Query 042217
Match_columns 270
No_of_seqs 139 out of 542
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 04:01:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/042217.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/042217hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3430 Dynein light chain typ 100.0 6.1E-31 1.3E-35 208.3 10.5 85 185-270 2-86 (90)
2 PTZ00059 dynein light chain; P 100.0 1.8E-30 4E-35 203.2 11.0 84 185-270 3-86 (90)
3 PLN03058 dynein light chain ty 100.0 2.8E-30 6.1E-35 215.5 11.7 89 182-270 29-118 (128)
4 PF01221 Dynein_light: Dynein 100.0 1.8E-29 3.9E-34 195.1 9.0 85 184-270 1-85 (89)
5 PF04155 Ground-like: Ground-l 92.9 0.91 2E-05 34.4 8.1 50 219-269 23-73 (76)
6 PF12006 DUF3500: Protein of u 54.8 40 0.00087 32.3 6.6 24 191-214 216-239 (313)
7 PF15650 Tox-REase-9: Restrict 45.0 16 0.00035 29.8 2.0 17 227-243 70-86 (89)
8 PF10703 MoaF: Molybdenum cofa 31.8 42 0.0009 32.0 2.8 29 238-269 182-210 (265)
9 COG4831 Roadblock/LC7 domain [ 25.8 3.5E+02 0.0075 22.9 6.8 62 189-255 26-96 (109)
10 PF13742 tRNA_anti_2: OB-fold 24.9 1.1E+02 0.0024 24.1 3.8 42 220-265 4-47 (99)
11 KOG2451 Aldehyde dehydrogenase 24.7 1.4E+02 0.003 30.8 5.1 46 187-232 49-94 (503)
12 PRK13007 succinyl-diaminopimel 23.2 2.8E+02 0.0061 25.3 6.6 39 196-234 1-40 (352)
13 PF06150 ChaB: ChaB; InterPro 21.6 1.8E+02 0.004 21.4 4.1 15 225-240 40-54 (57)
No 1
>KOG3430 consensus Dynein light chain type 1 [Cytoskeleton]
Probab=99.97 E-value=6.1e-31 Score=208.27 Aligned_cols=85 Identities=41% Similarity=0.771 Sum_probs=78.0
Q ss_pred ccCCcEEEeCCCCHHHHHHHHHHHHHHhHhhhcCCHHHHHHHHHHHhcccCCCceEEEEcCCceeeEEEccCcEEEEEeC
Q 042217 185 ASCGVKIVSVDMPPFMQIHAVDCARKTYDSLEKFTAKTLALTLKKEFDEVYGPAWHCIVGTSFGSFVTHSVGGFLYFSMD 264 (270)
Q Consensus 185 ~~~dV~Ii~SDMpeEMQ~eAIeiAkeAlk~~eK~~eKdIAk~IKkeFDKKYGptWHCIVGkSFGS~VTHE~~~FIyF~lg 264 (270)
....+.|..+|||++||++|+++|.+|++.++. ++++||.+||++||++||++||||||++|||+||||+++||||++|
T Consensus 2 ~~~~~~vk~tDM~~~mq~~a~~~a~~al~~f~~-~~k~iA~~iKkefDkkyG~~WhcivG~~FGs~vThe~g~Fiyf~~g 80 (90)
T KOG3430|consen 2 LERKAVVKATDMPEEMQQEAIELARQALEKFNV-IEKDIAAFIKKEFDKKYGPTWHCIVGRNFGSYVTHETGHFIYFYLG 80 (90)
T ss_pred CCccceEecCCCChHHHHHHHHHHHHHHHHcCC-ChHHHHHHHHHHHhhhcCCccEEEEcCCcceEEEeecCcEEEEEec
Confidence 446789999999999999999999999754433 4899999999999999999999999999999999999999999999
Q ss_pred CEEEEC
Q 042217 265 QKLYIL 270 (270)
Q Consensus 265 ~~afLL 270 (270)
.+++||
T Consensus 81 ~l~ill 86 (90)
T KOG3430|consen 81 VLAILL 86 (90)
T ss_pred eEEEEE
Confidence 999886
No 2
>PTZ00059 dynein light chain; Provisional
Probab=99.97 E-value=1.8e-30 Score=203.16 Aligned_cols=84 Identities=40% Similarity=0.772 Sum_probs=77.1
Q ss_pred ccCCcEEEeCCCCHHHHHHHHHHHHHHhHhhhcCCHHHHHHHHHHHhcccCCCceEEEEcCCceeeEEEccCcEEEEEeC
Q 042217 185 ASCGVKIVSVDMPPFMQIHAVDCARKTYDSLEKFTAKTLALTLKKEFDEVYGPAWHCIVGTSFGSFVTHSVGGFLYFSMD 264 (270)
Q Consensus 185 ~~~dV~Ii~SDMpeEMQ~eAIeiAkeAlk~~eK~~eKdIAk~IKkeFDKKYGptWHCIVGkSFGS~VTHE~~~FIyF~lg 264 (270)
...++.|+.+|||++||++|+++|.+|++.++ ++++||.+||++||++|||+||||||++|||++||++++||||+++
T Consensus 3 ~~~~~~i~~~dM~~emq~~a~~~~~~Al~~~~--~~kdiA~~IK~~fD~~yg~~WhciVG~~Fgs~vthe~~~~i~F~~~ 80 (90)
T PTZ00059 3 SDRKAVVKNADMSEDMQQDAIDCANQALEKFN--IEKDIAAYIKKEFDKKYNPTWHCIVGRNFGSYVTHETKHFIYFYLG 80 (90)
T ss_pred CCCccEEEECCCCHHHHHHHHHHHHHHHHHcC--chHHHHHHHHHHHHhhcCCCCEEEEecCeeEEEEEeCCcEEEEEEC
Confidence 34578899999999999999999999975432 3799999999999999999999999999999999999999999999
Q ss_pred CEEEEC
Q 042217 265 QKLYIL 270 (270)
Q Consensus 265 ~~afLL 270 (270)
+.+|||
T Consensus 81 ~~~vLl 86 (90)
T PTZ00059 81 QVAILL 86 (90)
T ss_pred CEEEEE
Confidence 999986
No 3
>PLN03058 dynein light chain type 1 family protein; Provisional
Probab=99.97 E-value=2.8e-30 Score=215.54 Aligned_cols=89 Identities=55% Similarity=0.955 Sum_probs=81.9
Q ss_pred hhhccCCcEEEeCCCCHHHHHHHHHHHHHHhHhhhcC-CHHHHHHHHHHHhcccCCCceEEEEcCCceeeEEEccCcEEE
Q 042217 182 DVLASCGVKIVSVDMPPFMQIHAVDCARKTYDSLEKF-TAKTLALTLKKEFDEVYGPAWHCIVGTSFGSFVTHSVGGFLY 260 (270)
Q Consensus 182 ~~m~~~dV~Ii~SDMpeEMQ~eAIeiAkeAlk~~eK~-~eKdIAk~IKkeFDKKYGptWHCIVGkSFGS~VTHE~~~FIy 260 (270)
.-..+.++.|+.+|||++||++|+++|.+|++.++.+ ++++||.+||++||++|||+||||||++|||+|||++++|||
T Consensus 29 ~~~~~~dv~Ik~sDM~~emQ~~ave~a~~Al~k~~~~~~ekdIA~~IKk~fDkkYG~tWHCIVGk~FGs~VTHe~~~fIy 108 (128)
T PLN03058 29 DQKDELNVRVRASDMPLVLQNRAFSCARDILDAMPGKLDSKRLALALKKEFDSAYGPAWHCIVGTSFGSYVTHSTGGFLY 108 (128)
T ss_pred hhccCCCCEEEECCCCHHHHHHHHHHHHHHHHHccccCCHHHHHHHHHHHHhhhhCCceEEEECCcEEEEEEEcCCcEEE
Confidence 3467789999999999999999999999998755433 479999999999999999999999999999999999999999
Q ss_pred EEeCCEEEEC
Q 042217 261 FSMDQKLYIL 270 (270)
Q Consensus 261 F~lg~~afLL 270 (270)
|++|+.+|||
T Consensus 109 F~ig~~aiLL 118 (128)
T PLN03058 109 FSIDKVYILL 118 (128)
T ss_pred EEECCEEEEE
Confidence 9999999986
No 4
>PF01221 Dynein_light: Dynein light chain type 1 ; InterPro: IPR001372 Dynein is a multisubunit microtubule-dependent motor enzyme that acts as the force generating protein of eukaryotic cilia and flagella. The cytoplasmic isoform of dynein acts as a motor for the intracellular retrograde motility of vesicles and organelles along microtubules. Dynein is composed of a number of ATP-binding large subunits (see IPR004273 from INTERPRO), intermediate size subunits and small subunits. Among the small subunits, there is a family of highly conserved proteins which make up this family [, ]. Both type 1 (DLC1) and 2 (DLC2) dynein light chains have a similar two-layer alpha-beta core structure consisting of beta-alpha(2)-beta-X-beta(2) [, ].; GO: 0007017 microtubule-based process, 0005875 microtubule associated complex; PDB: 1F95_A 1F96_A 1F3C_A 3P8M_B 2XQQ_C 1RE6_A 1CMI_A 1PWK_A 1PWJ_A 4DS1_C ....
Probab=99.96 E-value=1.8e-29 Score=195.13 Aligned_cols=85 Identities=41% Similarity=0.767 Sum_probs=76.9
Q ss_pred hccCCcEEEeCCCCHHHHHHHHHHHHHHhHhhhcCCHHHHHHHHHHHhcccCCCceEEEEcCCceeeEEEccCcEEEEEe
Q 042217 184 LASCGVKIVSVDMPPFMQIHAVDCARKTYDSLEKFTAKTLALTLKKEFDEVYGPAWHCIVGTSFGSFVTHSVGGFLYFSM 263 (270)
Q Consensus 184 m~~~dV~Ii~SDMpeEMQ~eAIeiAkeAlk~~eK~~eKdIAk~IKkeFDKKYGptWHCIVGkSFGS~VTHE~~~FIyF~l 263 (270)
|...+++|+.+||+++||++|+++|.+|++.++ ++++||++||++||++|||+||||||++|||++||++++||||++
T Consensus 1 m~~~~~~i~~~dM~~~~~~~~~~~~~~a~~~~~--~~~eiA~~iK~~lD~~yG~~Wh~IVG~~Fg~~~th~~~~~~~f~~ 78 (89)
T PF01221_consen 1 MSENKIVIKSSDMPEEMQEEAIELAKEALKKYQ--DEKEIAEFIKQELDKKYGPTWHCIVGKSFGSSVTHEPGTFLYFKI 78 (89)
T ss_dssp SGSCSEEEEEEES-HHHHHHHHHHHHHHHHHCS--SHHHHHHHHHHHHHHHHSS-EEEEEESEEEEEEEEETTEEEEEEE
T ss_pred CCCCccEEEECCCCHHHHHHHHHHHHHHHHHCC--cHHHHHHHHHHHHhcccCCceEEEECCcEEEEEEEcCCcEEEEEE
Confidence 566789999999999999999999999975332 489999999999999999999999999999999999999999999
Q ss_pred CCEEEEC
Q 042217 264 DQKLYIL 270 (270)
Q Consensus 264 g~~afLL 270 (270)
++..|||
T Consensus 79 ~~~~~li 85 (89)
T PF01221_consen 79 GNIAFLI 85 (89)
T ss_dssp TTEEEEE
T ss_pred CCEEEEE
Confidence 9999986
No 5
>PF04155 Ground-like: Ground-like domain; InterPro: IPR007284 This group of proteins contain one or more copies of the ground-like domain, which are specific to Caenorhabditis elegans and Caenorhabditis briggsae. It has been proposed that the ground-like domain containing proteins may bind and modulate the activity of Patched-like membrane molecules, reminiscent of the modulating activities of neuropeptides [].
Probab=92.90 E-value=0.91 Score=34.35 Aligned_cols=50 Identities=12% Similarity=0.183 Sum_probs=40.3
Q ss_pred CHHHHHHHHHHHhcccCCCceEEEEc-CCceeeEEEccCcEEEEEeCCEEEE
Q 042217 219 TAKTLALTLKKEFDEVYGPAWHCIVG-TSFGSFVTHSVGGFLYFSMDQKLYI 269 (270)
Q Consensus 219 ~eKdIAk~IKkeFDKKYGptWHCIVG-kSFGS~VTHE~~~FIyF~lg~~afL 269 (270)
+...+++.|...+.+.||+.|-||++ ++|... +|-...|.-+..+++.++
T Consensus 23 ~~~~s~~~Iq~~~e~~f~~~f~vIcs~~~Fsy~-~~~~~~~C~~~~~g~~c~ 73 (76)
T PF04155_consen 23 NLSISKRAIQKAAEKRFGGSFEVICSEGDFSYS-THTDDLYCKVEKNGVTCL 73 (76)
T ss_pred CHHHHHHHHHHHHHHHhCCCEEEEEeCCCceeE-EecccceeeeeeCCEEEE
Confidence 46789999999999999999999999 666555 444477777788887665
No 6
>PF12006 DUF3500: Protein of unknown function (DUF3500); InterPro: IPR021889 This family of proteins is functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 335 to 438 amino acids in length. This protein has a conserved GHH sequence motif. This protein has two completely conserved G residues that may be functionally important.
Probab=54.80 E-value=40 Score=32.28 Aligned_cols=24 Identities=4% Similarity=-0.007 Sum_probs=19.3
Q ss_pred EEeCCCCHHHHHHHHHHHHHHhHh
Q 042217 191 IVSVDMPPFMQIHAVDCARKTYDS 214 (270)
Q Consensus 191 Ii~SDMpeEMQ~eAIeiAkeAlk~ 214 (270)
|..++|+.+.|+.+..++..-+..
T Consensus 216 l~~s~Lt~~Qq~ll~~li~~y~~~ 239 (313)
T PF12006_consen 216 LAVSELTADQQELLLALIKEYLGR 239 (313)
T ss_pred cChhhCCHHHHHHHHHHHHHHHHh
Confidence 456999999999998888887543
No 7
>PF15650 Tox-REase-9: Restriction endonuclease fold toxin 9
Probab=45.00 E-value=16 Score=29.78 Aligned_cols=17 Identities=29% Similarity=0.868 Sum_probs=15.0
Q ss_pred HHHHhcccCCCceEEEE
Q 042217 227 LKKEFDEVYGPAWHCIV 243 (270)
Q Consensus 227 IKkeFDKKYGptWHCIV 243 (270)
-|++|...||.+|-|||
T Consensus 70 Y~~el~~~~G~~W~~~l 86 (89)
T PF15650_consen 70 YKQELEKIYGGGWKTRL 86 (89)
T ss_pred HHHHhcCccCCCeeEEe
Confidence 36789999999999998
No 8
>PF10703 MoaF: Molybdenum cofactor biosynthesis protein F; InterPro: IPR024724 Molybdenum cofactor biosynthesis protein F (MoaF) is essential for the production of the monoamine-inducible 30kDa protein in Klebsiella []. It is necessary for reconstituting organoautotrophic growth in Ralstonia eutropha []. MoaF is conserved in proteobacteria and some lower eukaryotes. The operon regulating the Moa genes is responsible for molybdenum cofactor biosynthesis.
Probab=31.82 E-value=42 Score=31.98 Aligned_cols=29 Identities=28% Similarity=0.749 Sum_probs=18.6
Q ss_pred ceEEEEcCCceeeEEEccCcEEEEEeCCEEEE
Q 042217 238 AWHCIVGTSFGSFVTHSVGGFLYFSMDQKLYI 269 (270)
Q Consensus 238 tWHCIVGkSFGS~VTHE~~~FIyF~lg~~afL 269 (270)
+|||+.|-.=|-. +...+=||++++..||
T Consensus 182 ~W~CL~G~e~Gla---D~D~c~~~Ki~d~lYl 210 (265)
T PF10703_consen 182 AWQCLSGVEKGLA---DTDRCHYYKIADNLYL 210 (265)
T ss_pred EEEEeeccccCCC---CccceEEEEecCCEEE
Confidence 8999999544422 3455666666665555
No 9
>COG4831 Roadblock/LC7 domain [Function unknown]
Probab=25.79 E-value=3.5e+02 Score=22.87 Aligned_cols=62 Identities=16% Similarity=0.115 Sum_probs=34.0
Q ss_pred cEEEeCCCCHHHHHHHHHHHHHHhHhhhcCCHHHHHHHHHHHhcccC---------CCceEEEEcCCceeeEEEcc
Q 042217 189 VKIVSVDMPPFMQIHAVDCARKTYDSLEKFTAKTLALTLKKEFDEVY---------GPAWHCIVGTSFGSFVTHSV 255 (270)
Q Consensus 189 V~Ii~SDMpeEMQ~eAIeiAkeAlk~~eK~~eKdIAk~IKkeFDKKY---------GptWHCIVGkSFGS~VTHE~ 255 (270)
..-...||+++|-.-+...|..- .-|. +-.|+---..--..| ||.|-|.|-+++|-||.-+.
T Consensus 26 Lv~Ykgdm~k~~A~maAkmcaAn-nmM~----~~qA~~~t~~sg~~w~P~~gwa~agg~yavci~Gn~GVFVe~~k 96 (109)
T COG4831 26 LVEYKGDMPKEMAEMAAKMCAAN-NMMG----DMQASGYTALSGMNWTPQNGWAVAGGKYAVCIMGNVGVFVELDK 96 (109)
T ss_pred eEEeeCCCCHHHHHHHHHHHHHH-HHHH----HHhhhhhhhhhcCccccccceEEecCceEEEEecceeEEEEcch
Confidence 44467899999887776655322 0011 111111111111112 77888888888998886543
No 10
>PF13742 tRNA_anti_2: OB-fold nucleic acid binding domain
Probab=24.94 E-value=1.1e+02 Score=24.13 Aligned_cols=42 Identities=19% Similarity=0.415 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHhccc--CCCceEEEEcCCceeeEEEccCcEEEEEeCC
Q 042217 220 AKTLALTLKKEFDEV--YGPAWHCIVGTSFGSFVTHSVGGFLYFSMDQ 265 (270)
Q Consensus 220 eKdIAk~IKkeFDKK--YGptWHCIVGkSFGS~VTHE~~~FIyF~lg~ 265 (270)
-.++..+||..++.. ++..| |.|.= |.++.-.+..+||.+.+
T Consensus 4 Vs~l~~~ik~~le~~~~~~~vw--V~GEI--s~~~~~~~gh~YftLkD 47 (99)
T PF13742_consen 4 VSELNNYIKDLLERDPPLPNVW--VEGEI--SNLKRHSSGHVYFTLKD 47 (99)
T ss_pred HHHHHHHHHHHHhcCCCcCCEE--EEEEE--eecEECCCceEEEEEEc
Confidence 357889999999998 56777 55632 22233377889998843
No 11
>KOG2451 consensus Aldehyde dehydrogenase [Energy production and conversion]
Probab=24.71 E-value=1.4e+02 Score=30.80 Aligned_cols=46 Identities=24% Similarity=0.234 Sum_probs=36.0
Q ss_pred CCcEEEeCCCCHHHHHHHHHHHHHHhHhhhcCCHHHHHHHHHHHhc
Q 042217 187 CGVKIVSVDMPPFMQIHAVDCARKTYDSLEKFTAKTLALTLKKEFD 232 (270)
Q Consensus 187 ~dV~Ii~SDMpeEMQ~eAIeiAkeAlk~~eK~~eKdIAk~IKkeFD 232 (270)
.++.-...||+-+.-++||+.|.+|+.....++.++=+..|++|+|
T Consensus 49 geii~~V~~~~V~e~~kAI~aA~EaF~s~~~~takeRs~lLrkwy~ 94 (503)
T KOG2451|consen 49 GEIIGKVADMTVEEAEKAIDAAYEAFKSYRNLTAKERSALLRKWYE 94 (503)
T ss_pred cchhhcccCCcHHHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHHHH
Confidence 3455568999999999999999999987655566666777777665
No 12
>PRK13007 succinyl-diaminopimelate desuccinylase; Reviewed
Probab=23.19 E-value=2.8e+02 Score=25.28 Aligned_cols=39 Identities=13% Similarity=0.036 Sum_probs=28.0
Q ss_pred CCHHHHHHHHHHHHHHhHhhhc-CCHHHHHHHHHHHhccc
Q 042217 196 MPPFMQIHAVDCARKTYDSLEK-FTAKTLALTLKKEFDEV 234 (270)
Q Consensus 196 MpeEMQ~eAIeiAkeAlk~~eK-~~eKdIAk~IKkeFDKK 234 (270)
|..+...++++...+.++.-.- .++.++|++|+++|.+.
T Consensus 1 ~~~~~~~~~~~~l~~li~ips~s~~e~~~~~~l~~~l~~~ 40 (352)
T PRK13007 1 MTLDLAADLAELTAALVDIPSVSGDEKALADAVEAALRAL 40 (352)
T ss_pred CccchHHHHHHHHHHHhcCCCCCchHHHHHHHHHHHHHhC
Confidence 5556677888888888652111 12678999999999875
No 13
>PF06150 ChaB: ChaB; InterPro: IPR009317 This family of proteins contain a conserved 60 residue region. This protein is known as ChaB in Escherichia coli and is found next to ChaA, which is a cation transporter protein. ChaB may be regulate ChaA function in some way.; PDB: 1SG7_A.
Probab=21.65 E-value=1.8e+02 Score=21.43 Aligned_cols=15 Identities=13% Similarity=0.592 Sum_probs=11.9
Q ss_pred HHHHHHhcccCCCceE
Q 042217 225 LTLKKEFDEVYGPAWH 240 (270)
Q Consensus 225 k~IKkeFDKKYGptWH 240 (270)
..+|+.+.+ -|+.|.
T Consensus 40 ~AVk~~Y~k-~~g~W~ 54 (57)
T PF06150_consen 40 AAVKRKYEK-VNGRWV 54 (57)
T ss_dssp HHHHHHEEE-SSS-EE
T ss_pred HHHHHHhee-cCCEee
Confidence 669999999 788896
Done!