Query 030789
Match_columns 171
No_of_seqs 35 out of 37
Neff 2.1
Searched_HMMs 46136
Date Fri Mar 29 04:36:12 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030789.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030789hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN00014 light-harvesting-like 100.0 4.9E-62 1.1E-66 412.3 10.0 165 4-170 1-170 (250)
2 PHA02337 putative high light i 89.3 0.093 2E-06 34.1 -0.3 11 160-170 3-13 (35)
3 PF14963 CAML: Calcium signal- 64.0 3.1 6.7E-05 36.9 0.9 12 119-130 6-17 (263)
4 PF10999 DUF2839: Protein of u 45.2 12 0.00025 27.2 1.1 24 121-151 3-26 (68)
5 PF09782 NDUF_B6: NADH:ubiquin 38.0 20 0.00043 29.4 1.5 21 122-144 29-49 (156)
6 PF14114 DUF4286: Domain of un 34.8 19 0.00041 26.2 0.9 17 149-165 15-31 (98)
7 PF05071 NDUFA12: NADH ubiquin 34.3 7.6 0.00016 28.9 -1.3 48 110-164 10-61 (105)
8 PF00504 Chloroa_b-bind: Chlor 32.9 10 0.00022 28.8 -0.8 14 157-170 131-144 (156)
9 COG4019 Uncharacterized protei 28.4 28 0.0006 29.0 0.9 14 153-166 55-68 (156)
10 PF06543 Lac_bphage_repr: Lact 26.4 36 0.00078 23.8 1.1 21 98-118 4-24 (49)
11 PRK08183 NADH dehydrogenase; V 26.0 20 0.00043 28.7 -0.3 36 121-165 48-87 (133)
12 PF05400 FliT: Flagellar prote 24.7 49 0.0011 21.7 1.5 19 112-130 8-26 (84)
13 PF12244 DUF3606: Protein of u 24.6 43 0.00093 22.7 1.2 14 152-165 25-38 (57)
14 PRK10548 flagellar biosynthesi 23.8 51 0.0011 25.5 1.6 19 112-130 28-46 (121)
15 PRK06630 hypothetical protein; 23.2 21 0.00045 27.9 -0.7 26 122-156 35-62 (99)
16 PF08557 Lipid_DES: Sphingolip 22.8 36 0.00078 22.5 0.5 14 121-134 16-29 (39)
17 PF14078 DUF4259: Domain of un 21.4 21 0.00047 25.9 -0.9 20 99-118 1-20 (128)
18 PF09701 Cas_Cmr5: CRISPR-asso 20.6 52 0.0011 24.5 1.0 11 147-157 107-117 (122)
19 PLN03182 xyloglucan 6-xylosylt 20.1 94 0.002 29.5 2.8 31 111-147 102-135 (429)
No 1
>PLN00014 light-harvesting-like protein 3; Provisional
Probab=100.00 E-value=4.9e-62 Score=412.28 Aligned_cols=165 Identities=46% Similarity=0.829 Sum_probs=131.5
Q ss_pred cccccccCCCCCCC-ccCCccccccCcceeecCCC-ccchhhhhccccCCCccC-CCcccccCCCccc--CCCCCCCCCC
Q 030789 4 SIDLLSFSPPPSSM-LSRTQFSFTHKPTFLLSSKK-ESFFTLRASAADNGAGVS-APAVTVEEPKVRE--ASEGPTESNG 78 (171)
Q Consensus 4 s~~ma~FSPp~~~~-~~~p~~~~~~k~~~~L~~~~-~~l~~~~ras~dnga~~s-a~a~~VE~Pkp~~--a~~~~~~sng 78 (171)
+|+|++++++.+++ +++|+ ..+++..+|.+++ .+++...+++++++..++ .++..++.++... ++-...+..+
T Consensus 1 ~~~~sl~~~~~~~~~~~k~~--~~~r~~~~l~~~~~~~~~~~~~~~~~~~~~~~r~~~pl~~gg~l~g~~a~gk~~~~aa 78 (250)
T PLN00014 1 MISMSLSRASSSTLVVSKPN--PQSRSSRSLGAKSEGSLVSVTVASTDGGGISERKPSPLERGGTLEGEAAAGKDPGPAA 78 (250)
T ss_pred CcccccCCCccccccccCCC--cccccccccccccccceEEEeecccCCCCccccCCCccccCCCcccccccccCccccc
Confidence 36778888776665 46888 8899999999999 889999999999875333 2333444443221 1111111112
Q ss_pred cccCcccccCCCccCCccccCccchhhhhhcCCcCchhhhhHHHHHhhhhhcCCCCCCCCCCeeeecCcchHHHHHHhhc
Q 030789 79 AVEAPEVKAVNKFEDPKWVNGTWDLKQFQKNGQTDWDAVIDAEARRRKWLENSPESSSNDDPVIFDTSIVPWWAWIKRFH 158 (171)
Q Consensus 79 A~~~~e~~~~~~f~D~RW~~GtWDl~qF~~~G~~dWDaVIdAE~~rRK~Led~Pe~s~n~epv~FdtsiiPWWaW~kRfh 158 (171)
++......+.++|+||||+||||||+||++||+||||+||||||+||||||||||+|+||||||||||||||||||||||
T Consensus 79 ~~~~~~~~~~~~f~d~RW~~GtWDl~qF~~dG~~DWd~vIdaEv~rRK~LE~nPe~s~n~epv~FdtSiiPWWaW~~rf~ 158 (250)
T PLN00014 79 AAKTSLAVSVGKFEDPRWKNGTWDLNQFKKDGKTDWDAVIDAEVVRRKWLEDNPETSSNDEPVLFDTSIIPWWAWVKRFH 158 (250)
T ss_pred ccccccccccccccCchhcCCcccHHHHhhcCCcchHHHHHHHHHHHHHHhhCccccCCCCCceeecccccHHHHHHhcc
Confidence 23333344689999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CchhhhhccccC
Q 030789 159 LPEAELLNGAAL 170 (171)
Q Consensus 159 LPEAE~lNGRAA 170 (171)
||+||++|||+|
T Consensus 159 l~~aE~lNGR~A 170 (250)
T PLN00014 159 LPEAELLNGRAA 170 (250)
T ss_pred CchhHhhhhHHH
Confidence 999999999997
No 2
>PHA02337 putative high light inducible protein
Probab=89.32 E-value=0.093 Score=34.08 Aligned_cols=11 Identities=55% Similarity=0.800 Sum_probs=10.0
Q ss_pred chhhhhccccC
Q 030789 160 PEAELLNGAAL 170 (171)
Q Consensus 160 PEAE~lNGRAA 170 (171)
|.||++|||+|
T Consensus 3 ~~aE~~NGRlA 13 (35)
T PHA02337 3 PEAEIFNGWLA 13 (35)
T ss_pred cHHHHHhhHHH
Confidence 68999999987
No 3
>PF14963 CAML: Calcium signal-modulating cyclophilin ligand
Probab=64.05 E-value=3.1 Score=36.91 Aligned_cols=12 Identities=75% Similarity=0.847 Sum_probs=10.6
Q ss_pred hHHHHHhhhhhc
Q 030789 119 DAEARRRKWLEN 130 (171)
Q Consensus 119 dAE~~rRK~Led 130 (171)
-||+||||+|+.
T Consensus 6 RaEaRRRKLLmN 17 (263)
T PF14963_consen 6 RAEARRRKLLMN 17 (263)
T ss_pred HHHHHHHHHHhh
Confidence 489999999985
No 4
>PF10999 DUF2839: Protein of unknown function (DUF2839); InterPro: IPR021262 This bacterial family of unknown function appear to be restricted to Cyanobacteria.
Probab=45.24 E-value=12 Score=27.17 Aligned_cols=24 Identities=42% Similarity=0.778 Sum_probs=15.5
Q ss_pred HHHHhhhhhcCCCCCCCCCCeeeecCcchHH
Q 030789 121 EARRRKWLENSPESSSNDDPVIFDTSIVPWW 151 (171)
Q Consensus 121 E~~rRK~Led~Pe~s~n~epv~FdtsiiPWW 151 (171)
|++|||=+-..|.. .+++. |+||=
T Consensus 3 EAKRRke~Gl~pr~-~k~~~------~~~wl 26 (68)
T PF10999_consen 3 EAKRRKELGLPPRY-KKEER------ILPWL 26 (68)
T ss_pred chhhhhhccCCCcc-CCccc------ccccC
Confidence 99999987554443 33343 77774
No 5
>PF09782 NDUF_B6: NADH:ubiquinone oxidoreductase, NDUFB6/B17 subunit; InterPro: IPR019174 The NADH dehydrogenase [ubiquinone] complex performs the first stage of electron transfer from NADH to the respiratory chain. This entry represents an accessory subunit that is not thought to be involved in catalysis [].
Probab=38.05 E-value=20 Score=29.42 Aligned_cols=21 Identities=38% Similarity=0.708 Sum_probs=16.0
Q ss_pred HHHhhhhhcCCCCCCCCCCeeee
Q 030789 122 ARRRKWLENSPESSSNDDPVIFD 144 (171)
Q Consensus 122 ~~rRK~Led~Pe~s~n~epv~Fd 144 (171)
+-|||||.|- --+-+|||+-.
T Consensus 29 a~Rr~WLkDQ--~Lsp~EPv~~p 49 (156)
T PF09782_consen 29 AWRRQWLKDQ--ELSPREPVLPP 49 (156)
T ss_pred HHHHHHHHhh--ccCCCCCcCCc
Confidence 5699999995 34567999765
No 6
>PF14114 DUF4286: Domain of unknown function (DUF4286)
Probab=34.84 E-value=19 Score=26.24 Aligned_cols=17 Identities=35% Similarity=0.860 Sum_probs=14.3
Q ss_pred hHHHHHHhhcCchhhhh
Q 030789 149 PWWAWIKRFHLPEAELL 165 (171)
Q Consensus 149 PWWaW~kRfhLPEAE~l 165 (171)
-|=.|||..|+|+....
T Consensus 15 ~wl~W~k~~hIp~vl~~ 31 (98)
T PF14114_consen 15 EWLNWMKEEHIPEVLAT 31 (98)
T ss_pred HHHHHHHHHHHHHHHhc
Confidence 37799999999998654
No 7
>PF05071 NDUFA12: NADH ubiquinone oxidoreductase subunit NDUFA12; InterPro: IPR007763 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. this entry represents the 17.2kDa subunit from NADH:ubiquinone oxidoreductase and its homologues []. This subunit is believed to be one of the 36 structural complex I proteins.; GO: 0008137 NADH dehydrogenase (ubiquinone) activity, 0009055 electron carrier activity, 0016020 membrane
Probab=34.33 E-value=7.6 Score=28.94 Aligned_cols=48 Identities=35% Similarity=0.756 Sum_probs=31.6
Q ss_pred CCcCchhhhhHHHHHhhhhhcCCCCCCCCCCeeeecCcch--HHHHHH--hhcCchhhh
Q 030789 110 GQTDWDAVIDAEARRRKWLENSPESSSNDDPVIFDTSIVP--WWAWIK--RFHLPEAEL 164 (171)
Q Consensus 110 G~~dWDaVIdAE~~rRK~Led~Pe~s~n~epv~FdtsiiP--WWaW~k--RfhLPEAE~ 164 (171)
|..=|..-.+..-+||+|.+-+... -||.|.|| |.+||+ |-+.|-.|.
T Consensus 10 GN~YyE~~~~~~~~~rRwV~y~~~~-------~~~~s~IPpeWh~WL~~~r~~pPt~~~ 61 (105)
T PF05071_consen 10 GNKYYENPRDEQGRRRRWVEYAGKS-------DYDPSQIPPEWHAWLHHTRDEPPTEEE 61 (105)
T ss_pred CCEEEeecCCCcCCCcEEEEcCCcc-------ccCcCccCcchHHHhccCcCCCCCccc
Confidence 4444444456677888898765443 46677887 999996 556665443
No 8
>PF00504 Chloroa_b-bind: Chlorophyll A-B binding protein; InterPro: IPR022796 The light-harvesting complex (LHC) consists of chlorophylls A and B and the chlorophyll A-B binding protein. LHC functions as a light receptor that captures and delivers excitation energy to photosystems I and II with which it is closely associated. Under changing light conditions, the reversible phosphorylation of light harvesting chlorophyll a/b binding proteins (LHCII) represents a system for balancing the excitation energy between the two photosystems []. The N terminus of the chlorophyll A-B binding protein extends into the stroma where it is involved with adhesion of granal membranes and photo-regulated by reversible phosphorylation of its threonine residues []. Both these processes are believed to mediate the distribution of excitation energy between photosystems I and II. This family also includes the photosystem II protein PsbS, which plays a role in energy-dependent quenching that increases thermal dissipation of excess absorbed light energy in the photosystem [].; PDB: 2O01_2 2WSF_2 2WSC_2 3LW5_2 2WSE_2 1RWT_D 2BHW_C 1VCR_A.
Probab=32.94 E-value=10 Score=28.81 Aligned_cols=14 Identities=36% Similarity=0.266 Sum_probs=11.4
Q ss_pred hcCchhhhhccccC
Q 030789 157 FHLPEAELLNGAAL 170 (171)
Q Consensus 157 fhLPEAE~lNGRAA 170 (171)
.....+|+.|||.|
T Consensus 131 ~~~~~~El~NGRlA 144 (156)
T PF00504_consen 131 EFMQLAELKNGRLA 144 (156)
T ss_dssp HCHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHH
Confidence 44568999999987
No 9
>COG4019 Uncharacterized protein conserved in archaea [Function unknown]
Probab=28.39 E-value=28 Score=29.01 Aligned_cols=14 Identities=50% Similarity=0.861 Sum_probs=12.0
Q ss_pred HHHhhcCchhhhhc
Q 030789 153 WIKRFHLPEAELLN 166 (171)
Q Consensus 153 W~kRfhLPEAE~lN 166 (171)
=|+||.|||||.|.
T Consensus 55 vlrrf~l~Eaeml~ 68 (156)
T COG4019 55 VLRRFCLAEAEMLD 68 (156)
T ss_pred HHHHhccchHHHhc
Confidence 48999999999873
No 10
>PF06543 Lac_bphage_repr: Lactococcus bacteriophage repressor; InterPro: IPR009498 This entry represents the C terminus of various Lactococcus bacteriophage repressor proteins.
Probab=26.40 E-value=36 Score=23.78 Aligned_cols=21 Identities=29% Similarity=0.593 Sum_probs=17.7
Q ss_pred cCccchhhhhhcCCcCchhhh
Q 030789 98 NGTWDLKQFQKNGQTDWDAVI 118 (171)
Q Consensus 98 ~GtWDl~qF~~~G~~dWDaVI 118 (171)
|-.-||..+..|.++|||-++
T Consensus 4 ~epiDLa~lvDd~kvdWd~wv 24 (49)
T PF06543_consen 4 NEPIDLADLVDDPKVDWDKWV 24 (49)
T ss_pred cCcccHHHHcCCcccchHHhe
Confidence 456799999999999999875
No 11
>PRK08183 NADH dehydrogenase; Validated
Probab=25.96 E-value=20 Score=28.66 Aligned_cols=36 Identities=25% Similarity=0.643 Sum_probs=24.8
Q ss_pred HHHHhhhhhcCCCCCCCCCCeeeecCcch--HHHHHHh--hcCchhhhh
Q 030789 121 EARRRKWLENSPESSSNDDPVIFDTSIVP--WWAWIKR--FHLPEAELL 165 (171)
Q Consensus 121 E~~rRK~Led~Pe~s~n~epv~FdtsiiP--WWaW~kR--fhLPEAE~l 165 (171)
.-+||+|.+-+- .+|.|.|| |.+||.. -+.|..|.+
T Consensus 48 ~~~~rRWV~Y~~---------~~d~s~IPpeWh~WLh~~~d~pPt~~~~ 87 (133)
T PRK08183 48 DGRERRWVIYNG---------YAEASRIPPEWHGWLHHTVDVPPTKEPY 87 (133)
T ss_pred CCCceEEEEeCC---------CCCccccCchHHhhhccCcCCCCCcccc
Confidence 467888988432 25778897 9999964 366765544
No 12
>PF05400 FliT: Flagellar protein FliT; InterPro: IPR008622 This entry represents the bacterial flagellar FliT family of dual-function proteins. Together with FlgN, FliT has been proposed to act as a substrate-specific export chaperone, facilitating the incorporation of the enterobacterial hook-associated axial proteins (HAPs) FlgK/FlgL and FliD into the growing flagellum []. FliT has also been shown to act as a transcriptional regulator in Salmonella typhimurium [].; GO: 0019861 flagellum; PDB: 3A7M_A 3H3M_B 3NKZ_C 2G42_A 2FZT_B.
Probab=24.73 E-value=49 Score=21.66 Aligned_cols=19 Identities=26% Similarity=0.580 Sum_probs=15.8
Q ss_pred cCchhhhhHHHHHhhhhhc
Q 030789 112 TDWDAVIDAEARRRKWLEN 130 (171)
Q Consensus 112 ~dWDaVIdAE~~rRK~Led 130 (171)
=|||.|+.-+..|...++.
T Consensus 8 ~dWe~l~~l~~~R~~ll~~ 26 (84)
T PF05400_consen 8 GDWEELEELLDERQELLER 26 (84)
T ss_dssp T-HHHHHHHHHHHHHHHHH
T ss_pred CcHHHHHHHHHHHHHHHHH
Confidence 3899999999999999853
No 13
>PF12244 DUF3606: Protein of unknown function (DUF3606); InterPro: IPR022037 This family of proteins is found in bacteria. Proteins in this family are typically between 58 and 85 amino acids in length. There is a single completely conserved residue G that may be functionally important.
Probab=24.60 E-value=43 Score=22.70 Aligned_cols=14 Identities=43% Similarity=0.802 Sum_probs=12.0
Q ss_pred HHHHhhcCchhhhh
Q 030789 152 AWIKRFHLPEAELL 165 (171)
Q Consensus 152 aW~kRfhLPEAE~l 165 (171)
-|.|+|+++++++.
T Consensus 25 ywa~~~gvt~~~L~ 38 (57)
T PF12244_consen 25 YWAKRFGVTEEQLR 38 (57)
T ss_pred HHHHHHCcCHHHHH
Confidence 48899999999875
No 14
>PRK10548 flagellar biosynthesis protein FliT; Provisional
Probab=23.81 E-value=51 Score=25.52 Aligned_cols=19 Identities=26% Similarity=0.536 Sum_probs=16.7
Q ss_pred cCchhhhhHHHHHhhhhhc
Q 030789 112 TDWDAVIDAEARRRKWLEN 130 (171)
Q Consensus 112 ~dWDaVIdAE~~rRK~Led 130 (171)
=|||.||+.|..-.+.+|.
T Consensus 28 g~Wd~Li~lE~~y~~~Ve~ 46 (121)
T PRK10548 28 GQWDELIEQEVAYVQAVEE 46 (121)
T ss_pred CCHHHHHHHHHHHHHHHHH
Confidence 4899999999999988873
No 15
>PRK06630 hypothetical protein; Provisional
Probab=23.21 E-value=21 Score=27.86 Aligned_cols=26 Identities=23% Similarity=0.758 Sum_probs=19.3
Q ss_pred HHHhhhhhcCCCCCCCCCCeeeecCcch--HHHHHHh
Q 030789 122 ARRRKWLENSPESSSNDDPVIFDTSIVP--WWAWIKR 156 (171)
Q Consensus 122 ~~rRK~Led~Pe~s~n~epv~FdtsiiP--WWaW~kR 156 (171)
-+||+|.+-+- .+|.|-|| |+.||-.
T Consensus 35 gr~rRWViY~g---------~~daS~VPpeWHgWLHh 62 (99)
T PRK06630 35 GRPRRFVIYKN---------VNEPTKIPPSWHAWLHH 62 (99)
T ss_pred CCceEEEEeCC---------CCccccCCcchhhhhcc
Confidence 35678887643 36789998 9999954
No 16
>PF08557 Lipid_DES: Sphingolipid Delta4-desaturase (DES); InterPro: IPR013866 Sphingolipids are important membrane signalling molecules involved in many different cellular functions in eukaryotes. Sphingolipid delta 4-desaturase catalyses the formation of (E)-sphing-4-enine []. Some proteins in this entry have bifunctional delta 4-desaturase/C-4-hydroxylase activity. Delta 4-desaturated sphingolipids may play a role in early signalling required for entry into meiotic and spermatid differentiation pathways during Drosophila spermatogenesis []. This small protein associates with FA_desaturase IPR005804 from INTERPRO and appears to be specific to sphingolipid delta 4-desaturase. ; GO: 0016705 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 0006633 fatty acid biosynthetic process, 0055114 oxidation-reduction process, 0016021 integral to membrane
Probab=22.81 E-value=36 Score=22.48 Aligned_cols=14 Identities=36% Similarity=0.662 Sum_probs=11.7
Q ss_pred HHHHhhhhhcCCCC
Q 030789 121 EARRRKWLENSPES 134 (171)
Q Consensus 121 E~~rRK~Led~Pe~ 134 (171)
-.|||.+|+.+||.
T Consensus 16 ~~RRk~IL~k~PeI 29 (39)
T PF08557_consen 16 ASRRKEILKKHPEI 29 (39)
T ss_pred HHHHHHHHHhChHH
Confidence 36899999999984
No 17
>PF14078 DUF4259: Domain of unknown function (DUF4259)
Probab=21.40 E-value=21 Score=25.93 Aligned_cols=20 Identities=20% Similarity=0.536 Sum_probs=17.4
Q ss_pred CccchhhhhhcCCcCchhhh
Q 030789 99 GTWDLKQFQKNGQTDWDAVI 118 (171)
Q Consensus 99 GtWDl~qF~~~G~~dWDaVI 118 (171)
|+|+..-|..|+..||=.-+
T Consensus 1 GaWg~g~FdnD~a~D~l~el 20 (128)
T PF14078_consen 1 GAWGTGPFDNDTALDFLDEL 20 (128)
T ss_pred CCCCCCCCCCchHHHHHHHH
Confidence 89999999999999995544
No 18
>PF09701 Cas_Cmr5: CRISPR-associated protein (Cas_Cmr5); InterPro: IPR010160 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. This entry represents a family of Cas proteins as represented by TM1791.1 from Thermotoga maritima. This family of Cas proteins are found in both archaeal and bacterial species.; PDB: 2OEB_A 2ZOP_A.
Probab=20.58 E-value=52 Score=24.55 Aligned_cols=11 Identities=36% Similarity=1.084 Sum_probs=9.2
Q ss_pred cchHHHHHHhh
Q 030789 147 IVPWWAWIKRF 157 (171)
Q Consensus 147 iiPWWaW~kRf 157 (171)
++-++.|+|||
T Consensus 107 ~La~l~WlKRf 117 (122)
T PF09701_consen 107 ALAFLNWLKRF 117 (122)
T ss_dssp HHHHHHHHHHH
T ss_pred HHHHHHHHHHH
Confidence 46789999998
No 19
>PLN03182 xyloglucan 6-xylosyltransferase; Provisional
Probab=20.13 E-value=94 Score=29.47 Aligned_cols=31 Identities=35% Similarity=0.709 Sum_probs=22.0
Q ss_pred CcCchhhhhHHHHHhhhhhcCCCCCCC---CCCeeeecCc
Q 030789 111 QTDWDAVIDAEARRRKWLENSPESSSN---DDPVIFDTSI 147 (171)
Q Consensus 111 ~~dWDaVIdAE~~rRK~Led~Pe~s~n---~epv~Fdtsi 147 (171)
-+||| .+|+.||+.||..... ..+||.=|..
T Consensus 102 i~~wd------~~R~~wl~~~p~~~~~~~g~prVviVT~s 135 (429)
T PLN03182 102 ISDWD------EQRRRWLRKNPGFPSFVNGKPRVLLVTGS 135 (429)
T ss_pred CCCHH------HHHHHHHHhCCCCCCccCCCCCEEEEeCC
Confidence 46787 5899999999997643 3456655543
Done!