Query 003912
Match_columns 787
No_of_seqs 219 out of 338
Neff 3.9
Searched_HMMs 46136
Date Thu Mar 28 14:14:22 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/003912.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/003912hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1213 Sister chromatid cohes 100.0 7.5E-59 1.6E-63 525.3 27.8 122 1-123 1-122 (614)
2 PF04825 Rad21_Rec8_N: N termi 100.0 2.1E-34 4.5E-39 265.3 4.5 111 1-112 1-111 (111)
3 PF04824 Rad21_Rec8: Conserved 99.7 1.5E-17 3.3E-22 137.1 2.7 52 729-780 4-55 (55)
4 PF02616 ScpA_ScpB: ScpA/B pro 95.9 0.0094 2E-07 61.6 4.9 48 729-776 194-241 (242)
5 PRK00104 scpA segregation and 94.7 0.054 1.2E-06 56.9 5.9 50 729-778 190-239 (242)
6 COG1354 scpA Rec8/ScpA/Scc1-li 91.2 0.36 7.7E-06 51.0 5.7 49 730-778 191-240 (248)
7 PRK00478 scpA segregation and 77.6 2.3 5E-05 49.7 4.0 49 729-777 361-413 (505)
8 PF06278 DUF1032: Protein of u 73.1 2.5 5.4E-05 50.1 2.8 40 729-768 493-532 (565)
9 PF06278 DUF1032: Protein of u 38.0 49 0.0011 39.6 5.3 31 58-88 7-37 (565)
10 KOG2359 Uncharacterized conser 22.2 47 0.001 39.6 1.6 50 729-783 536-585 (688)
11 COG1965 CyaY Protein implicate 20.2 43 0.00094 32.2 0.7 21 4-24 47-67 (106)
No 1
>KOG1213 consensus Sister chromatid cohesion complex Cohesin, subunit RAD21/SCC1 [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=7.5e-59 Score=525.25 Aligned_cols=122 Identities=52% Similarity=0.783 Sum_probs=118.5
Q ss_pred CCccchhhccCCchhhhHHhhhcCCCCCchhhccCChHHHHHHHhccCCCcchhhhhhhhccceEEEEecchhHHHhhHH
Q 003912 1 MFYSRSLLSRKGPLGAIWVAAYCFKRLKKAQVFETNIPSSVDEILEEELDVMTYRVLAYLLLGLVRIYSKKVEYLFDDCN 80 (787)
Q Consensus 1 MFYS~~LLskkGpLa~IWLAAt~~kKLsKkqIl~~dI~~s~~~Il~p~~p~iALRLSG~LLlGVVRIYsrKv~YLl~Dcn 80 (787)
|||||.||+||||||+|||||||+|||+|+||++|||+++|+.|++|.+| ||||||||||+||||||||||+|||+|||
T Consensus 1 MFYs~~vLakKGPLa~IWlAAh~~kKL~K~qv~~tdI~~sve~Il~p~~~-lALRtSghLLlGVVRIYSrK~~YLl~Dcn 79 (614)
T KOG1213|consen 1 MFYSHFVLAKKGPLAKIWLAAHWEKKLSKAQVFETDIPQSVEEILQPKVP-LALRTSGHLLLGVVRIYSRKVKYLLDDCN 79 (614)
T ss_pred CcchhhhHhhcCchhhhhHHhHHhhhcchhheeeccHHHHHHHHhCcccc-eehhhhcccceeeEEeehhhHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999998 99999999999999999999999999999
Q ss_pred HHHHHHHhhhcccccccCCCCCCCCCcccccCCCccCCccChh
Q 003912 81 DAVVKINNFLVSEKSMKNLGNLCAPYCSITLPESFELDAFDLE 123 (787)
Q Consensus 81 ~al~kIk~~f~~~~~dlp~~~~~A~~~aITLPd~f~ld~~Dl~ 123 (787)
++|.|||++|+.+++++|.........+||||++|+++++|+.
T Consensus 80 eal~kIk~afr~~~vd~p~~~~~~~~~siTLPE~~~d~d~~l~ 122 (614)
T KOG1213|consen 80 EALLKIKMAFRSGQVDLPELAPRLPTHSITLPETFEDDDFDLP 122 (614)
T ss_pred HHHHHHHHHhccccccCCCcccccccccccchhhhcccccccc
Confidence 9999999999999999999888888899999999998888876
No 2
>PF04825 Rad21_Rec8_N: N terminus of Rad21 / Rec8 like protein; InterPro: IPR006910 This domain represents a conserved N-terminal region found in eukaryotic cohesins of the Rad21, Rec8 and Scc1 families. Rad21/Rec8 like proteins mediate sister chromatid cohesion during mitosis and meiosis, as part of the cohesin complex []. Cohesion is necessary for homologous recombination (including double-strand break repair) and correct chromatid segregation. These proteins may also be involved in chromosome condensation. Dissociation at the metaphase to anaphase transition causes loss of cohesion and chromatid segregation [].; GO: 0005515 protein binding
Probab=100.00 E-value=2.1e-34 Score=265.35 Aligned_cols=111 Identities=43% Similarity=0.702 Sum_probs=107.8
Q ss_pred CCccchhhccCCchhhhHHhhhcCCCCCchhhccCChHHHHHHHhccCCCcchhhhhhhhccceEEEEecchhHHHhhHH
Q 003912 1 MFYSRSLLSRKGPLGAIWVAAYCFKRLKKAQVFETNIPSSVDEILEEELDVMTYRVLAYLLLGLVRIYSKKVEYLFDDCN 80 (787)
Q Consensus 1 MFYS~~LLskkGpLa~IWLAAt~~kKLsKkqIl~~dI~~s~~~Il~p~~p~iALRLSG~LLlGVVRIYsrKv~YLl~Dcn 80 (787)
||||++||+|+|+|++||+|||+++||+|++|+++||+++|++|++|+.| +|||+||+||+||||||+||++||++||+
T Consensus 1 MFy~~~iL~k~~~l~~vWlaat~~~kl~k~~i~~vdI~~~c~~I~~~~~~-~sLRlss~LL~Gvv~Iy~kKv~yLl~D~~ 79 (111)
T PF04825_consen 1 MFYSHDILSKKGPLATVWLAATLGKKLSKKQILQVDIPKICEEIIEPENP-LSLRLSSQLLYGVVRIYSKKVEYLLSDCN 79 (111)
T ss_pred CCccHHHHhcCCcHHHHHHHHhccCCCCHHHHHhCCHHHHHHHHhCCCcC-eeHHHHhHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999998 99999999999999999999999999999
Q ss_pred HHHHHHHhhhcccccccCCCCCCCCCcccccC
Q 003912 81 DAVVKINNFLVSEKSMKNLGNLCAPYCSITLP 112 (787)
Q Consensus 81 ~al~kIk~~f~~~~~dlp~~~~~A~~~aITLP 112 (787)
+++.+|++++.....+++.++..|++++||||
T Consensus 80 ~~~~~l~~~~~~~~~dl~~~~~~~~~~~it~p 111 (111)
T PF04825_consen 80 ELLSKLKRAFRPKKIDLPKDKTKASRNAITLP 111 (111)
T ss_pred HHHHHHHHHhcccccCCCccccCCChhhccCc
Confidence 99999999887777888988999999999998
No 3
>PF04824 Rad21_Rec8: Conserved region of Rad21 / Rec8 like protein; InterPro: IPR006909 This domain represents a conserved C-terminal region found in eukaryotic cohesins of the Rad21, Rec8 and Scc1 families. Rad21/Rec8 like proteins mediate sister chromatid cohesion during mitosis and meiosis, as part of the cohesin complex []. Cohesion is necessary for homologous recombination (including double-strand break repair) and correct chromatid segregation. These proteins may also be involved in chromosome condensation. Dissociation at the metaphase to anaphase transition causes loss of cohesion and chromatid segregation [].; GO: 0000228 nuclear chromosome; PDB: 1W1W_E.
Probab=99.67 E-value=1.5e-17 Score=137.14 Aligned_cols=52 Identities=52% Similarity=0.820 Sum_probs=37.5
Q ss_pred cccchhhhhccchHHHHHHHHHHHHhhccCCceeecccCCCcCeEEecCccH
Q 003912 729 EAIKLLPLLEGRTVKETARIFYEILVLQTKGIVNVKQDDAYGDILVVKAPWW 780 (787)
Q Consensus 729 ~~vsl~~lL~g~TRKeAAr~FfE~LVLkT~g~IdV~Q~epYgDI~I~~~p~L 780 (787)
+.++|++|++|+||++|||+||++|||+|+|||+|+|++|||||.|+++|+|
T Consensus 4 ~~~~~~~l~~~~tr~~AA~~Fy~~LvL~t~~~I~v~Q~~pygdI~I~~~~~~ 55 (55)
T PF04824_consen 4 ESLSLSQLPEGMTRKEAARAFYELLVLATKGYIDVKQEEPYGDIEISPGPKF 55 (55)
T ss_dssp HHTT----------HHHHHHHHHHHHHHHHTSEEEEESSTT--EEEEE-GGG
T ss_pred cccHHHHhhCCCCHHHHHHHHHHHHHHhhCCeEEeecCCCCCCeEEeeCCCC
Confidence 5789999999999999999999999999999999999999999999999986
No 4
>PF02616 ScpA_ScpB: ScpA/B protein; InterPro: IPR003768 This family represents ScpA, which along with ScpB (IPR005234 from INTERPRO) interacts with SMC in vivo forming a complex that is required for chromosome condensation and segregation [, ]. The SMC-Scp complex appears to be similar to the MukB-MukE-Muk-F complex in Escherichia coli [], where MukB (IPR007406 from INTERPRO) is the homologue of SMC. ScpA and ScpB have little sequence similarity to MukE (IPR007385 from INTERPRO) or MukF (IPR005582 from INTERPRO), they are predicted to be structurally similar, being predominantly alpha-helical with coiled coil regions. In general scpA and scpB form an operon in most bacterial genomes. Flanking genes are highly variable suggesting that the operon has moved throughout evolution. Bacteria containing an smc gene also contain scpA or scpB but not necessarily both. An exception is found in Deinococcus radiodurans, which contains scpB but neither smc nor scpA. In the archaea the gene order SMC-ScpA is conserved in nearly all species, as is the very short distance between the two genes, indicating co-transcription of the both in different archaeal genera and arguing that interaction of the gene products is not confined to the homologues in Bacillus subtilis. It would seem probable that, in light of all the studies, SMC, ScpA and ScpB proteins or homologues act together in chromosome condensation and segregation in all prokaryotes [].
Probab=95.92 E-value=0.0094 Score=61.58 Aligned_cols=48 Identities=23% Similarity=0.442 Sum_probs=46.0
Q ss_pred cccchhhhhccchHHHHHHHHHHHHhhccCCceeecccCCCcCeEEec
Q 003912 729 EAIKLLPLLEGRTVKETARIFYEILVLQTKGIVNVKQDDAYGDILVVK 776 (787)
Q Consensus 729 ~~vsl~~lL~g~TRKeAAr~FfE~LVLkT~g~IdV~Q~epYgDI~I~~ 776 (787)
+.++|++|+.+.+|.+..-.|--+|-|...|.|++.|+++||||.|..
T Consensus 194 ~~~~f~~l~~~~~r~~~V~tFLAlLeL~k~~~i~i~Q~e~fgdI~I~~ 241 (242)
T PF02616_consen 194 GWVSFSELFEEPSRSEVVVTFLALLELVKQGKIEIEQEEPFGDIYIEL 241 (242)
T ss_pred CceeHHHHcCcCCcCeeHHHHHHHHHHhhcCcEEEEEcCCCCceEEEe
Confidence 589999999999999999999999999999999999999999999974
No 5
>PRK00104 scpA segregation and condensation protein A; Reviewed
Probab=94.74 E-value=0.054 Score=56.94 Aligned_cols=50 Identities=20% Similarity=0.337 Sum_probs=46.8
Q ss_pred cccchhhhhccchHHHHHHHHHHHHhhccCCceeecccCCCcCeEEecCc
Q 003912 729 EAIKLLPLLEGRTVKETARIFYEILVLQTKGIVNVKQDDAYGDILVVKAP 778 (787)
Q Consensus 729 ~~vsl~~lL~g~TRKeAAr~FfE~LVLkT~g~IdV~Q~epYgDI~I~~~p 778 (787)
+.++|.+|+.+.+|.+..-.|--+|-|...|-|.+.|+++||+|.|..+.
T Consensus 190 ~~~~f~~l~~~~~~~~~v~tFLAlLEL~k~~~i~l~Q~~~f~~I~i~~~~ 239 (242)
T PRK00104 190 KRLSFSELFKEPSKNEFVVTFLALLELIKLQEIIVEQEENFGEIYLEKGE 239 (242)
T ss_pred CcEeHHHHhCCCCchhhHHHHHHHHHHHhcCeeEEEEcCCCCeEEEEeCC
Confidence 46999999999999999999999999999999999999999999997653
No 6
>COG1354 scpA Rec8/ScpA/Scc1-like protein (kleisin family) [Replication, recombination, and repair]
Probab=91.24 E-value=0.36 Score=50.99 Aligned_cols=49 Identities=22% Similarity=0.433 Sum_probs=40.1
Q ss_pred ccchhhhhccchHHHHHH-HHHHHHhhccCCceeecccCCCcCeEEecCc
Q 003912 730 AIKLLPLLEGRTVKETAR-IFYEILVLQTKGIVNVKQDDAYGDILVVKAP 778 (787)
Q Consensus 730 ~vsl~~lL~g~TRKeAAr-~FfE~LVLkT~g~IdV~Q~epYgDI~I~~~p 778 (787)
.+.|..++.-.+++...- .|--+|-|...|-|++.|+++||||.|..+.
T Consensus 191 ~~~~~~~~~~~~~~~~vv~~FlAlLeL~k~~~v~l~Qee~fgdI~i~~~~ 240 (248)
T COG1354 191 VLRFSDLFSPEERKDEVVSTFLALLELVKEGKVELEQEEPFGDIYIRLLG 240 (248)
T ss_pred cccHHHhcccccchhHHHHHHHHHHHHHhcCceEEEecccccceEEEecC
Confidence 677888777344444444 8888999999999999999999999999865
No 7
>PRK00478 scpA segregation and condensation protein A/unknown domain fusion protein; Provisional
Probab=77.56 E-value=2.3 Score=49.67 Aligned_cols=49 Identities=14% Similarity=0.222 Sum_probs=44.4
Q ss_pred cccchhhhhcc----chHHHHHHHHHHHHhhccCCceeecccCCCcCeEEecC
Q 003912 729 EAIKLLPLLEG----RTVKETARIFYEILVLQTKGIVNVKQDDAYGDILVVKA 777 (787)
Q Consensus 729 ~~vsl~~lL~g----~TRKeAAr~FfE~LVLkT~g~IdV~Q~epYgDI~I~~~ 777 (787)
+.++|.+|+.+ .+|.+..-.|--+|.|...|-|.+.|.++||+|.|...
T Consensus 361 ~~~~F~~L~~~~~~~~sr~evVvtFLAlLEL~K~~~I~i~Q~~~f~~I~i~~~ 413 (505)
T PRK00478 361 NQVSLKRVLLKINHKISLMYFVTAFVALLVLVNNQKIDLEQKNDDEELYICLL 413 (505)
T ss_pred CeEEhHHHhhhcccCCCcceEehHHHHHHHHhccCeEEEEEcCCCCeEEEEEc
Confidence 35899999984 48888899999999999999999999999999999875
No 8
>PF06278 DUF1032: Protein of unknown function (DUF1032); InterPro: IPR009378 This entry includes a regulatory subunit of Non-SMC condensin II complex called H2. Non-SMC condensin II complex seems to provide chromosomes with an additional level of organisation and rigidity and in establishing mitotic chromosome architecture. May play a role in lineage-specific role in T-cell development.
Probab=73.07 E-value=2.5 Score=50.05 Aligned_cols=40 Identities=30% Similarity=0.454 Sum_probs=37.1
Q ss_pred cccchhhhhccchHHHHHHHHHHHHhhccCCceeecccCC
Q 003912 729 EAIKLLPLLEGRTVKETARIFYEILVLQTKGIVNVKQDDA 768 (787)
Q Consensus 729 ~~vsl~~lL~g~TRKeAAr~FfE~LVLkT~g~IdV~Q~ep 768 (787)
+..+|.+|.+|+..-+.+|.|+-+|-|++.|=|++.|...
T Consensus 493 ~~~~f~~vv~~~~~~ev~R~fla~LqLaN~~nv~i~~~~~ 532 (565)
T PF06278_consen 493 EKATFADVVEGKPPYEVCRYFLASLQLANDGNVEISQDPG 532 (565)
T ss_pred CeeeHHHHhCCCChhHHHHHHHHHHHHhcCCCeeeccCCc
Confidence 4679999999999999999999999999999999998754
No 9
>PF06278 DUF1032: Protein of unknown function (DUF1032); InterPro: IPR009378 This entry includes a regulatory subunit of Non-SMC condensin II complex called H2. Non-SMC condensin II complex seems to provide chromosomes with an additional level of organisation and rigidity and in establishing mitotic chromosome architecture. May play a role in lineage-specific role in T-cell development.
Probab=37.99 E-value=49 Score=39.64 Aligned_cols=31 Identities=39% Similarity=0.554 Sum_probs=27.8
Q ss_pred hhhccceEEEEecchhHHHhhHHHHHHHHHh
Q 003912 58 AYLLLGLVRIYSKKVEYLFDDCNDAVVKINN 88 (787)
Q Consensus 58 G~LLlGVVRIYsrKv~YLl~Dcn~al~kIk~ 88 (787)
+.|+.|.+-||||||+|||.-+-.++.-|..
T Consensus 7 alliQgsa~vYskKVeyly~lv~~~l~~l~~ 37 (565)
T PF06278_consen 7 ALLIQGSACVYSKKVEYLYSLVYQALDFLSG 37 (565)
T ss_pred HHHHhcchhhHHHHHHHHHHHHHHHHHHHhc
Confidence 5688999999999999999999999988875
No 10
>KOG2359 consensus Uncharacterized conserved protein [Function unknown]
Probab=22.21 E-value=47 Score=39.64 Aligned_cols=50 Identities=24% Similarity=0.151 Sum_probs=40.2
Q ss_pred cccchhhhhccchHHHHHHHHHHHHhhccCCceeecccCCCcCeEEecCccHhhh
Q 003912 729 EAIKLLPLLEGRTVKETARIFYEILVLQTKGIVNVKQDDAYGDILVVKAPWWDQS 783 (787)
Q Consensus 729 ~~vsl~~lL~g~TRKeAAr~FfE~LVLkT~g~IdV~Q~epYgDI~I~~~p~L~~~ 783 (787)
+.-+|.+|..|.++-|-+|.||-.|-|.+-|=|+++|- |+...-|-|..|
T Consensus 536 ~~~~F~eL~a~Q~~fEV~Ra~~A~LQL~N~~dVel~~~-----~n~~~~P~l~~A 585 (688)
T KOG2359|consen 536 MAPNFLELDALQTDFEVPRAEYAPLQLENIDDVELNSV-----INLPALPLLKKA 585 (688)
T ss_pred CCCcHHHHhcCCcccccchhhhcceeeccCCceeeccc-----CCCccchhHHHh
Confidence 56779999999999999999999999999999999982 344444555443
No 11
>COG1965 CyaY Protein implicated in iron transport, frataxin homolog [Inorganic ion transport and metabolism]
Probab=20.20 E-value=43 Score=32.17 Aligned_cols=21 Identities=29% Similarity=0.610 Sum_probs=18.2
Q ss_pred cchhhccCCchhhhHHhhhcC
Q 003912 4 SRSLLSRKGPLGAIWVAAYCF 24 (787)
Q Consensus 4 S~~LLskkGpLa~IWLAAt~~ 24 (787)
|+.++.|+.|+-+||||+-.+
T Consensus 47 s~iiINkQ~P~~qiWlAs~~g 67 (106)
T COG1965 47 SQIIINKQEPLQQIWLASKVG 67 (106)
T ss_pred cEEEEeCCChHHHHHhhccCC
Confidence 566788999999999999776
Done!