Query psy8283
Match_columns 285
No_of_seqs 191 out of 343
Neff 4.1
Searched_HMMs 46136
Date Fri Aug 16 23:31:52 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8283.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8283hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1213|consensus 100.0 2.3E-47 5E-52 385.2 10.0 150 1-150 1-153 (614)
2 PF04825 Rad21_Rec8_N: N termi 100.0 8.4E-41 1.8E-45 273.1 5.4 111 1-111 1-111 (111)
3 PF06278 DUF1032: Protein of u 72.8 1.5 3.3E-05 45.6 0.9 31 57-87 7-37 (565)
4 PF05786 Cnd2: Condensin compl 55.1 19 0.00042 38.2 5.1 70 17-86 82-153 (725)
5 TIGR03422 mito_frataxin fratax 42.6 6.7 0.00015 31.9 -0.5 19 4-22 46-64 (97)
6 KOG2359|consensus 41.7 22 0.00048 37.6 2.9 36 50-85 57-92 (688)
7 COG1965 CyaY Protein implicate 41.4 9.4 0.0002 32.0 0.2 21 4-24 47-67 (106)
8 TIGR03421 FeS_CyaY iron donor 37.6 7.5 0.00016 31.9 -1.0 21 4-24 44-64 (102)
9 cd00503 Frataxin Frataxin is a 36.9 8.9 0.00019 31.5 -0.6 21 4-24 47-67 (105)
10 KOG2328|consensus 36.5 44 0.00095 35.9 4.1 71 17-87 65-137 (702)
11 PRK00446 cyaY frataxin-like pr 32.1 8.9 0.00019 31.6 -1.3 21 4-24 46-66 (105)
12 PRK01379 cyaY frataxin-like pr 26.5 17 0.00037 30.1 -0.6 17 6-22 48-64 (103)
13 PF03417 AAT: Acyl-coenzyme A: 25.9 52 0.0011 29.0 2.3 29 252-280 181-213 (225)
No 1
>KOG1213|consensus
Probab=100.00 E-value=2.3e-47 Score=385.16 Aligned_cols=150 Identities=61% Similarity=0.937 Sum_probs=144.9
Q ss_pred CccchhhhhccCChhhHHHhhhccCccchhhhhccCHHHHHHHhcCCCCcchhhhhhccccceEEEEecchhHHHHHHHH
Q psy8283 1 MFYAQFVLAKKGPLARIWLAAHWDKKLTKAHVFETNIEKSVDGILQPKVKMALRTSGHLLLGVVRIYSRKAKYLLADCNE 80 (285)
Q Consensus 1 MFYS~~lLskkgpLa~IWLAAt~~kKLsKk~Il~vdI~~sce~Il~P~~p~ALRLSg~LLlGVVRIYsrKv~YLl~Dc~~ 80 (285)
|||||.||+||||||+|||||||+|||+|+||++|||+++|+.|++|.+|||||+|||||+||||||+|||+||++|||+
T Consensus 1 MFYs~~vLakKGPLa~IWlAAh~~kKL~K~qv~~tdI~~sve~Il~p~~~lALRtSghLLlGVVRIYSrK~~YLl~Dcne 80 (614)
T KOG1213|consen 1 MFYSHFVLAKKGPLAKIWLAAHWEKKLSKAQVFETDIPQSVEEILQPKVPLALRTSGHLLLGVVRIYSRKVKYLLDDCNE 80 (614)
T ss_pred CcchhhhHhhcCchhhhhHHhHHhhhcchhheeeccHHHHHHHHhCcccceehhhhcccceeeEEeehhhHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhcCCCcCCCCccccccccccccCCccCCcccCCC-CCCccCcCcccccCCCc--cccceeccCCC
Q psy8283 81 AFVKIKMAFRPGMVDLPEDNREAAVNAITLPEVFHDFETTMP-EINSVQFEPVKSLAPPT--KRLMHWKESGG 150 (285)
Q Consensus 81 ~l~kik~afr~~~vdLp~~~~~A~~~aITLPe~~~d~d~~lP-~ld~~D~~~~~~lnqsr--~edITLkEd~g 150 (285)
++.|||++||+++||+|..+..+...+|||||.|.++|..+| +++++|+..+|++.+.+ .+++++.+++.
T Consensus 81 al~kIk~afr~~~vd~p~~~~~~~~~siTLPE~~~d~d~~l~~~~~~~~~~~~~~~~~~~~~lde~~~~~~~~ 153 (614)
T KOG1213|consen 81 ALLKIKMAFRSGQVDLPELAPRLPTHSITLPETFEDDDFDLPDEITDIDLYDDFSIPQSRNNLDEITLLEDIE 153 (614)
T ss_pred HHHHHHHHhccccccCCCcccccccccccchhhhccccccccccccccccccccCccccccchhhhhcccCCC
Confidence 999999999999999999888888999999999999999888 78889988889999988 89999999886
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=8.4e-41 Score=273.06 Aligned_cols=111 Identities=53% Similarity=0.917 Sum_probs=109.9
Q ss_pred CccchhhhhccCChhhHHHhhhccCccchhhhhccCHHHHHHHhcCCCCcchhhhhhccccceEEEEecchhHHHHHHHH
Q psy8283 1 MFYAQFVLAKKGPLARIWLAAHWDKKLTKAHVFETNIEKSVDGILQPKVKMALRTSGHLLLGVVRIYSRKAKYLLADCNE 80 (285)
Q Consensus 1 MFYS~~lLskkgpLa~IWLAAt~~kKLsKk~Il~vdI~~sce~Il~P~~p~ALRLSg~LLlGVVRIYsrKv~YLl~Dc~~ 80 (285)
||||++||+|+|+|++||+|||+++||+|++|+++||+++|++|++|++|+|||+|||||+||||||+||++||++||+.
T Consensus 1 MFy~~~iL~k~~~l~~vWlaat~~~kl~k~~i~~vdI~~~c~~I~~~~~~~sLRlss~LL~Gvv~Iy~kKv~yLl~D~~~ 80 (111)
T PF04825_consen 1 MFYSHDILSKKGPLATVWLAATLGKKLSKKQILQVDIPKICEEIIEPENPLSLRLSSQLLYGVVRIYSKKVEYLLSDCNE 80 (111)
T ss_pred CCccHHHHhcCCcHHHHHHHHhccCCCCHHHHHhCCHHHHHHHHhCCCcCeeHHHHhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhcCCCcCCCCccccccccccccC
Q psy8283 81 AFVKIKMAFRPGMVDLPEDNREAAVNAITLP 111 (285)
Q Consensus 81 ~l~kik~afr~~~vdLp~~~~~A~~~aITLP 111 (285)
++.+|++++++..+|+|+++..|++++||||
T Consensus 81 ~~~~l~~~~~~~~~dl~~~~~~~~~~~it~p 111 (111)
T PF04825_consen 81 LLSKLKRAFRPKKIDLPKDKTKASRNAITLP 111 (111)
T ss_pred HHHHHHHHhcccccCCCccccCCChhhccCc
Confidence 9999999999999999999999999999998
No 3
>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=72.80 E-value=1.5 Score=45.58 Aligned_cols=31 Identities=26% Similarity=0.371 Sum_probs=26.6
Q ss_pred hccccceEEEEecchhHHHHHHHHHHHHHHH
Q psy8283 57 GHLLLGVVRIYSRKAKYLLADCNEAFVKIKM 87 (285)
Q Consensus 57 g~LLlGVVRIYsrKv~YLl~Dc~~~l~kik~ 87 (285)
+-|+-|.+-||||||+||++-+-.++.-|..
T Consensus 7 alliQgsa~vYskKVeyly~lv~~~l~~l~~ 37 (565)
T PF06278_consen 7 ALLIQGSACVYSKKVEYLYSLVYQALDFLSG 37 (565)
T ss_pred HHHHhcchhhHHHHHHHHHHHHHHHHHHHhc
Confidence 3467799999999999999999998887765
No 4
>PF05786 Cnd2: Condensin complex subunit 2; InterPro: IPR022816 This entry represents eukaryotic condensin complex subunit 2 proteins. Included in this group are several Barren protein homologues from several eukaryotic organisms. In Drosophila Barren (barr) is required for sister-chromatid segregation in mitosis. barr encodes a novel protein that is present in proliferating cells and has homologues in yeast and human. Mitotic defects in barr embryos become apparent during cycle 16, resulting in a loss of PNS and CNS neurons. Centromeres move apart at the metaphase-anaphase transition and Cyclin B is degraded, but sister chromatids remain connected, resulting in chromatin bridging. Barren protein localises to chromatin throughout mitosis. Colocalisation and biochemical experiments indicate that Barren associates with Topoisomerase II throughout mitosis and alters the activity of Topoisomerase II. It has been suggested that this association is required for proper chromosomal segregation by facilitating the decatenation of chromatids at anaphase [].
Probab=55.05 E-value=19 Score=38.19 Aligned_cols=70 Identities=9% Similarity=0.171 Sum_probs=59.1
Q ss_pred HHHhhhccCccchhhhhccCHHHHHHHhcCC--CCcchhhhhhccccceEEEEecchhHHHHHHHHHHHHHH
Q psy8283 17 IWLAAHWDKKLTKAHVFETNIEKSVDGILQP--KVKMALRTSGHLLLGVVRIYSRKAKYLLADCNEAFVKIK 86 (285)
Q Consensus 17 IWLAAt~~kKLsKk~Il~vdI~~sce~Il~P--~~p~ALRLSg~LLlGVVRIYsrKv~YLl~Dc~~~l~kik 86 (285)
=|+-...+-||+.|--+++.+......|+.- ..-+..--.|--|-|-|+||+-.|.-++.++-+++..|.
T Consensus 82 ~~ikl~~~NKIn~~Naw~~~lID~~~~~~~~~~~~~~nFq~As~tLd~~~KIy~~RVDsv~~~t~k~l~~l~ 153 (725)
T PF05786_consen 82 ECIKLATENKINAKNAWNLALIDYFHDLIDKKDGDMINFQKASCTLDASVKIYSSRVDSVHTETYKLLSGLA 153 (725)
T ss_pred HHHHHHhhCCcccccccchhHHHHHHHHHhccccccchHHHhhhheeeeeeEEeeeehHHHHHHHHHHHhcc
Confidence 4666666789999999999998888887642 334566677889999999999999999999999999986
No 5
>TIGR03422 mito_frataxin frataxin. Frataxin is a mitochondrial protein, mutation of which leads to the disease Friedreich's ataxia. Its orthologs are widely distributed in the bacteria, associated with the ISC system for iron-sulfur cluster assembly, and designated CyaY. This exception-type model allows those examples of frataxin per se that score above the trusted cutoff to the CyaY equivalog-type model (TIGR03421) to be named appropriately.
Probab=42.57 E-value=6.7 Score=31.95 Aligned_cols=19 Identities=32% Similarity=0.765 Sum_probs=16.8
Q ss_pred chhhhhccCChhhHHHhhh
Q psy8283 4 AQFVLAKKGPLARIWLAAH 22 (285)
Q Consensus 4 S~~lLskkgpLa~IWLAAt 22 (285)
++.|++|+.|..+|||||-
T Consensus 46 ~~~VINkQ~p~~QIWlsSp 64 (97)
T TIGR03422 46 GTYVINKQPPNKQIWLSSP 64 (97)
T ss_pred CEEEEeCCChhhHHheecC
Confidence 4678899999999999994
No 6
>KOG2359|consensus
Probab=41.73 E-value=22 Score=37.55 Aligned_cols=36 Identities=11% Similarity=0.207 Sum_probs=27.2
Q ss_pred cchhhhhhccccceEEEEecchhHHHHHHHHHHHHH
Q psy8283 50 KMALRTSGHLLLGVVRIYSRKAKYLLADCNEAFVKI 85 (285)
Q Consensus 50 p~ALRLSg~LLlGVVRIYsrKv~YLl~Dc~~~l~ki 85 (285)
+.-.--.+-|+.|-|-||+|||+|+|.=+-.++.-+
T Consensus 57 ~~~f~~a~~~~qgs~~vy~~kv~~~y~l~~~~~~~~ 92 (688)
T KOG2359|consen 57 TYDFQRACRIIQGSCAVYGRKVDHVYELTISVVDLV 92 (688)
T ss_pred cccHHHHHHHHhcchhhhhhhhHHHHHHHHHHHHHH
Confidence 455555677899999999999999998665554433
No 7
>COG1965 CyaY Protein implicated in iron transport, frataxin homolog [Inorganic ion transport and metabolism]
Probab=41.37 E-value=9.4 Score=32.03 Aligned_cols=21 Identities=38% Similarity=0.809 Sum_probs=18.1
Q ss_pred chhhhhccCChhhHHHhhhcc
Q psy8283 4 AQFVLAKKGPLARIWLAAHWD 24 (285)
Q Consensus 4 S~~lLskkgpLa~IWLAAt~~ 24 (285)
|+.|+.|+.|+-.||||+-.+
T Consensus 47 s~iiINkQ~P~~qiWlAs~~g 67 (106)
T COG1965 47 SQIIINKQEPLQQIWLASKVG 67 (106)
T ss_pred cEEEEeCCChHHHHHhhccCC
Confidence 466888999999999999774
No 8
>TIGR03421 FeS_CyaY iron donor protein CyaY. Members of this protein family are the iron-sulfur cluster (FeS) metabolism protein CyaY, a homolog of eukaryotic frataxin. ISC is one of several bacterial systems for FeS assembly; we find by Partial Phylogenetic Profiling vs. the ISC system that CyaY most like work with the ISC system for FeS cluster biosynthesis. A study of of cyaY mutants in Salmonella enterica bears this out. Although the trusted cutoff is set low enough to include eukaryotic frataxin sequences, a narrower, exception-type model (TIGR03421) identifies identifies members of that specific set.
Probab=37.58 E-value=7.5 Score=31.85 Aligned_cols=21 Identities=43% Similarity=0.809 Sum_probs=17.8
Q ss_pred chhhhhccCChhhHHHhhhcc
Q psy8283 4 AQFVLAKKGPLARIWLAAHWD 24 (285)
Q Consensus 4 S~~lLskkgpLa~IWLAAt~~ 24 (285)
++.|++|..|..+|||||-.+
T Consensus 44 ~~~VINkQ~p~~QIWlaspsG 64 (102)
T TIGR03421 44 SQIIINKQEPLHQIWLAAKSG 64 (102)
T ss_pred CEEEEeCCchhhhheeecCCC
Confidence 457889999999999999753
No 9
>cd00503 Frataxin Frataxin is a nuclear-encoded mitochondrial protein implicated in Friedreich's ataxia (FRDA), an human autosomal recessive neurodegenerative disease; Frataxin is found in eukaryotes and in purple bacteria; lack of frataxin causes iron to accumulate in the mitochondrial matrix suggesting that frataxin is involved in mitochondrial iron homeostasis and possibly in iron transport; the domain has an alpha-beta fold consisting of two helices flanking an antiparallel beta sheet.
Probab=36.86 E-value=8.9 Score=31.48 Aligned_cols=21 Identities=33% Similarity=0.757 Sum_probs=17.8
Q ss_pred chhhhhccCChhhHHHhhhcc
Q psy8283 4 AQFVLAKKGPLARIWLAAHWD 24 (285)
Q Consensus 4 S~~lLskkgpLa~IWLAAt~~ 24 (285)
++.|++|..|..+|||||-.+
T Consensus 47 ~~~VINkQ~p~~QIWlaSp~G 67 (105)
T cd00503 47 STIVINRQEPLRQIWLASKVG 67 (105)
T ss_pred CEEEEeCCchhhhhheecCCC
Confidence 456889999999999999764
No 10
>KOG2328|consensus
Probab=36.50 E-value=44 Score=35.94 Aligned_cols=71 Identities=11% Similarity=0.189 Sum_probs=60.5
Q ss_pred HHHhhhccCccchhhhhccCHHHHHHHhcC--CCCcchhhhhhccccceEEEEecchhHHHHHHHHHHHHHHH
Q psy8283 17 IWLAAHWDKKLTKAHVFETNIEKSVDGILQ--PKVKMALRTSGHLLLGVVRIYSRKAKYLLADCNEAFVKIKM 87 (285)
Q Consensus 17 IWLAAt~~kKLsKk~Il~vdI~~sce~Il~--P~~p~ALRLSg~LLlGVVRIYsrKv~YLl~Dc~~~l~kik~ 87 (285)
=|+-...+.||+.|--++..+....-.|+. -+.++-.-..|-=|-|-|+||+-.|.-+..|+-+++..|-.
T Consensus 65 ~cIKLateNKIntkNtWnl~LID~f~~i~~~kd~e~iNFqkAs~TLdacvKIYs~RVDSV~tea~rlL~GL~~ 137 (702)
T KOG2328|consen 65 NCIKLATENKINTKNTWNLALIDHFANILKLKDGENINFQKASCTLDACVKIYSSRVDSVHTEAMRLLGGLGA 137 (702)
T ss_pred HHHHHhhcCccccccchhHHHHHHHHHHHHhhccCCcchhhhccccccceeeeeeehhHHHHHHHHHhhcccc
Confidence 377777789999999999998888777765 34567777888889999999999999999999999998864
No 11
>PRK00446 cyaY frataxin-like protein; Provisional
Probab=32.11 E-value=8.9 Score=31.61 Aligned_cols=21 Identities=29% Similarity=0.746 Sum_probs=17.6
Q ss_pred chhhhhccCChhhHHHhhhcc
Q psy8283 4 AQFVLAKKGPLARIWLAAHWD 24 (285)
Q Consensus 4 S~~lLskkgpLa~IWLAAt~~ 24 (285)
++.|++|..|..+|||||-.+
T Consensus 46 ~~~VINkQ~p~~QIWlas~sG 66 (105)
T PRK00446 46 SKIIINRQEPLHELWLAAKSG 66 (105)
T ss_pred CEEEEeCCCchhheeEecCCC
Confidence 456889999999999999653
No 12
>PRK01379 cyaY frataxin-like protein; Provisional
Probab=26.48 E-value=17 Score=30.07 Aligned_cols=17 Identities=29% Similarity=0.755 Sum_probs=15.3
Q ss_pred hhhhccCChhhHHHhhh
Q psy8283 6 FVLAKKGPLARIWLAAH 22 (285)
Q Consensus 6 ~lLskkgpLa~IWLAAt 22 (285)
.|++|..|..+||||+-
T Consensus 48 ~VINkQ~p~~QIWlASp 64 (103)
T PRK01379 48 YVINKQSAAKEIWLSSP 64 (103)
T ss_pred EEEeCCChhhhheeecc
Confidence 57889999999999995
No 13
>PF03417 AAT: Acyl-coenzyme A:6-aminopenicillanic acid acyl-transferase This family belongs to family C45 of the peptidase classification.; InterPro: IPR005079 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to MEROPS peptidase family C45 (clan PB(C)). The active site residue for members of this family and family T1 is C-terminal to the autolytic cleavage site. They represent a family of enzymes which catalyse the final step in penicillin biosynthesis []. ; GO: 0042318 penicillin biosynthetic process; PDB: 3GVZ_A 2X1D_D 2X1E_B 2X1C_A.
Probab=25.86 E-value=52 Score=29.03 Aligned_cols=29 Identities=38% Similarity=0.474 Sum_probs=21.1
Q ss_pred CCCCCCCCCC----CCCCCCccceeeEEeeeec
Q psy8283 252 DDDHFGGPAS----PMGHPRSRTIHSIVYSVKT 280 (285)
Q Consensus 252 ~~~~~~~p~s----~~~~~~~~~~~~~~~~~~~ 280 (285)
--||.++|-| +-+..+..|++|+||....
T Consensus 181 l~D~~~~p~~ic~~~~~~~~~~T~~s~v~~~~~ 213 (225)
T PF03417_consen 181 LSDHEDGPYSICRHPDFKSRFSTLASVVYDPEA 213 (225)
T ss_dssp CT--TTTTTSSSS-BTTCCSCEEEEEEEECTTT
T ss_pred hcCccCCCCceeccCCCCCCCccEEEEEEECCC
Confidence 5677777766 5667799999999997654
Done!