Query psy16695
Match_columns 101
No_of_seqs 109 out of 407
Neff 4.0
Searched_HMMs 46136
Date Fri Aug 16 19:38:32 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16695.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16695hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04099 Sybindin: Sybindin-li 99.8 3.3E-21 7.2E-26 138.8 4.7 74 23-100 68-142 (142)
2 KOG3369|consensus 99.7 1.1E-18 2.4E-23 133.7 5.4 74 23-100 124-197 (199)
3 PF04628 Sedlin_N: Sedlin, N-t 99.7 1.2E-17 2.6E-22 118.2 3.8 77 23-100 55-132 (132)
4 COG5122 TRS23 Transport protei 99.7 6.9E-17 1.5E-21 117.4 4.8 75 23-101 60-134 (134)
5 KOG3368|consensus 99.7 1.2E-16 2.7E-21 117.5 5.7 67 30-100 69-138 (140)
6 COG5603 TRS20 Subunit of TRAPP 99.4 3.6E-13 7.9E-18 98.3 5.6 75 23-101 61-135 (136)
7 KOG3487|consensus 99.2 1.8E-11 3.8E-16 90.1 5.3 75 23-101 62-136 (139)
8 KOG3444|consensus 98.0 8.4E-06 1.8E-10 59.1 3.8 55 27-82 65-120 (121)
9 PF03288 Pox_D5: Poxvirus D5 p 65.4 11 0.00025 23.9 3.5 34 63-99 25-58 (86)
10 smart00678 WWE Domain in Delte 33.6 13 0.00029 23.2 -0.1 25 2-26 1-25 (73)
11 PF13198 DUF4014: Protein of u 31.1 32 0.0007 23.2 1.4 27 59-86 41-67 (72)
12 PHA00743 helix-turn-helix prot 30.5 56 0.0012 20.7 2.4 22 55-76 5-26 (51)
13 PF09888 DUF2115: Uncharacteri 29.2 78 0.0017 23.6 3.4 19 67-85 107-125 (163)
14 PF12780 AAA_8: P-loop contain 28.5 14 0.0003 29.3 -0.8 15 27-41 243-257 (268)
15 PF07599 DUF1563: Protein of u 26.0 73 0.0016 19.4 2.2 19 60-78 12-30 (43)
16 PF10100 DUF2338: Uncharacteri 21.2 77 0.0017 27.7 2.3 33 51-83 290-329 (429)
17 KOG1299|consensus 21.1 68 0.0015 28.8 2.0 30 54-83 111-141 (549)
18 PF02257 RFX_DNA_binding: RFX 20.8 1.6E+02 0.0036 19.9 3.4 31 64-98 28-58 (85)
19 PF10040 DUF2276: Uncharacteri 20.6 1E+02 0.0023 20.3 2.4 32 35-71 3-36 (121)
No 1
>PF04099 Sybindin: Sybindin-like family ; InterPro: IPR007233 Sybindin is a physiological syndecan-2 ligand on dendritic spines, the small protrusions on the surface of dendrites that receive the vast majority of excitatory synapses. Syndecan-2 induces spine formation by recruiting intracellular vesicles toward postsynaptic sites through the interaction with synbindin []. ; GO: 0006888 ER to Golgi vesicle-mediated transport, 0005801 cis-Golgi network; PDB: 3CUE_C 2J3T_C 2ZMV_B 2JSN_A.
Probab=99.83 E-value=3.3e-21 Score=138.82 Aligned_cols=74 Identities=42% Similarity=0.680 Sum_probs=56.9
Q ss_pred hhhhhhcccceeeecccccccCCCCCCCCCCCchHH-HHHHHHHHHHHHhhHhcCCCCCCCCcccchhHHHHHHHHHhh
Q psy16695 23 HLIQQQEQHRHIDVAPTNYQRSGSNEPGRNLASSGL-DLILKKIYELYADYALKNPFYSLEMPIRCELFDTHLQNLLQQ 100 (101)
Q Consensus 23 ~~~~~~~~~~~~~~~p~~~~~~~~~~~~s~~~~~~I-r~~fq~VYeLYVdYVvKNPFY~~d~PI~SelFd~~V~~lvrk 100 (101)
..++.....+|+++|||.+||+ +.+|++.+.. ..+++.+|++|+|||+|||||++||||+|++||.+|++++++
T Consensus 68 ~~~~T~~yklh~~eT~TGlKFv----l~td~~~~~~~~~l~~~~~~lY~dyV~KNPfy~~~~pI~~~lF~~~l~~~~~~ 142 (142)
T PF04099_consen 68 ESFETDTYKLHCFETPTGLKFV----LITDPNVPSLRDELLRIYYELYVDYVVKNPFYSLEMPIRCELFDTKLDQYVKS 142 (142)
T ss_dssp EEEEESS-EEEEEE-TTS-EEE----EEE-TTCCHCHHHHHHHHHHHHHHHHHS-TTS-TTS----HHHHHHHHHHHHC
T ss_pred EEEEeCCEEEEEEEcCcCcEEE----EEecCCCccHHHHHHHHHHHHHHHHHhhCCCCCCCCcEehHHHHHHHHHHHhC
Confidence 6678889999999999999999 9999999444 556677779999999999999999999999999999999874
No 2
>KOG3369|consensus
Probab=99.75 E-value=1.1e-18 Score=133.73 Aligned_cols=74 Identities=47% Similarity=0.747 Sum_probs=69.8
Q ss_pred hhhhhhcccceeeecccccccCCCCCCCCCCCchHHHHHHHHHHHHHHhhHhcCCCCCCCCcccchhHHHHHHHHHhh
Q psy16695 23 HLIQQQEQHRHIDVAPTNYQRSGSNEPGRNLASSGLDLILKKIYELYADYALKNPFYSLEMPIRCELFDTHLQNLLQQ 100 (101)
Q Consensus 23 ~~~~~~~~~~~~~~~p~~~~~~~~~~~~s~~~~~~Ir~~fq~VYeLYVdYVvKNPFY~~d~PI~SelFd~~V~~lvrk 100 (101)
-++|...-..|||-|=|-.||| ..+++....++.+|+++|++|+|||+|||||+++|||||++||.+++.++.+
T Consensus 124 e~LetdtF~l~~~QTlTG~KFV----vis~~~~~~aD~lLrKiYelYsDyvlKNPfYSlEMPIRc~lFDe~lk~~le~ 197 (199)
T KOG3369|consen 124 EVLETDTFTLHIFQTLTGTKFV----VIAEPGTQGADSLLRKIYELYSDYVLKNPFYSLEMPIRCELFDEKLKFLLES 197 (199)
T ss_pred EEEEeccEEEEEEEccCCcEEE----EEecCCchhHHHHHHHHHHHHHHHhhcCCccCcccceeHHHhhHHHHHHHhh
Confidence 5777788899999999999999 8899999999999999999999999999999999999999999999998865
No 3
>PF04628 Sedlin_N: Sedlin, N-terminal conserved region; InterPro: IPR006722 Sedlin is a 140 amino-acid protein with a putative role in endoplasmic reticulum-to-Golgi transport. Several missense mutations and deletion mutations in the SEDL gene, which result in protein truncation by frame shift, are responsible for spondyloepiphyseal dysplasia tarda, a progressive skeletal disorder (OMIM:313400). [].; GO: 0006888 ER to Golgi vesicle-mediated transport, 0005622 intracellular; PDB: 3PR6_A 2J3W_A 1H3Q_A.
Probab=99.69 E-value=1.2e-17 Score=118.17 Aligned_cols=77 Identities=23% Similarity=0.347 Sum_probs=62.9
Q ss_pred hhhhhhcccceeeecccccccCCCCC-CCCCCCchHHHHHHHHHHHHHHhhHhcCCCCCCCCcccchhHHHHHHHHHhh
Q psy16695 23 HLIQQQEQHRHIDVAPTNYQRSGSNE-PGRNLASSGLDLILKKIYELYADYALKNPFYSLEMPIRCELFDTHLQNLLQQ 100 (101)
Q Consensus 23 ~~~~~~~~~~~~~~~p~~~~~~~~~~-~~s~~~~~~Ir~~fq~VYeLYVdYVvKNPFY~~d~PI~SelFd~~V~~lvrk 100 (101)
.|-.+++.-++-|+|+|.+|++--.+ .....++++||.||++||++|++ +++||||.+++||+|+.|+++|+++++|
T Consensus 55 ~l~~~~~~~vygyvT~t~~Kfvl~~~~~~~~~~d~~ik~fF~~vh~~Y~~-~~~NPF~~~~~~I~S~~Fd~~v~~l~~k 132 (132)
T PF04628_consen 55 LLDPFEDYKVYGYVTNTGIKFVLVHDMSDNSIRDEDIKQFFKEVHELYVK-ALCNPFYQPGTPIKSPKFDSRVRALAKK 132 (132)
T ss_dssp EEEEETTEEEEEEETTT--EEEEEECGGG-S--HHHHHHHHHHHHHHHHH-HHTSTTCGCT-HHHHHHHHHHHHHHHHH
T ss_pred ceehhhhHHHHhhhccCceeEEEEEecccCCcchHHHHHHHHHHHHHHHH-HccCCCCCCCCCcCCHHHHHHHHHHhcC
Confidence 56777999999999999999983222 23358999999999999999999 8899999999999999999999999986
No 4
>COG5122 TRS23 Transport protein particle (TRAPP) complex subunit [Intracellular trafficking and secretion]
Probab=99.66 E-value=6.9e-17 Score=117.40 Aligned_cols=75 Identities=36% Similarity=0.549 Sum_probs=68.6
Q ss_pred hhhhhhcccceeeecccccccCCCCCCCCCCCchHHHHHHHHHHHHHHhhHhcCCCCCCCCcccchhHHHHHHHHHhhC
Q psy16695 23 HLIQQQEQHRHIDVAPTNYQRSGSNEPGRNLASSGLDLILKKIYELYADYALKNPFYSLEMPIRCELFDTHLQNLLQQH 101 (101)
Q Consensus 23 ~~~~~~~~~~~~~~~p~~~~~~~~~~~~s~~~~~~Ir~~fq~VYeLYVdYVvKNPFY~~d~PI~SelFd~~V~~lvrk~ 101 (101)
-++++..-+.||+-|-|-.||| ..+.-+..+.+--+|++|++|+|||+|||||+++|||+|.+||.+|++++..|
T Consensus 60 ~~l~~~~f~m~I~qT~TG~kFV----~~~~k~t~na~~ql~kiY~lYsdYV~knPfys~EMPI~c~lFde~lkrm~e~~ 134 (134)
T COG5122 60 LVLYFRNFVMTIFQTTTGTKFV----FVAEKRTVNALFQLQKIYSLYSDYVTKNPFYSPEMPIQCSLFDEHLKRMFEGH 134 (134)
T ss_pred EEEEeccEEEEEEEecCCcEEE----EEecCCchhHHHHHHHHHHHHHHHhhcCCCCCcccceehhhhhHHHHHHhcCC
Confidence 5678888899999999999999 77777777888889999999999999999999999999999999999998764
No 5
>KOG3368|consensus
Probab=99.66 E-value=1.2e-16 Score=117.45 Aligned_cols=67 Identities=30% Similarity=0.541 Sum_probs=64.1
Q ss_pred ccceeeecccccccCCCCCCCCCCCchHHHHHHHHHHH-HHHhhHhcCCCCC--CCCcccchhHHHHHHHHHhh
Q psy16695 30 QHRHIDVAPTNYQRSGSNEPGRNLASSGLDLILKKIYE-LYADYALKNPFYS--LEMPIRCELFDTHLQNLLQQ 100 (101)
Q Consensus 30 ~~~~~~~~p~~~~~~~~~~~~s~~~~~~Ir~~fq~VYe-LYVdYVvKNPFY~--~d~PI~SelFd~~V~~lvrk 100 (101)
--.|.|||||..|++ +++|++..++|++||+||. +|||||+|||+|+ +++||+||.|..++++++++
T Consensus 69 YklhfyeTptglk~v----l~Tdpk~~~ir~vLq~IYs~lyVE~Vvknpl~~~~~~~~i~~E~fr~~ld~~vrs 138 (140)
T KOG3368|consen 69 YKLHFYETPTGLKFV----LNTDPKAGSIRDVLQYIYSHLYVEYVVKNPLYTYDPGSPIRSELFRKILDRFVRS 138 (140)
T ss_pred eEEEEEEcCCCcEEE----EecCCCcccHHHHHHHHHHHHHHHHHHcCcccccCCCCccchHHHHHHHHhhhcc
Confidence 457999999999999 9999999999999999996 9999999999999 99999999999999999875
No 6
>COG5603 TRS20 Subunit of TRAPP, an ER-Golgi tethering complex [Cell motility and secretion]
Probab=99.41 E-value=3.6e-13 Score=98.33 Aligned_cols=75 Identities=23% Similarity=0.320 Sum_probs=63.5
Q ss_pred hhhhhhcccceeeecccccccCCCCCCCCCCCchHHHHHHHHHHHHHHhhHhcCCCCCCCCcccchhHHHHHHHHHhhC
Q psy16695 23 HLIQQQEQHRHIDVAPTNYQRSGSNEPGRNLASSGLDLILKKIYELYADYALKNPFYSLEMPIRCELFDTHLQNLLQQH 101 (101)
Q Consensus 23 ~~~~~~~~~~~~~~~p~~~~~~~~~~~~s~~~~~~Ir~~fq~VYeLYVdYVvKNPFY~~d~PI~SelFd~~V~~lvrk~ 101 (101)
+|=+|-+--|--|+||+..||.-- --+.+++++|.||++||++|++ .++||||++++||+|++||.+|+++.|++
T Consensus 61 ~~d~f~~l~IsAYi~pSgmkf~~i---H~n~s~~N~rsF~qevHely~k-tLmspfy~~~~pirsqafd~~Vr~~ar~~ 135 (136)
T COG5603 61 CLDSFGDLRISAYIMPSGMKFLFI---HQNQSRKNARSFLQEVHELYAK-TLMSPFYEPDEPIRSQAFDDGVREAARVC 135 (136)
T ss_pred HHHhhCCeEEEEEEccCCceEEEE---eccchhhhHHHHHHHHHHHHHH-HhhCcccCCCccccchhhhhhHHHHHHhh
Confidence 444555666888999999999832 2233688999999999999999 88999999999999999999999998864
No 7
>KOG3487|consensus
Probab=99.22 E-value=1.8e-11 Score=90.13 Aligned_cols=75 Identities=27% Similarity=0.417 Sum_probs=63.6
Q ss_pred hhhhhhcccceeeecccccccCCCCCCCCCCCchHHHHHHHHHHHHHHhhHhcCCCCCCCCcccchhHHHHHHHHHhhC
Q psy16695 23 HLIQQQEQHRHIDVAPTNYQRSGSNEPGRNLASSGLDLILKKIYELYADYALKNPFYSLEMPIRCELFDTHLQNLLQQH 101 (101)
Q Consensus 23 ~~~~~~~~~~~~~~~p~~~~~~~~~~~~s~~~~~~Ir~~fq~VYeLYVdYVvKNPFY~~d~PI~SelFd~~V~~lvrk~ 101 (101)
|.=.|-|-=|-.|+|+....|.- +-.+-.+++++.||+++|++|++ .++||||.+++||+|++||.+|+.+.++|
T Consensus 62 tVDkfne~~VSAyvTas~i~f~m---lh~~~~~~~ik~Ffqev~elyik-~lmnpFy~~~dpirs~afd~kv~~~~rkh 136 (139)
T KOG3487|consen 62 TVDKFNELFVSAYVTASHIRFIM---LHINRADDNIKLFFQEVHELYIK-TLMNPFYEINDPIRSPAFDHKVRGLARKH 136 (139)
T ss_pred HHHhhcceeEEEEEccCcEEEEE---EeeccccccHHHHHHHHHHHHHH-HHhCcccccCCccccHHHHHHHHHHHHHH
Confidence 44466777788999999997762 23344588999999999999999 77899999999999999999999998875
No 8
>KOG3444|consensus
Probab=97.97 E-value=8.4e-06 Score=59.06 Aligned_cols=55 Identities=16% Similarity=0.129 Sum_probs=45.8
Q ss_pred hhcccceeeecccccccCCCC-CCCCCCCchHHHHHHHHHHHHHHhhHhcCCCCCCC
Q psy16695 27 QQEQHRHIDVAPTNYQRSGSN-EPGRNLASSGLDLILKKIYELYADYALKNPFYSLE 82 (101)
Q Consensus 27 ~~~~~~~~~~~p~~~~~~~~~-~~~s~~~~~~Ir~~fq~VYeLYVdYVvKNPFY~~d 82 (101)
-+.+.+--|+|-|.+||.--. ..+.+.++.++|++||.+|-+|++ ++|||||.|+
T Consensus 65 ted~kvYgfvtNTkVKFIlvvdssd~avreteiRsv~r~~h~l~td-~~~npfy~pg 120 (121)
T KOG3444|consen 65 TEDYKVYGFVTNTKVKFILVVDSSDYAVRETEIRSVFRILHLLYTD-LSCNPFYLPG 120 (121)
T ss_pred ccceeEEEEEeccEEEEEEEEcCCcceehhHHHHHHHHHHHHHHHH-heecceeccC
Confidence 356677788999999985211 146788999999999999999999 9999999986
No 9
>PF03288 Pox_D5: Poxvirus D5 protein-like; InterPro: IPR004968 This domain is found at the C terminus of phage P4 alpha protein and related proteins. Phage P4 DNA replication depends on the product of the alpha gene, which has origin recognition ability, DNA helicase activity, and DNA primase activity. The structure of the protein can be summarised as follows: The N terminus provides the primase activity, the central region is the helicase/nucleoside triphosphatase domain and the ori DNA recognition resides in the C-terminal 1/3 of the protein []. The domain is also found at the C terminus of a number of proteins from orthopox viruses including vaccinia virus D5. D5 encodes a 90kDa protein that is transiently expressed at early times after infection. It has an nucleoside triphosphatase activity which is independent of common nucleic acid cofactors and it can hydrolyse all the common ribo- and deoxyribonucleoside triphosphates to diphosphates in the presence of a divalent cation [].; PDB: 1KA8_E.
Probab=65.39 E-value=11 Score=23.89 Aligned_cols=34 Identities=21% Similarity=0.548 Sum_probs=23.6
Q ss_pred HHHHHHHHhhHhcCCCCCCCCcccchhHHHHHHHHHh
Q psy16695 63 KKIYELYADYALKNPFYSLEMPIRCELFDTHLQNLLQ 99 (101)
Q Consensus 63 q~VYeLYVdYVvKNPFY~~d~PI~SelFd~~V~~lvr 99 (101)
..||++|..|+-.|=... ++....|..++++++.
T Consensus 25 ~~lY~~Y~~wc~~ng~~~---~ls~~~F~~~L~~~~~ 58 (86)
T PF03288_consen 25 KDLYDAYKEWCEENGYKP---PLSKRKFGKELKQYFP 58 (86)
T ss_dssp TBHHHHHHHHHHHTT-S-------HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHhCCCc---ccCHHHHHHHHHHHhh
Confidence 568888888887775554 6899999999998864
No 10
>smart00678 WWE Domain in Deltex and TRIP12 homologues. Possibly involved in regulation of ubiquitin-mediated proteolysis.
Probab=33.57 E-value=13 Score=23.19 Aligned_cols=25 Identities=20% Similarity=0.563 Sum_probs=19.4
Q ss_pred CccccccccccccccCCCCcchhhh
Q psy16695 2 WSWNYLVPSLRWNEYHPVDNTHLIQ 26 (101)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~ 26 (101)
|.|-|.-.+-.|..|+|..+..|=+
T Consensus 1 ~~W~w~~~~g~W~~Y~~~~~~~IE~ 25 (73)
T smart00678 1 YVWEYEGRNGKWWPYDPRVSEDIEE 25 (73)
T ss_pred CEEEEECCCCCeeeCChHHHHHHHH
Confidence 5688888888899999987765443
No 11
>PF13198 DUF4014: Protein of unknown function (DUF4014)
Probab=31.15 E-value=32 Score=23.19 Aligned_cols=27 Identities=37% Similarity=0.641 Sum_probs=21.5
Q ss_pred HHHHHHHHHHHHhhHhcCCCCCCCCccc
Q psy16695 59 DLILKKIYELYADYALKNPFYSLEMPIR 86 (101)
Q Consensus 59 r~~fq~VYeLYVdYVvKNPFY~~d~PI~ 86 (101)
-..+..+.++|.+ +++|||-.++..|.
T Consensus 41 ~~~~E~l~e~Y~~-~~w~~F~~Lhnkin 67 (72)
T PF13198_consen 41 GKIIEPLFELYKD-WFWNPFNALHNKIN 67 (72)
T ss_pred HHHHHHHHHHHHH-HHHHhHHHHhcccc
Confidence 3467788899999 88999998877663
No 12
>PHA00743 helix-turn-helix protein
Probab=30.47 E-value=56 Score=20.72 Aligned_cols=22 Identities=18% Similarity=0.212 Sum_probs=19.3
Q ss_pred chHHHHHHHHHHHHHHhhHhcC
Q psy16695 55 SSGLDLILKKIYELYADYALKN 76 (101)
Q Consensus 55 ~~~Ir~~fq~VYeLYVdYVvKN 76 (101)
|+++|.+|.-+|++-+|.++-|
T Consensus 5 D~~iReLLs~iheIKID~i~~~ 26 (51)
T PHA00743 5 DEDVRELLSIIHEIKIDIITQS 26 (51)
T ss_pred HHHHHHHHHHHHHHhhhhhccc
Confidence 6789999999999999977655
No 13
>PF09888 DUF2115: Uncharacterized protein conserved in archaea (DUF2115); InterPro: IPR019215 This entry represents various hypothetical archaeal proteins, has no known function.
Probab=29.21 E-value=78 Score=23.60 Aligned_cols=19 Identities=32% Similarity=0.611 Sum_probs=17.5
Q ss_pred HHHHhhHhcCCCCCCCCcc
Q psy16695 67 ELYADYALKNPFYSLEMPI 85 (101)
Q Consensus 67 eLYVdYVvKNPFY~~d~PI 85 (101)
.+|+-||++-|.+.+|||.
T Consensus 107 s~Y~~FI~~~PlHPvG~~F 125 (163)
T PF09888_consen 107 SPYLIFILKEPLHPVGMPF 125 (163)
T ss_pred HHHHHHHhCCCCCCCCCCC
Confidence 6899999999999999875
No 14
>PF12780 AAA_8: P-loop containing dynein motor region D4; InterPro: IPR024317 The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four (D1 - D4) correspond to the ATP binding sites with P-loop signatures described previously, and two (D5, D6) are modules in which the P loop has been lost in evolution. This particular entry represents the D4 ATP-binding domain of the motor [].; PDB: 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A.
Probab=28.55 E-value=14 Score=29.27 Aligned_cols=15 Identities=40% Similarity=0.468 Sum_probs=7.0
Q ss_pred hhcccceeeeccccc
Q psy16695 27 QQEQHRHIDVAPTNY 41 (101)
Q Consensus 27 ~~~~~~~~~~~p~~~ 41 (101)
.+|.++|.|+||+.+
T Consensus 243 ~~~~~r~~yvTP~sy 257 (268)
T PF12780_consen 243 LQELRRYNYVTPKSY 257 (268)
T ss_dssp HHHCS------HHHH
T ss_pred HHHcCCcceECcHHH
Confidence 357899999999987
No 15
>PF07599 DUF1563: Protein of unknown function (DUF1563); InterPro: IPR011457 This is a small family of short hypothetical proteins in Leptospira interrogans.
Probab=25.97 E-value=73 Score=19.40 Aligned_cols=19 Identities=37% Similarity=0.754 Sum_probs=13.7
Q ss_pred HHHHHHHHHHHhhHhcCCC
Q psy16695 60 LILKKIYELYADYALKNPF 78 (101)
Q Consensus 60 ~~fq~VYeLYVdYVvKNPF 78 (101)
..|..+|.-||+|-+|--|
T Consensus 12 ~TLeNlYatyve~~lkq~f 30 (43)
T PF07599_consen 12 ETLENLYATYVEYFLKQTF 30 (43)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 4567888899998876433
No 16
>PF10100 DUF2338: Uncharacterized protein conserved in bacteria (DUF2338); InterPro: IPR016935 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=21.19 E-value=77 Score=27.66 Aligned_cols=33 Identities=24% Similarity=0.474 Sum_probs=25.4
Q ss_pred CCCCchHHHHHH-----HHHHHHHHhh--HhcCCCCCCCC
Q psy16695 51 RNLASSGLDLIL-----KKIYELYADY--ALKNPFYSLEM 83 (101)
Q Consensus 51 s~~~~~~Ir~~f-----q~VYeLYVdY--VvKNPFY~~d~ 83 (101)
...+..+|..|- ++-|-+||+| .+-.||.+||.
T Consensus 290 eslsr~~Ie~F~~l~~i~QEYLLYVRYtsiLIDPFS~PD~ 329 (429)
T PF10100_consen 290 ESLSRDDIESFEELPAIHQEYLLYVRYTSILIDPFSEPDE 329 (429)
T ss_pred hhCCHHHHhhhhcCChHHhhHHHHHHhhhheeCCCCCCCC
Confidence 456677787763 5667799999 67899999985
No 17
>KOG1299|consensus
Probab=21.07 E-value=68 Score=28.77 Aligned_cols=30 Identities=30% Similarity=0.542 Sum_probs=23.4
Q ss_pred CchHHHHHHHHHHHHHHhhHhcCCC-CCCCC
Q psy16695 54 ASSGLDLILKKIYELYADYALKNPF-YSLEM 83 (101)
Q Consensus 54 ~~~~Ir~~fq~VYeLYVdYVvKNPF-Y~~d~ 83 (101)
.+.+-.+..++|+|+|.||+.-||+ ++++.
T Consensus 111 AesD~~E~V~eVqE~y~Df~~~n~~Lfsln~ 141 (549)
T KOG1299|consen 111 AESDEQEVVREVQEIYLDFFKVNPDLFSLNI 141 (549)
T ss_pred HhcchHHHHHHHHHHHHhhhccCCceeecCC
Confidence 4455677899999999999999996 44553
No 18
>PF02257 RFX_DNA_binding: RFX DNA-binding domain; InterPro: IPR003150 RFX is a regulatory factor which binds to the X box of MHC class II genes and is essential for their expression. The DNA-binding domain of RFX is the central domain of the protein and binds ssDNA as either a monomer or homodimer [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1DP7_P 2KW3_A.
Probab=20.80 E-value=1.6e+02 Score=19.90 Aligned_cols=31 Identities=19% Similarity=0.470 Sum_probs=21.8
Q ss_pred HHHHHHHhhHhcCCCCCCCCcccchhHHHHHHHHH
Q psy16695 64 KIYELYADYALKNPFYSLEMPIRCELFDTHLQNLL 98 (101)
Q Consensus 64 ~VYeLYVdYVvKNPFY~~d~PI~SelFd~~V~~lv 98 (101)
.||+.|+++.-+|- -.|+.+..|-+-|+...
T Consensus 28 ~lY~~Y~~~C~~~~----~~pln~AsFGKlir~vF 58 (85)
T PF02257_consen 28 DLYAHYLSFCEKNG----IKPLNAASFGKLIRQVF 58 (85)
T ss_dssp HHHHHHHHHHHHTT---------HHHHHHHHHHHS
T ss_pred HHHHHHHHHHHHhC----CCCCchHHHHHHHHHHc
Confidence 78999999887765 25789999999888763
No 19
>PF10040 DUF2276: Uncharacterized conserved protein (DUF2276); InterPro: IPR019267 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes []. CRISPRs appear to provide acquired resistance against bacteriophages, possibly acting with an RNA interference-like mechanism to inhibit gene functions of invasive DNA elements [, ]. Differences in the number and type of spacers between CRISPR repeats correlate with phage sensitivity. It is thought that following phage infection, bacteria integrate new spacers derived from phage genomic sequences, and that the removal or addition of particular spacers modifies the phage-resistance phenotype of the cell. Therefore, the specificity of CRISPRs may be determined by spacer-phage sequence similarity. In addition, there are many protein families known as CRISPR-associated sequences (Cas), which are encoded in the vicinity of CRISPR loci []. CRISPR/cas gene regions can be quite large, with up to 20 different, tandem-arranged cas genes next to a CRISPR cluster or filling the region between two repeat clusters. Cas genes and CRISPRs are found on mobile genetic elements such as plasmids, and have undergone extensive horizontal transfer. Cas proteins are thought to be involved in the propagation and functioning of CRISPRs. Some Cas proteins show similarity to helicases and repair proteins, although the functions of most are unknown. Cas families can be divided into subtypes according to operon organisation and phylogeny. Cas6 is a member of the RAMP (repeat-associated mysterious protein) superfamily []. It is among the most widely distributed Cas proteins and is found in both bacteria and archaea []. Cas6 functions in the generation of CRISPR-derived guide RNAs for invader defense in prokaryotes []. This entry represents a domain found in some CRISPR-associated proteins Cas6 and in uncharacterised proteins.
Probab=20.61 E-value=1e+02 Score=20.31 Aligned_cols=32 Identities=16% Similarity=0.376 Sum_probs=22.2
Q ss_pred eecccccccCCCCCCCCCCC--chHHHHHHHHHHHHHHh
Q psy16695 35 DVAPTNYQRSGSNEPGRNLA--SSGLDLILKKIYELYAD 71 (101)
Q Consensus 35 ~~~p~~~~~~~~~~~~s~~~--~~~Ir~~fq~VYeLYVd 71 (101)
+.|||+.+..+. ... .++...+|+.+...+..
T Consensus 3 F~TPt~~~~~~~-----~~~~~~P~~~~i~~sl~~r~~~ 36 (121)
T PF10040_consen 3 FLTPTRFKQRGR-----YVPRFFPSPRLIFRSLLRRWNA 36 (121)
T ss_pred EECCeeEEECCE-----eeeccCCCHHHHHHHHHHHHHH
Confidence 679999988633 233 45567778888777766
Done!