Query 036568
Match_columns 168
No_of_seqs 103 out of 136
Neff 3.8
Searched_HMMs 46136
Date Fri Mar 29 03:17:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/036568.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/036568hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF09478 CBM49: Carbohydrate b 96.3 0.014 3.1E-07 41.5 6.0 74 65-152 1-79 (80)
2 PLN02171 endoglucanase 82.8 2.1 4.7E-05 41.6 5.0 77 62-153 534-615 (629)
3 PF14016 DUF4232: Protein of u 45.7 1.2E+02 0.0027 22.7 6.9 77 60-154 1-82 (131)
4 PF07705 CARDB: CARDB; InterP 41.5 48 0.001 22.5 3.7 69 63-155 2-72 (101)
5 PLN02340 endoglucanase 37.6 28 0.0006 34.1 2.7 78 61-151 518-600 (614)
6 PF10633 NPCBM_assoc: NPCBM-as 29.5 1E+02 0.0022 21.1 3.8 48 80-151 7-57 (78)
7 PF02933 CDC48_2: Cell divisio 29.4 29 0.00063 23.3 1.0 27 136-163 15-41 (64)
8 COG3900 Predicted periplasmic 27.3 40 0.00087 29.9 1.7 20 72-91 206-225 (262)
9 PF09270 BTD: Beta-trefoil DNA 15.8 1.6E+02 0.0035 24.3 2.9 50 101-154 71-124 (158)
10 PF03293 Pox_RNA_pol: Poxvirus 14.8 2.5E+02 0.0055 23.3 3.8 48 103-150 94-141 (160)
No 1
>PF09478 CBM49: Carbohydrate binding domain CBM49; InterPro: IPR019028 A carbohydrate-binding module (CBM) is defined as a contiguous amino acid sequence within a carbohydrate-active enzyme with a discreet fold having carbohydrate-binding activity. A few exceptions are CBMs in cellulosomal scaffolding proteins and rare instances of independent putative CBMs. The requirement of CBMs existing as modules within larger enzymes sets this class of carbohydrate-binding protein apart from other non-catalytic sugar binding proteins such as lectins and sugar transport proteins. CBMs were previously classified as cellulose-binding domains (CBDs) based on the initial discovery of several modules that bound cellulose [, ]. However, additional modules in carbohydrate-active enzymes are continually being found that bind carbohydrates other than cellulose yet otherwise meet the CBM criteria, hence the need to reclassify these polypeptides using more inclusive terminology. Previous classification of cellulose-binding domains were based on amino acid similarity. Groupings of CBDs were called "Types" and numbered with roman numerals (e.g. Type I or Type II CBDs). In keeping with the glycoside hydrolase classification, these groupings are now called families and numbered with Arabic numerals. Families 1 to 13 are the same as Types I to XIII. For a detailed review on the structure and binding modes of CBMs see []. This domain is found at the C-terminal of cellulases and in vitro binding studies have shown it to binds to crystalline cellulose []. ; GO: 0030246 carbohydrate binding, 0005576 extracellular region
Probab=96.31 E-value=0.014 Score=41.46 Aligned_cols=74 Identities=19% Similarity=0.260 Sum_probs=54.2
Q ss_pred eeEEecccCCCCC-Ccc--cEEEEEecccccCCCCCCCCcccccEEEEcCCcc-cceeeCCcceeeecCCceEe-cCCcc
Q 036568 65 IVIYQGSTAPLPN-GIP--ACTVQILNTCTCVSESESGGCSICNIHVNCGWFS-SARLVNPQVFRRIHYDDCLV-NDGEA 139 (168)
Q Consensus 65 I~V~Q~~TG~~v~-G~P--ey~VtI~N~C~~~~~~~~~~C~~snV~L~CggF~-Sa~~VDP~vfrrl~~ddCLV-NdG~p 139 (168)
|+|.|..+..+.. |.+ +|.|+|+|.+. =+++++++....+. +.= .+-+ ..++..-+ ..-.+
T Consensus 1 i~i~q~~~~sW~~~g~~y~qy~v~I~N~~~---------~~I~~~~i~~~~l~~~iW----~l~~-~~~~~y~lPs~~~~ 66 (80)
T PF09478_consen 1 ITITQTLVNSWTENGQTYTQYDVTITNNGS---------KPIKSLKISIDNLYGSIW----GLDK-VSGNTYTLPSYQPT 66 (80)
T ss_pred CEEEEEEEeEEEeCCEEEEEEEEEEEECCC---------CeEEEEEEEECccchhhe----eEEe-ccCCEEECCccccc
Confidence 6788988877554 543 79999999997 68999999998774 221 1222 45566666 33349
Q ss_pred CCCCCeeEEEEec
Q 036568 140 LPPGQALSFQYAN 152 (168)
Q Consensus 140 I~~g~~VsF~YAw 152 (168)
|.+|++.+|-|-.
T Consensus 67 i~pg~s~~FGYI~ 79 (80)
T PF09478_consen 67 IKPGQSFTFGYIS 79 (80)
T ss_pred cCCCCEEEEEEEe
Confidence 9999999999953
No 2
>PLN02171 endoglucanase
Probab=82.80 E-value=2.1 Score=41.62 Aligned_cols=77 Identities=17% Similarity=0.221 Sum_probs=52.9
Q ss_pred CCceeEEecccCCCCC---CcccEEEEEecccccCCCCCCCCcccccEEEEcCCc-ccceeeCCcceeeecCCceEecCC
Q 036568 62 KDDIVIYQGSTAPLPN---GIPACTVQILNTCTCVSESESGGCSICNIHVNCGWF-SSARLVNPQVFRRIHYDDCLVNDG 137 (168)
Q Consensus 62 ~sDI~V~Q~~TG~~v~---G~Pey~VtI~N~C~~~~~~~~~~C~~snV~L~CggF-~Sa~~VDP~vfrrl~~ddCLVNdG 137 (168)
.+.|+|.|..++.+.. +.-+|.|+|+|++. .+++++++.=..+ -+.- .+.+ .++...+=+-
T Consensus 534 ~~ei~i~q~v~~sW~~~g~~y~qy~v~I~N~s~---------~~ik~i~i~~~~~~~~iW----~v~~--~~ngytlPs~ 598 (629)
T PLN02171 534 SSPIEIEQKATASWKAKGRTYYRYSTTVTNRSA---------KTLKELHLGISKLYGPLW----GLTK--AGYGYVLPSW 598 (629)
T ss_pred cceeEEEEEEEEEEEcCCceEEEEEEEEEECCC---------Cceeeeeeeeccccccch----heee--cCCcccCchh
Confidence 3379999999987664 35589999999997 9999999975333 2221 1111 1223333333
Q ss_pred c-cCCCCCeeEEEEecC
Q 036568 138 E-ALPPGQALSFQYANT 153 (168)
Q Consensus 138 ~-pI~~g~~VsF~YAws 153 (168)
. .|.+|+..+|-|-+.
T Consensus 599 ~~sL~aG~s~tFgyI~~ 615 (629)
T PLN02171 599 MPSLPAGKSLEFVYVHS 615 (629)
T ss_pred hcccCCCCeeEEEeecC
Confidence 2 788899999999965
No 3
>PF14016 DUF4232: Protein of unknown function (DUF4232)
Probab=45.70 E-value=1.2e+02 Score=22.70 Aligned_cols=77 Identities=17% Similarity=0.222 Sum_probs=48.8
Q ss_pred CCCCceeEEecccCCCCCCcccEEEEEecccccCCCCCCCCcccccEEEEcCCcccceeeCCcceeeec-----CCceEe
Q 036568 60 CSKDDIVIYQGSTAPLPNGIPACTVQILNTCTCVSESESGGCSICNIHVNCGWFSSARLVNPQVFRRIH-----YDDCLV 134 (168)
Q Consensus 60 Cs~sDI~V~Q~~TG~~v~G~Pey~VtI~N~C~~~~~~~~~~C~~snV~L~CggF~Sa~~VDP~vfrrl~-----~ddCLV 134 (168)
|...|+.++-..... ..|...+.|+++|+=. .-|.+ .||..+.++|..=-. +. .+. -
T Consensus 1 C~~~~L~~~~~~~~~-~~g~~~~~l~~tN~s~-------~~C~l-------~G~P~v~~~~~~g~~-~~~~~~~~~~--~ 62 (131)
T PF14016_consen 1 CTAADLSVTVGPVDA-GAGQRHATLTFTNTSD-------TPCTL-------YGYPGVALVDADGAP-LGVPAVREGP--P 62 (131)
T ss_pred CCcccEEEEEecccC-CCCccEEEEEEEECCC-------CcEEe-------ccCCcEEEECCCCCc-CCccccccCC--C
Confidence 888898888866533 3577799999999653 45766 567666665543221 11 111 1
Q ss_pred cCCccCCCCCeeEEEEecCC
Q 036568 135 NDGEALPPGQALSFQYANTF 154 (168)
Q Consensus 135 NdG~pI~~g~~VsF~YAws~ 154 (168)
..--.|.+|++..|.-.|..
T Consensus 63 ~~~vtL~PG~sA~a~l~~~~ 82 (131)
T PF14016_consen 63 PRPVTLAPGGSAYAGLRWSN 82 (131)
T ss_pred CCcEEECCCCEEEEEEEEec
Confidence 11235778999888887754
No 4
>PF07705 CARDB: CARDB; InterPro: IPR011635 The APHP (acidic peptide-dependent hydrolases/peptidase) domain is found in a variety of different proteins.; PDB: 2KUT_A 2L0D_A 3IDU_A 2KL6_A.
Probab=41.47 E-value=48 Score=22.49 Aligned_cols=69 Identities=22% Similarity=0.318 Sum_probs=33.3
Q ss_pred CceeE-EecccCCCCCCcc-cEEEEEecccccCCCCCCCCcccccEEEEcCCcccceeeCCcceeeecCCceEecCCccC
Q 036568 63 DDIVI-YQGSTAPLPNGIP-ACTVQILNTCTCVSESESGGCSICNIHVNCGWFSSARLVNPQVFRRIHYDDCLVNDGEAL 140 (168)
Q Consensus 63 sDI~V-~Q~~TG~~v~G~P-ey~VtI~N~C~~~~~~~~~~C~~snV~L~CggF~Sa~~VDP~vfrrl~~ddCLVNdG~pI 140 (168)
-||.| ..........|.+ .+.|+|.|.=. -...++.+. .+.+-..+ . .-.+ ..|
T Consensus 2 pDL~v~~~~~~~~~~~g~~~~i~~~V~N~G~---------~~~~~~~v~--~~~~~~~~-----~-----~~~i---~~L 57 (101)
T PF07705_consen 2 PDLTVSITVSPSNVVPGEPVTITVTVKNNGT---------ADAENVTVR--LYLDGNSV-----S-----TVTI---PSL 57 (101)
T ss_dssp --EEE-EEEC-SEEETTSEEEEEEEEEE-SS---------S-BEEEEEE--EEETTEEE-----E-----EEEE---SEB
T ss_pred CCEEEEEeeCCCcccCCCEEEEEEEEEECCC---------CCCCCEEEE--EEECCcee-----c-----cEEE---CCc
Confidence 36677 2222233334555 79999999754 334455554 11221111 1 1122 588
Q ss_pred CCCCeeEEEEecCCc
Q 036568 141 PPGQALSFQYANTFQ 155 (168)
Q Consensus 141 ~~g~~VsF~YAws~~ 155 (168)
.+|+...|++.|..+
T Consensus 58 ~~g~~~~v~~~~~~~ 72 (101)
T PF07705_consen 58 APGESETVTFTWTPP 72 (101)
T ss_dssp -TTEEEEEEEEEE-S
T ss_pred CCCcEEEEEEEEEeC
Confidence 888887777777654
No 5
>PLN02340 endoglucanase
Probab=37.59 E-value=28 Score=34.08 Aligned_cols=78 Identities=21% Similarity=0.224 Sum_probs=51.0
Q ss_pred CCCceeEEecccCCCCCC---cccEEEEEecccccCCCCCCCCcccccEEEEcCCc-ccceeeCCcceeeecCCceEecC
Q 036568 61 SKDDIVIYQGSTAPLPNG---IPACTVQILNTCTCVSESESGGCSICNIHVNCGWF-SSARLVNPQVFRRIHYDDCLVND 136 (168)
Q Consensus 61 s~sDI~V~Q~~TG~~v~G---~Pey~VtI~N~C~~~~~~~~~~C~~snV~L~CggF-~Sa~~VDP~vfrrl~~ddCLVNd 136 (168)
+..++.+.|.-+..+..+ .-+|.|+|+|+|. =|++.+++.=..+ -..--|.|.+=+ +...+-+
T Consensus 518 ~~~~~e~~~~~~~sw~~~g~~y~~~~v~i~N~s~---------~pi~~l~~~~~~l~g~lwgl~~~~~~----~~y~~p~ 584 (614)
T PLN02340 518 SGAPVEFVHSITNTWTAGGTTYYRHKVIIKNKSQ---------KPITDLKLVIEDLSGPIWGLNPTKEK----NTYELPQ 584 (614)
T ss_pred CCCchhhhhhheeeeecCCceEEEEEEEEEeCCC---------CCchhhhhhhhhcccchhcceecccc----CCccCch
Confidence 355667778887765543 3479999999997 7899988876333 333233332212 3333333
Q ss_pred C-ccCCCCCeeEEEEe
Q 036568 137 G-EALPPGQALSFQYA 151 (168)
Q Consensus 137 G-~pI~~g~~VsF~YA 151 (168)
= ..|.+|+.++|.|-
T Consensus 585 ~~~tl~~g~~~~f~yi 600 (614)
T PLN02340 585 WQKVLQPGSQLSFVYV 600 (614)
T ss_pred hhhccCCCCeeEEEec
Confidence 3 47888999999998
No 6
>PF10633 NPCBM_assoc: NPCBM-associated, NEW3 domain of alpha-galactosidase; InterPro: IPR018905 This domain has been named NEW3, but its function is not known. It is found on proteins which are bacterial galactosidases [].; PDB: 1EUT_A 2BZD_A 1WCQ_C 2BER_A 1W8O_A 1EUU_A 1W8N_A.
Probab=29.47 E-value=1e+02 Score=21.06 Aligned_cols=48 Identities=21% Similarity=0.448 Sum_probs=24.2
Q ss_pred ccEEEEEecccccCCCCCCCCcccccEEEEc---CCcccceeeCCcceeeecCCceEecCCccCCCCCeeEEEEe
Q 036568 80 PACTVQILNTCTCVSESESGGCSICNIHVNC---GWFSSARLVNPQVFRRIHYDDCLVNDGEALPPGQALSFQYA 151 (168)
Q Consensus 80 Pey~VtI~N~C~~~~~~~~~~C~~snV~L~C---ggF~Sa~~VDP~vfrrl~~ddCLVNdG~pI~~g~~VsF~YA 151 (168)
-.++++|.|.+. -+..++.|+- .|+. ...+|.-+. .|++|++.++++.
T Consensus 7 ~~~~~tv~N~g~---------~~~~~v~~~l~~P~GW~--~~~~~~~~~-------------~l~pG~s~~~~~~ 57 (78)
T PF10633_consen 7 VTVTLTVTNTGT---------APLTNVSLSLSLPEGWT--VSASPASVP-------------SLPPGESVTVTFT 57 (78)
T ss_dssp EEEEEEEE--SS---------S-BSS-EEEEE--TTSE-----EEEEE---------------B-TTSEEEEEEE
T ss_pred EEEEEEEEECCC---------CceeeEEEEEeCCCCcc--ccCCccccc-------------cCCCCCEEEEEEE
Confidence 379999999996 5677777765 3444 122332111 6677777766653
No 7
>PF02933 CDC48_2: Cell division protein 48 (CDC48), domain 2; InterPro: IPR004201 This domain has a double psi-beta barrel fold and includes VCP-like ATPase and N-ethylmaleimide sensitive fusion protein N-terminal domains. Both the VAT and NSF N-terminal functional domains consist of two structural domains of which this is at the C terminus. The VAT-N domain found in AAA ATPases (IPR003959 from INTERPRO) is a substrate 185-residue recognition domain [].; GO: 0005524 ATP binding; PDB: 1QDN_B 1QCS_A 1CR5_C 3QQ8_A 3HU2_A 3HU1_E 3HU3_A 3QWZ_A 3TIW_B 3QQ7_A ....
Probab=29.43 E-value=29 Score=23.31 Aligned_cols=27 Identities=22% Similarity=0.509 Sum_probs=20.7
Q ss_pred CCccCCCCCeeEEEEecCCcccccccee
Q 036568 136 DGEALPPGQALSFQYANTFQYPLSVSSV 163 (168)
Q Consensus 136 dG~pI~~g~~VsF~YAws~~f~L~~ssv 163 (168)
.|+|+..|+.|.|.|. ...++|.+.++
T Consensus 15 ~~~pv~~Gd~i~~~~~-~~~~~~~V~~~ 41 (64)
T PF02933_consen 15 EGRPVTKGDTIVFPFF-GQALPFKVVST 41 (64)
T ss_dssp TTEEEETT-EEEEEET-TEEEEEEEEEE
T ss_pred cCCCccCCCEEEEEeC-CcEEEEEEEEE
Confidence 3599999999999996 57778877544
No 8
>COG3900 Predicted periplasmic protein [Function unknown]
Probab=27.26 E-value=40 Score=29.94 Aligned_cols=20 Identities=30% Similarity=0.159 Sum_probs=17.7
Q ss_pred cCCCCCCcccEEEEEecccc
Q 036568 72 TAPLPNGIPACTVQILNTCT 91 (168)
Q Consensus 72 TG~~v~G~Pey~VtI~N~C~ 91 (168)
|.+++.|-|||+|++.|.=.
T Consensus 206 Tsk~v~g~PqYtv~fsnwks 225 (262)
T COG3900 206 TSKDVPGEPQYTVVFSNWKS 225 (262)
T ss_pred EecccCCCCcEEEEEccccc
Confidence 56778899999999999985
No 9
>PF09270 BTD: Beta-trefoil DNA-binding domain; InterPro: IPR015350 This DNA-binding domain adopt a beta-trefoil fold, that is, a capped beta-barrel with internal pseudo threefold symmetry. In the DNA-binding protein LAG-1, it also is the site of mutually exclusive interactions with NotchIC (and the viral protein EBNA2) and corepressors (SMRT/N-Cor and CIR) []. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 2FO1_A 3NBN_A 2F8X_C 3V79_C 3IAG_C 3BRG_C.
Probab=15.81 E-value=1.6e+02 Score=24.35 Aligned_cols=50 Identities=16% Similarity=0.253 Sum_probs=36.0
Q ss_pred cccccEEEEc--CCcccceeeCCcceeeecCCceEecC--CccCCCCCeeEEEEecCC
Q 036568 101 CSICNIHVNC--GWFSSARLVNPQVFRRIHYDDCLVND--GEALPPGQALSFQYANTF 154 (168)
Q Consensus 101 C~~snV~L~C--ggF~Sa~~VDP~vfrrl~~ddCLVNd--G~pI~~g~~VsF~YAws~ 154 (168)
|.=+-|.|-| .|.+| +|-++|+++.+.=++.. |+|+...+.+-|+-....
T Consensus 71 ~YGs~V~Lv~~~TGv~s----ppliIRKVdk~~~~ld~~~~ePVSQLhK~Afq~~d~~ 124 (158)
T PF09270_consen 71 HYGSTVVLVCSVTGVSS----PPLIIRKVDKQQVVLDAASDEPVSQLHKCAFQMIDGE 124 (158)
T ss_dssp BTTSEEEEEETTT-EBE----EEEEEEEEETTEEESSGGTTSB-BTTEEEEEEETTST
T ss_pred ecCCEEEEEECCCCccc----CceEEEEecCCceeecccccchhhhhheeeEEecCCC
Confidence 4455678888 45555 58899999866555555 899999999999988843
No 10
>PF03293 Pox_RNA_pol: Poxvirus DNA-directed RNA polymerase, 18 kD subunit; InterPro: IPR004973 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. The Poxvirus DNA-directed RNA polymerase (2.7.7.6 from EC) catalyses DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. The enzyme consists of at least eight subunits, this is the 18 kDa subunit.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0019083 viral transcription
Probab=14.76 E-value=2.5e+02 Score=23.33 Aligned_cols=48 Identities=19% Similarity=0.272 Sum_probs=28.6
Q ss_pred cccEEEEcCCcccceeeCCcceeeecCCceEecCCccCCCCCeeEEEE
Q 036568 103 ICNIHVNCGWFSSARLVNPQVFRRIHYDDCLVNDGEALPPGQALSFQY 150 (168)
Q Consensus 103 ~snV~L~CggF~Sa~~VDP~vfrrl~~ddCLVNdG~pI~~g~~VsF~Y 150 (168)
-+||.+.|+..-=-..=|..-..--+.--|++.||..-..|..|+-.-
T Consensus 94 ESni~V~CgDLiCkl~rdsGtVSf~dsKYCfirNg~vY~ngs~Vsv~L 141 (160)
T PF03293_consen 94 ESNITVQCGDLICKLSRDSGTVSFNDSKYCFIRNGVVYDNGSEVSVVL 141 (160)
T ss_pred cCceEEEcCcEEEEeeccCCeEEecCceEEEEECCEEecCCCEEEEEe
Confidence 468888887653211112211111011249999999999999987654
Done!