Query 047317
Match_columns 299
No_of_seqs 66 out of 68
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 09:55:59 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/047317.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/047317hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF14953 DUF4504: Domain of un 100.0 1.2E-71 2.7E-76 519.9 25.5 263 8-299 2-270 (270)
2 COG0742 N6-adenine-specific me 56.8 27 0.00058 31.9 5.6 61 31-109 59-121 (187)
3 PF12672 DUF3793: Protein of u 32.2 1.5E+02 0.0033 26.3 6.4 63 30-97 4-72 (176)
4 cd07042 STAS_SulP_like_sulfate 31.4 1.7E+02 0.0037 22.0 5.9 65 69-139 5-71 (107)
5 PF09651 Cas_APE2256: CRISPR-a 20.9 35 0.00075 29.0 0.2 22 187-208 105-126 (136)
6 COG2819 Predicted hydrolase of 18.2 51 0.0011 31.7 0.7 16 200-215 39-54 (264)
7 TIGR02886 spore_II_AA anti-sig 17.8 1.9E+02 0.004 22.4 3.7 42 72-113 7-49 (106)
8 COG4678 Muramidase (phage lamb 17.3 56 0.0012 29.6 0.7 29 257-285 117-152 (180)
9 PF03602 Cons_hypoth95: Conser 16.2 2.3E+02 0.005 25.1 4.3 52 9-60 30-88 (183)
10 cd01684 Tet_like_IV EF-G_domai 15.8 64 0.0014 26.3 0.6 11 193-204 69-79 (115)
No 1
>PF14953 DUF4504: Domain of unknown function (DUF4504)
Probab=100.00 E-value=1.2e-71 Score=519.88 Aligned_cols=263 Identities=41% Similarity=0.628 Sum_probs=230.9
Q ss_pred HHHHHhhcccccccchhhhhHHHHHHHhcCCceeEEeecCCC-hHHHHHHHHHHHHHhhhcCC-CCCCeEEEEECCeEEE
Q 047317 8 LESSLSHIKWRLKSSSKLRLEIDILALCTGMRPVIMVDYGGK-MPELQEHLCELLKRCQKESP-SFEHLRVMVIEDMIYL 85 (299)
Q Consensus 8 ~~~~~~~~~~rl~~~~~~~La~dVlaV~~GLRPAvL~Dy~~~-~~qlq~~L~~LL~~~q~~~~-~~~~Lrvl~i~d~i~l 85 (299)
.++|++++|||+++++|++|++||+||++|||||+||||+++ ++|+|+||++|+.++++... .+++||||+|+||+||
T Consensus 2 ~~~~~~~~~~~l~~~~~~~L~~dilaV~~GLRpa~L~Dy~~~~~~~lq~~L~~L~~~~~q~~~~~~~~L~vl~I~~~~~l 81 (270)
T PF14953_consen 2 QRTCLMGKRWRLSSSSCLRLARDILAVCSGLRPAVLYDYNGAGAPQLQEYLCSLLRLAQQESGLLFQNLRVLVIDDNILL 81 (270)
T ss_pred hhhhhCcCCcCCcHHHHHHHHHHHHHHHcCCccEEEEEcCCCCHHHHHHHHHHhhhhhhcccchhccceEEEEEcCcEEE
Confidence 578999999999999999999999999999999999999999 55999999999999887655 8999999999999999
Q ss_pred EehhHHHHHHHhhccCCCceEEEEccCCC--CccccccccchHHHHHHHHHHHhhccccCCCCcccccCCCCCccccccc
Q 047317 86 IHVKGLAEYVSSSLSSEAELHFVDLEQDP--PKMITLKEKSSVGMQLISVQKLFSLVFPLNGMTDEIRLPNRTDHTIEAT 163 (299)
Q Consensus 86 In~~~l~e~l~~~l~s~~~~~FVDvs~s~--P~l~~~~e~~~~~~~l~~i~~~~~~~f~~~~~~~~~r~~~~~~~~~~~~ 163 (299)
||++++++|+++++.++.. ||||+.+. |++++.++.+++++++++++++|++ .. ..+ ++
T Consensus 82 vn~~~~~~~le~~l~s~~~--lvdVs~~~~~P~l~~~~~~~~~~~~l~~i~~~l~~---~~----------~~~----~~ 142 (270)
T PF14953_consen 82 VNPKELLEHLESSLRSNDL--LVDVSLSLSPPKLCSQDQESDLKSQLQSIQDHLSQ---FN----------ASN----NN 142 (270)
T ss_pred EeHHHHHHHHHHHhcCCCE--EEEEeCCCCCCccccccchhHHHHHHHHHHHHHhh---hc----------ccc----cc
Confidence 9999999999999998644 55555555 9999998889999999999999996 11 001 00
Q ss_pred CCccccCCCCcceecCCCcccCCCccccceeeeecCCceEEEecCCCchhhhccccCCceEEEEEEEEecCCCCCCCCce
Q 047317 164 SSNITISPQSTEVVDLSSCICDSQVTIPTLNGWLLGYPVVYLFDKEHIADAIYNLSTQSLRIFKILVTRNGPFSKGSMPE 243 (299)
Q Consensus 164 s~~~~~s~~~~~viDls~~l~~s~~~lpTL~G~LLGYPVvY~f~~~~~~~n~~cLS~~pL~vf~v~v~~~~~~~~~~~~~ 243 (299)
.+........+|+++++++++||+||||||||||||||||++++.++| ||||+||+||+|.++++....++++++
T Consensus 143 ---~~~~~~~~~~~~~~~~l~~~~~nl~TL~G~LLGYPvvY~f~~~~~~~n--cLs~~pL~V~~v~~~~~~~~~~~~~~~ 217 (270)
T PF14953_consen 143 ---ASELSESSESIDSSSGLESSDWNLPTLFGWLLGYPVVYWFDQEQSSDN--CLSMTPLRVFTVQASRSWLSDQPQHRE 217 (270)
T ss_pred ---cchhcccccccccccccccCCCCcchhhhhhhCCCEEEEeccccchhh--hhccCceEEEEEEEeccccccCcccce
Confidence 122233445578889999999999999999999999999999999999 999999999999996554455566899
Q ss_pred eEEeeecccccCCCCC--chhHHHHHHHHHHHHhhhccccceeeeeeeeeeecccccC
Q 047317 244 ELMSFSVPYELSMEGS--NEPWAEMFLAKMQSKWAKCKPTWRTLQMEVSECFPQAIAL 299 (299)
Q Consensus 244 ~L~SFSVP~~L~~~~~--~e~W~~~fl~~~~~k~~~~~~~w~~~~~ev~~~~~~~~~~ 299 (299)
+|||||||++|++++. +|+|+++|+++|+++ ++|++++|++|+|++||++|
T Consensus 218 ~L~SFSvP~~L~~~~~~~le~W~~~l~~~~~~q-----~~~~~l~~~~~~~~~~sv~l 270 (270)
T PF14953_consen 218 ELYSFSVPESLFPELSSHLENWIESLLERFQQQ-----NVWADLSISSETVTLPSVVL 270 (270)
T ss_pred eEEEeeCchhhccCccHHHHHHHHHHHHHHHhh-----cCCCceEEEEEEEeccceeC
Confidence 9999999999999554 599999999999997 99999999999999999987
No 2
>COG0742 N6-adenine-specific methylase [DNA replication, recombination, and repair]
Probab=56.82 E-value=27 Score=31.86 Aligned_cols=61 Identities=25% Similarity=0.288 Sum_probs=40.7
Q ss_pred HHHHhcCCceeEEeecCCChH-HHHHHHHHHHHHhhhcCCCCCCeEEEEECCeEEEEehhHHHHHHHhhccC-CCceEEE
Q 047317 31 ILALCTGMRPVIMVDYGGKMP-ELQEHLCELLKRCQKESPSFEHLRVMVIEDMIYLIHVKGLAEYVSSSLSS-EAELHFV 108 (299)
Q Consensus 31 VlaV~~GLRPAvL~Dy~~~~~-qlq~~L~~LL~~~q~~~~~~~~Lrvl~i~d~i~lIn~~~l~e~l~~~l~s-~~~~~FV 108 (299)
+=|+++|.+.|+++|-+.... .+++++..| ..+++.=+++.+.. ..+++.-.. .-++.|+
T Consensus 59 lEAlSRGA~~~~~vE~~~~a~~~l~~N~~~l-----------------~~~~~~~~~~~da~-~~L~~~~~~~~FDlVfl 120 (187)
T COG0742 59 LEALSRGAARVVFVEKDRKAVKILKENLKAL-----------------GLEGEARVLRNDAL-RALKQLGTREPFDLVFL 120 (187)
T ss_pred HHHHhCCCceEEEEecCHHHHHHHHHHHHHh-----------------CCccceEEEeecHH-HHHHhcCCCCcccEEEe
Confidence 558999999999999998766 677776666 22344444455555 555555443 2378887
Q ss_pred E
Q 047317 109 D 109 (299)
Q Consensus 109 D 109 (299)
|
T Consensus 121 D 121 (187)
T COG0742 121 D 121 (187)
T ss_pred C
Confidence 6
No 3
>PF12672 DUF3793: Protein of unknown function (DUF3793); InterPro: IPR024523 This family of bacterial proteins is functionally uncharacterised. The proteins in this family contain two conserved sequence motifs: PHE and LGYP.
Probab=32.24 E-value=1.5e+02 Score=26.35 Aligned_cols=63 Identities=19% Similarity=0.294 Sum_probs=41.0
Q ss_pred HHHHHhcCCceeEEeecCCCh-HHHHHHHHHHHHHhhhcCCCCCCeEEEEE---CC--eEEEEehhHHHHHHHh
Q 047317 30 DILALCTGMRPVIMVDYGGKM-PELQEHLCELLKRCQKESPSFEHLRVMVI---ED--MIYLIHVKGLAEYVSS 97 (299)
Q Consensus 30 dVlaV~~GLRPAvL~Dy~~~~-~qlq~~L~~LL~~~q~~~~~~~~Lrvl~i---~d--~i~lIn~~~l~e~l~~ 97 (299)
..--+-.|+|||-|+=+.... .++.+.+++. .+. ....++++..+ ++ -+|+-+++.+.+++.+
T Consensus 4 ~cAPtL~g~Kpa~L~~~~~~~~~~~~~~~~~~----~~~-l~~~gl~~~~L~~~~~~~lilvYr~~~L~~~L~~ 72 (176)
T PF12672_consen 4 HCAPTLAGIKPANLFSFSKSDGENLYELWEKY----NRE-LNPKGLSFRILKECEGRVLILVYREKLLERYLSD 72 (176)
T ss_pred hhHHHHhCCCeEeEEEEECCchHHHHHHHHHH----HHH-hhhcCcEEEEEEecCCeEEEEEEeHHHHHHHHCC
Confidence 334577899999999998543 3666655555 222 22666776665 33 2366699998888764
No 4
>cd07042 STAS_SulP_like_sulfate_transporter Sulphate Transporter and Anti-Sigma factor antagonist domain of SulP-like sulfate transporters, plays a role in the function and regulation of the transport activity, proposed general NTP binding function. The SulP family is a large and diverse family of anion transporters, with members from eubacteria, plants, fungi, and mammals. They contain 10 to 14 transmembrane helices which form the catalytic core of the protein and a C-terminal extension, the STAS (Sulphate Transporter and AntiSigma factor antagonist) domain which plays a role in the function and regulation of the transport activity. The STAS domain is found in the C-terminal region of sulphate transporters and bacterial anti-sigma factor antagonists. It has been suggested that this domain may have a general NTP binding function.
Probab=31.37 E-value=1.7e+02 Score=21.99 Aligned_cols=65 Identities=9% Similarity=0.105 Sum_probs=43.8
Q ss_pred CCCCCeEEEEECCeEEEEehhHHHHHHHhhccCC--CceEEEEccCCCCccccccccchHHHHHHHHHHHhhc
Q 047317 69 PSFEHLRVMVIEDMIYLIHVKGLAEYVSSSLSSE--AELHFVDLEQDPPKMITLKEKSSVGMQLISVQKLFSL 139 (299)
Q Consensus 69 ~~~~~Lrvl~i~d~i~lIn~~~l~e~l~~~l~s~--~~~~FVDvs~s~P~l~~~~e~~~~~~~l~~i~~~~~~ 139 (299)
...++..++.+.|.+++-|.+.+.+.+....... ...+.+|.+.-. .+ + ......|..+.+.+..
T Consensus 5 ~~~~~~~v~~l~G~l~~~~~~~l~~~~~~~~~~~~~~~~lilD~~~v~-~i----D-ss~~~~L~~~~~~~~~ 71 (107)
T cd07042 5 EEPPGVLIYRIDGPLFFGNAEYFKDRLLRLVDEDPPLKVVILDLSAVN-FI----D-STAAEALEELVKDLRK 71 (107)
T ss_pred ccCCCEEEEEecCceEeehHHHHHHHHHHHhccCCCceEEEEECCCCc-hh----h-HHHHHHHHHHHHHHHH
Confidence 3456788999999999999999999988877643 245677776531 11 1 2244556666666554
No 5
>PF09651 Cas_APE2256: CRISPR-associated protein (Cas_APE2256); InterPro: IPR013442 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 conserved region of about 150 amino acids found in a family of Cas proteins in at least five archaeal and three bacterial species. In six of eight species, the protein is encoded the vicinity of a CRISPR/Cas locus.; PDB: 3QYF_A.
Probab=20.90 E-value=35 Score=29.05 Aligned_cols=22 Identities=41% Similarity=0.768 Sum_probs=16.7
Q ss_pred CccccceeeeecCCceEEEecC
Q 047317 187 QVTIPTLNGWLLGYPVVYLFDK 208 (299)
Q Consensus 187 ~~~lpTL~G~LLGYPVvY~f~~ 208 (299)
....-++.|+++|+||.|-|..
T Consensus 105 ~~~~~~~~g~~~~~~v~Yi~E~ 126 (136)
T PF09651_consen 105 EIAYLTLLGMLYGDPVYYIFEE 126 (136)
T ss_dssp HHHHHHHHHHHT--EEEEEETT
T ss_pred HHHHHHHHHHHcCCCEEEEEcC
Confidence 3456699999999999999985
No 6
>COG2819 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]
Probab=18.19 E-value=51 Score=31.67 Aligned_cols=16 Identities=38% Similarity=0.939 Sum_probs=12.9
Q ss_pred CceEEEecCCCchhhh
Q 047317 200 YPVVYLFDKEHIADAI 215 (299)
Q Consensus 200 YPVvY~f~~~~~~~n~ 215 (299)
|||+|.-|-+..+++.
T Consensus 39 YpVlY~lDGn~vf~~~ 54 (264)
T COG2819 39 YPVLYMLDGNAVFNAL 54 (264)
T ss_pred CcEEEEecchhhhchH
Confidence 9999999987766553
No 7
>TIGR02886 spore_II_AA anti-sigma F factor antagonist. The anti-sigma F factor antagonist, also called stage II sporulation protein AA, is a protein universal among endospore-forming bacteria, all of which belong to the Firmcutes
Probab=17.78 E-value=1.9e+02 Score=22.40 Aligned_cols=42 Identities=2% Similarity=0.086 Sum_probs=32.8
Q ss_pred CCeEEEEECCeEEEEehhHHHHHHHhhcc-CCCceEEEEccCC
Q 047317 72 EHLRVMVIEDMIYLIHVKGLAEYVSSSLS-SEAELHFVDLEQD 113 (299)
Q Consensus 72 ~~Lrvl~i~d~i~lIn~~~l~e~l~~~l~-s~~~~~FVDvs~s 113 (299)
+++.++.++|..++-|.+.+.+.+.+.+. +.++.+.+|.+.-
T Consensus 7 ~~~~vi~l~G~L~f~~~~~~~~~l~~~~~~~~~~~vilDls~v 49 (106)
T TIGR02886 7 GDVLIVRLSGELDHHTAERVRRKIDDAIERRPIKHLILNLKNV 49 (106)
T ss_pred CCEEEEEEecccchhhHHHHHHHHHHHHHhCCCCEEEEECCCC
Confidence 46778889999999999999999887765 3445677777653
No 8
>COG4678 Muramidase (phage lambda lysozyme) [Carbohydrate transport and metabolism]
Probab=17.28 E-value=56 Score=29.62 Aligned_cols=29 Identities=28% Similarity=0.460 Sum_probs=19.3
Q ss_pred CCCchhHH--HHHHHHHH-----HHhhhccccceee
Q 047317 257 EGSNEPWA--EMFLAKMQ-----SKWAKCKPTWRTL 285 (299)
Q Consensus 257 ~~~~e~W~--~~fl~~~~-----~k~~~~~~~w~~~ 285 (299)
+-..=+|. ..+++.++ .-+.||+++|+||
T Consensus 117 D~va~~~i~d~~al~~i~aG~i~qal~k~s~~WaSL 152 (180)
T COG4678 117 DAVAYRWIRDRDALADIQAGRIDQALRKLSNTWASL 152 (180)
T ss_pred hHHHHHHHHhcChHhHHhcccHHHHHHHhcchhhcc
Confidence 44555663 34555443 4688999999998
No 9
>PF03602 Cons_hypoth95: Conserved hypothetical protein 95; InterPro: IPR004398 This entry contains Ribosomal RNA small subunit methyltransferase D as well as the putative rRNA methyltransferase YlbH. They methylate the guanosine in position 966 of 16S rRNA in the assembled 30S particle [].; GO: 0008168 methyltransferase activity, 0031167 rRNA methylation; PDB: 3P9N_A 2ESR_B 2IFT_A 1WS6_A 2FPO_B 2FHP_A.
Probab=16.24 E-value=2.3e+02 Score=25.11 Aligned_cols=52 Identities=25% Similarity=0.335 Sum_probs=32.0
Q ss_pred HHHHhhcccc-cccchhhhhHH-----HHHHHhcCCceeEEeecCCChH-HHHHHHHHH
Q 047317 9 ESSLSHIKWR-LKSSSKLRLEI-----DILALCTGMRPVIMVDYGGKMP-ELQEHLCEL 60 (299)
Q Consensus 9 ~~~~~~~~~r-l~~~~~~~La~-----dVlaV~~GLRPAvL~Dy~~~~~-qlq~~L~~L 60 (299)
+|--+-+..+ +.-+..++|.. =+=|+.+|-+-+++||.+.... .+++.+..+
T Consensus 30 ealFniL~~~~~~g~~vLDLFaGSGalGlEALSRGA~~v~fVE~~~~a~~~i~~N~~~l 88 (183)
T PF03602_consen 30 EALFNILQPRNLEGARVLDLFAGSGALGLEALSRGAKSVVFVEKNRKAIKIIKKNLEKL 88 (183)
T ss_dssp HHHHHHHHCH-HTT-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHHHH
T ss_pred HHHHHHhcccccCCCeEEEcCCccCccHHHHHhcCCCeEEEEECCHHHHHHHHHHHHHh
Confidence 3334444444 55555555522 2448999999999999998655 677777666
No 10
>cd01684 Tet_like_IV EF-G_domain IV_RPP domain is a part of bacterial ribosomal protected proteins (RPP) family. RPPs such as tetracycline resistance proteins Tet(M) and Tet(O) mediate tetracycline resistance in both gram-positive and -negative species. Tetracyclines inhibit the accommodation of aminoacyl-tRNA into ribosomal A site and therefore prevent the addition of new amino acids to the growing polypeptide. RPPs Tet(M) confer tetracycline resistance by releasing tetracycline from the ribosome and thereby freeing the ribosome from inhibitory effects of the drug, such that aa-tRNA can bind to the A site and protein synthesis can continue.
Probab=15.83 E-value=64 Score=26.35 Aligned_cols=11 Identities=27% Similarity=0.480 Sum_probs=8.9
Q ss_pred eeeeecCCceEE
Q 047317 193 LNGWLLGYPVVY 204 (299)
Q Consensus 193 L~G~LLGYPVvY 204 (299)
-.|.| ||||+-
T Consensus 69 ~~G~l-G~pv~d 79 (115)
T cd01684 69 QQGLY-GWEVTD 79 (115)
T ss_pred hcCCC-CCCEee
Confidence 45899 999975
Done!