Consensus 89 la~llgv~~~d~~~f~~~~q~nF~~i 114 (144)
T PF11220_consen 89 LAELLGVPAEDRAAFGAVLQENFASI 114 (144)
T ss_pred HHHHhCCCHhhHHHHHHHHHHHHHHh
Confidence 34444455689999999987 67654
No 3
>COG3098 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.76 E-value=97 Score=26.08 Aligned_cols=39 Identities=31% Similarity=0.376 Sum_probs=33.8
Q ss_pred CCCCCCCcchhhhhhhhhhhhhchhhHHHHHHHHHHHHHHHHH
Q psy6677 275 SLPNHPDLNIYLSIALSKFRRSTRDDRQEFGAVLQNFGAVLQN 317 (320)
Q Consensus 275 slpnhpdlniylsialskfrrstrddrqefgavlqnfgavlqn 317 (320)
.|||--.+.-|+..|+..+ +++|+..-|+||.|-+++++
T Consensus 68 ~lP~~fai~PY~EeAl~~~----~~~~a~lLa~l~~ld~L~~~ 106 (109)
T COG3098 68 ALPNAFAIAPYYEEALAGD----HPQRAALLAVLQELDALFAK 106 (109)
T ss_pred CCCcchhhhHHHHHHHhcc----chHHHHHHHHHHHHHHHHcC
Confidence 5788888888999999876 57899999999999999875
No 4
>PRK09928 choline transport protein BetT; Provisional
Probab=23.48 E-value=61 Score=33.24 Aligned_cols=39 Identities=23% Similarity=0.361 Sum_probs=33.0
Q ss_pred CcchhhhhhhhhhhhhchhhHHHHHHHHHHHHHHHHHhh
Q psy6677 281 DLNIYLSIALSKFRRSTRDDRQEFGAVLQNFGAVLQNIL 319 (320)
Q Consensus 281 dlniylsialskfrrstrddrqefgavlqnfgavlqnil 319 (320)
++|+||.++|--|---.-.-.--+....||+|..+||+.
T Consensus 264 ~lN~~La~~LllfVli~GPT~fil~~~~~siG~yl~~f~ 302 (679)
T PRK09928 264 ELNVLLALGLILFVLFMGDTSFLLNALVLNVGDYVNRFM 302 (679)
T ss_pred HHHHHHHHHHHheeeeccCHHHHHHHHHHHHHHHHHHHH
Confidence 579999999988877777777788889999999999975
No 5
>cd07603 BAR_ACAPs The Bin/Amphiphysin/Rvs (BAR) domain of ArfGAP with Coiled-coil, ANK repeat and PH domain containing proteins. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. This subfamily is composed of ACAPs (ArfGAP with Coiled-coil, ANK repeat and PH domain containing proteins), which are Arf GTPase activating proteins (GAPs) containing an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, an Arf GAP domain, and C-terminal ankyrin (ANK) repeats. Vertebrates contain at least three members, ACAP1, ACAP2, and ACAP3. ACAP1 and ACAP2 are Arf6-specific GAPs, involved in the regulation of endocytosis, phagocytosis, cell adhesion and migration, by mediating Arf6 signaling. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions.
Probab=20.72 E-value=1.1e+02 Score=26.16 Aligned_cols=35 Identities=23% Similarity=0.242 Sum_probs=25.8
Q ss_pred hhhhhhhhhhhhhchhhHHHHHHHHHHHHHHHHHhh
Q psy6677 284 IYLSIALSKFRRSTRDDRQEFGAVLQNFGAVLQNIL 319 (320)
Q Consensus 284 iylsialskfrrstrddrqefgavlqnfgavlqnil 319 (320)
.-++.+|..|.-..+||- ..+.+|+.||.+|+.|.
T Consensus 40 ~~F~~~L~~~~~~~~~d~-~i~~~l~kF~~~l~el~ 74 (200)
T cd07603 40 SLFVNSLNDLSDYFRDDS-LVQNCLNKFIQALQEMN 74 (200)
T ss_pred HHHHHHHHHHhcccCCcH-HHHHHHHHHHHHHHHHH
Confidence 345566777776666664 77899999999998873
No 6
>cd07604 BAR_ASAPs The Bin/Amphiphysin/Rvs (BAR) domain of ArfGAP with SH3 domain, ANK repeat and PH domain containing proteins. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. This subfamily is composed of ASAPs (ArfGAP with SH3 domain, ANK repeat and PH domain containing proteins), which are Arf GTPase activating proteins (GAPs) with similarity to ACAPs (ArfGAP with Coiled-coil, ANK repeat and PH domain containing proteins) in that they contain an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, an Arf GAP domain, and ankyrin (ANK) repeats. However, ASAPs contain an additional C-terminal SH3 domain. ASAPs function in regulating cell growth, migration, and invasion. Vertebrates contain at least three members, ASAP1, ASAP2, and ASAP3. ASAP1 and ASAP2 shows GTPase activating protein (GAP) activity towards Arf1 and Arf5. They do not show GAP activity towards Arf6, but is able to mediate
Probab=19.05 E-value=1.1e+02 Score=26.68 Aligned_cols=36 Identities=17% Similarity=0.355 Sum_probs=24.9
Q ss_pred hhhhhhhhhhhhhchhhH-HHHHHHHHHHHHHHHHhh
Q psy6677 284 IYLSIALSKFRRSTRDDR-QEFGAVLQNFGAVLQNIL 319 (320)
Q Consensus 284 iylsialskfrrstrddr-qefgavlqnfgavlqnil 319 (320)
.-++-+|.+|--...+|- .+.|.+|++|+.+++.|.
T Consensus 40 ~~F~~aL~~~g~~~~~~~~~~i~~~l~kF~~~l~El~ 76 (215)
T cd07604 40 LQFAEALEKLGSKALSREEEDLGAAFLKFSVFTKELA 76 (215)
T ss_pred HHHHHHHHHHhccccCcccHHHHHHHHHHHHHHHHHH
Confidence 345566777766554332 368999999999998764
No 7
>PF13424 TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 4A1S_B 3CEQ_B 3EDT_H ....
Probab=18.86 E-value=2.3e+02 Score=18.66 Aligned_cols=31 Identities=23% Similarity=0.300 Sum_probs=18.7
Q ss_pred hhhhhhhhhhhchhhHHHHHHHHHHHHHHHHH
Q psy6677 286 LSIALSKFRRSTRDDRQEFGAVLQNFGAVLQN 317 (320)
Q Consensus 286 lsialskfrrstrddrqefgavlqnfgavlqn 317 (320)
+..||.. .+...++.-+++..+.|.|.+...
T Consensus 28 ~~~al~~-~~~~~~~~~~~a~~~~~lg~~~~~ 58 (78)
T PF13424_consen 28 YEKALDI-EEQLGDDHPDTANTLNNLGECYYR 58 (78)
T ss_dssp HHHHHHH-HHHTTTHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHH-HHHHCCCCHHHHHHHHHHHHHHHH
Confidence 3344444 444455555667888888877653
No 8
>PF07328 VirD1: T-DNA border endonuclease VirD1; InterPro: IPR009933 This family consists of several T-DNA border endonuclease VirD1 proteins, which appear to be found exclusively in Agrobacterium species. Agrobacterium, a plant pathogen, is capable to stably transform the plant cell with a segment of its own DNA called T-DNA (transferred DNA). This process depends, among others, on the specialised bacterial virulence proteins VirD1 and VirD2 that excise the T-DNA from its adjacent sequences. VirD1 is thought to interact with VirD2 in this process [].; GO: 0004519 endonuclease activity
Probab=18.00 E-value=1.3e+02 Score=26.35 Aligned_cols=22 Identities=36% Similarity=0.747 Sum_probs=16.1
Q ss_pred hhhHHHHHHHHHHHHHHHHHhh
Q psy6677 298 RDDRQEFGAVLQNFGAVLQNIL 319 (320)
Q Consensus 298 rddrqefgavlqnfgavlqnil 319 (320)
+..|+.||..+...-++|+-||
T Consensus 109 ~aER~~fGk~fA~ld~lLr~iL 130 (147)
T PF07328_consen 109 RAERKAFGKEFADLDALLRSIL 130 (147)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 4567777777777777777776
No 9
>cd07602 BAR_RhoGAP_OPHN1-like The Bin/Amphiphysin/Rvs (BAR) domain of Oligophrenin1-like Rho GTPase Activating Proteins. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. This subfamily is composed of Rho and Rac GTPase activating proteins (GAPs) with similarity to oligophrenin1 (OPHN1). Members contain an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, and a Rho GAP domain. Some members contain a C-terminal SH3 domain. Vertebrates harbor at least three Rho GAPs in this subfamily including OPHN1, GTPase Regulator Associated with Focal adhesion kinase (GRAF), GRAF2, and an uncharacterized protein called GAP10-like. OPHN1, GRAF and GRAF2 show GAP activity towards RhoA and Cdc42. In addition, OPHN1 is active towards Rac. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The BAR domains of OPHN1
Probab=16.35 E-value=1.7e+02 Score=25.87 Aligned_cols=22 Identities=27% Similarity=0.581 Sum_probs=17.2
Q ss_pred hhhHHHHHHHHHHHHHHHHHhh
Q psy6677 298 RDDRQEFGAVLQNFGAVLQNIL 319 (320)
Q Consensus 298 rddrqefgavlqnfgavlqnil 319 (320)
.||-..++..|+.||.+|++|.
T Consensus 59 tDDe~~i~~~L~kF~~~l~ei~ 80 (207)
T cd07602 59 TDDEIEIAESLKEFGRLIETVE 80 (207)
T ss_pred cccHHHHHHHHHHHHHHHHHHH
Confidence 4444557899999999999874
No 10
>PF13512 TPR_18: Tetratricopeptide repeat
Probab=16.09 E-value=2.1e+02 Score=24.03 Aligned_cols=39 Identities=26% Similarity=0.569 Sum_probs=23.9
Q ss_pred CCCCCcc-hhhhhhhhhhhh----------hchhhHHHHHHHHHHHHHHHH
Q psy6677 277 PNHPDLN-IYLSIALSKFRR----------STRDDRQEFGAVLQNFGAVLQ 316 (320)
Q Consensus 277 pnhpdln-iylsialskfrr----------strddrqefgavlqnfgavlq 316 (320)
|+||++- .|..++|+.|+. +.||- +.....+..|..|++
T Consensus 78 P~hp~vdYa~Y~~gL~~~~~~~~~~~~~~~~drD~-~~~~~A~~~f~~lv~ 127 (142)
T PF13512_consen 78 PTHPNVDYAYYMRGLSYYEQDEGSLQSFFRSDRDP-TPARQAFRDFEQLVR 127 (142)
T ss_pred CCCCCccHHHHHHHHHHHHHhhhHHhhhcccccCc-HHHHHHHHHHHHHHH
Confidence 7888864 566788888874 33433 334455556665554
Done!