Query 031983
Match_columns 149
No_of_seqs 124 out of 149
Neff 3.0
Searched_HMMs 46136
Date Fri Mar 29 08:01:58 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031983.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031983hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4149 Uncharacterized conser 100.0 4.9E-33 1.1E-37 215.1 4.2 64 52-115 52-115 (129)
2 PF07802 GCK: GCK domain; Int 98.1 1.9E-06 4.2E-11 61.9 1.9 61 58-118 2-65 (76)
3 PF06747 CHCH: CHCH domain; I 97.0 0.00071 1.5E-08 40.2 2.5 35 70-106 1-35 (35)
4 PF07802 GCK: GCK domain; Int 64.9 4.9 0.00011 29.0 1.9 20 88-107 9-28 (76)
5 PF12225 MTHFR_C: Methylene-te 55.3 5.4 0.00012 29.9 0.7 32 58-96 37-71 (97)
6 PF05051 COX17: Cytochrome C o 47.1 13 0.00027 25.3 1.4 34 70-107 12-45 (49)
7 KOG0568 Molecular chaperone (D 45.9 16 0.00034 32.6 2.3 38 31-68 205-244 (342)
8 PF11326 DUF3128: Protein of u 44.0 29 0.00063 24.4 3.0 40 69-108 6-51 (84)
9 cd00307 RuBisCO_small_like Rib 36.2 26 0.00055 25.6 1.7 21 93-113 44-64 (84)
10 PF08583 Cmc1: Cytochrome c ox 35.7 22 0.00048 23.2 1.2 40 67-108 10-50 (69)
11 PF05254 UPF0203: Uncharacteri 34.9 42 0.00091 23.5 2.6 20 89-108 34-53 (68)
12 KOG0983 Mitogen-activated prot 28.0 66 0.0014 29.6 3.3 52 21-73 50-108 (391)
13 PF09350 DUF1992: Domain of un 26.6 56 0.0012 22.7 2.1 16 31-46 2-17 (71)
14 COG4802 FtrB Ferredoxin-thiore 24.2 81 0.0018 24.6 2.7 11 53-63 61-71 (110)
15 KOG4477 RING1 interactor RYBP 24.0 60 0.0013 27.9 2.2 33 76-108 37-72 (228)
16 PF00101 RuBisCO_small: Ribulo 23.8 55 0.0012 24.4 1.7 20 94-113 59-78 (99)
17 cd03527 RuBisCO_small Ribulose 22.5 61 0.0013 24.3 1.7 20 94-113 60-79 (99)
18 COG0723 QcrA Rieske Fe-S prote 22.0 36 0.00078 26.4 0.4 10 55-64 124-133 (177)
19 PF10200 Ndufs5: NADH:ubiquino 20.6 96 0.0021 23.4 2.4 48 66-113 29-76 (96)
No 1
>KOG4149 consensus Uncharacterized conserved protein [Function unknown]
Probab=99.97 E-value=4.9e-33 Score=215.13 Aligned_cols=64 Identities=42% Similarity=0.928 Sum_probs=59.3
Q ss_pred HHhhhcCCCcccCCCCCCchHHHHhhhhcccccCCCcCCCCChHhHHHHHHHHHhCccchhhhh
Q 031983 52 KAQKALECPCIADLRSGPCGAQFSEAFLCFLKSTSEEKGSDCVHPFVALQNCIKANPSAFSKDI 115 (149)
Q Consensus 52 ~~~iNwdCPCLggMa~GPCG~eFkeAFSCF~~S~eE~KGsDC~e~F~amq~Cm~~~Pd~y~~el 115 (149)
..+|||+|||||||++||||++||+|||||+||++++||+||+++|++||+||++||+.+....
T Consensus 52 DG~INwdCpClg~m~a~pCG~eFreA~sCf~~s~~e~kg~dC~~qf~a~~~C~qk~p~~~~eq~ 115 (129)
T KOG4149|consen 52 DGTINWDCPCLGGLVAGPCGEEFREAFSCFKYSDTEPKGGDCVKQFVAMQECMQKYPREEEEQC 115 (129)
T ss_pred CCceeecCccccccccCccHHHHHHHHhhccccCCCcCccchHHHHHHHHHHHHhCchHHHHHh
Confidence 3579999999999999999999999999999999999999999999999999999997665443
No 2
>PF07802 GCK: GCK domain; InterPro: IPR012891 This domain is found in proteins carrying other domains known to be involved in intracellular signalling pathways (such as IPR001806 from INTERPRO) indicating that it might also be involved in these pathways. It has 4 highly conserved cysteine residues, suggesting that it can bind zinc ions. Moreover, it is found repeated in some members of this family (such as Q9LMF3 from SWISSPROT); this may indicate that these domains are able to interact with one another, raising the possibility that this domain mediates heterodimerisation.
Probab=98.06 E-value=1.9e-06 Score=61.85 Aligned_cols=61 Identities=21% Similarity=0.429 Sum_probs=48.8
Q ss_pred CCCcccCCCCCCchHHHHhhhhccccc---CCCcCCCCChHhHHHHHHHHHhCccchhhhhhhh
Q 031983 58 ECPCIADLRSGPCGAQFSEAFLCFLKS---TSEEKGSDCVHPFVALQNCIKANPSAFSKDILEE 118 (149)
Q Consensus 58 dCPCLggMa~GPCG~eFkeAFSCF~~S---~eE~KGsDC~e~F~amq~Cm~~~Pd~y~~el~e~ 118 (149)
+|+-..=|..|||++.|..-..|.-.. .+......|.+.|.+|..||..|||+|..-|...
T Consensus 2 ec~fc~FMkgG~Cke~F~awe~C~~ea~~~~~~d~v~kC~e~~~~L~kCM~ahsdYY~P~La~~ 65 (76)
T PF07802_consen 2 ECGFCKFMKGGGCKESFTAWEDCVDEAEKNKEEDFVEKCFEATAALRKCMEAHSDYYEPILAAE 65 (76)
T ss_pred cchHHHHhcCCChhHHHHHHHHHHHHHHhccCCchHHHHHHHHHHHHHHHHhchhHHHHHHHHH
Confidence 455566799999999999999997432 2224567999999999999999999998766543
No 3
>PF06747 CHCH: CHCH domain; InterPro: IPR010625 A conserved motif was identified in the LOC118487 protein was called the CHCH motif. Alignment of this protein with related members showed the presence of three subgroups of proteins, which are called the S (Small), N (N-terminal extended) and C (C-terminal extended) subgroups. All three sub-groups of proteins have in common that they contain a predicted conserved [coiled coil 1]-[helix 1]-[coiled coil 2]-[helix 2] domain (CHCH domain). Within each helix of the CHCH domain, there are two cysteines present in a C-X9-C motif. The N-group contains an additional double helix domain, and each helix contains the C-X9-C motif. This family contains a number of characterised proteins: Cox19 protein - a nuclear gene of Saccharomyces cerevisiae, codes for an 11 kDa protein (Cox19p) required for expression of cytochrome oxidase. Because cox19 mutants are able to synthesise the mitochondrial and nuclear gene products of cytochrome oxidase, Cox19p probably functions post-translationally during assembly of the enzyme. Cox19p is present in the cytoplasm and mitochondria, where it exists as a soluble intermembrane protein. This dual location is similar to what was previously reported for Cox17p, a low molecular weight copper protein thought to be required for maturation of the CuA centre of subunit 2 of cytochrome oxidase. Cox19p have four conserved potential metal ligands, these are three cysteines and one histidine. Mrp10 - belongs to the class of yeast mitochondrial ribosomal proteins that are essential for translation []. Eukaryotic NADH-ubiquinone oxidoreductase 19 kDa (NDUFA8) subunit []. The CHCH domain was previously called DUF657 []. ; PDB: 2ZXT_A 3A3C_A 2L0Y_A 2K3J_A.
Probab=96.95 E-value=0.00071 Score=40.21 Aligned_cols=35 Identities=20% Similarity=0.511 Sum_probs=31.0
Q ss_pred chHHHHhhhhcccccCCCcCCCCChHhHHHHHHHHHh
Q 031983 70 CGAQFSEAFLCFLKSTSEEKGSDCVHPFVALQNCIKA 106 (149)
Q Consensus 70 CG~eFkeAFSCF~~S~eE~KGsDC~e~F~amq~Cm~~ 106 (149)
|+.+|+..+.|+..++.+ .+.|.+.|+++++|+++
T Consensus 1 C~~e~~~~~~Cl~~n~~~--~~~C~~~~~~~~~C~~~ 35 (35)
T PF06747_consen 1 CAEEMKAYLACLKENNFD--WSKCRKEFKAYKECRMK 35 (35)
T ss_dssp THHHHHHHHHHHHCH-SS--TCCCHHHHHHHHHHHCC
T ss_pred CHHHHHHHHHHHHHCCCc--HHhhHHHHHHHHHHhhC
Confidence 899999999998888875 89999999999999863
No 4
>PF07802 GCK: GCK domain; InterPro: IPR012891 This domain is found in proteins carrying other domains known to be involved in intracellular signalling pathways (such as IPR001806 from INTERPRO) indicating that it might also be involved in these pathways. It has 4 highly conserved cysteine residues, suggesting that it can bind zinc ions. Moreover, it is found repeated in some members of this family (such as Q9LMF3 from SWISSPROT); this may indicate that these domains are able to interact with one another, raising the possibility that this domain mediates heterodimerisation.
Probab=64.87 E-value=4.9 Score=28.99 Aligned_cols=20 Identities=30% Similarity=0.772 Sum_probs=17.3
Q ss_pred cCCCCChHhHHHHHHHHHhC
Q 031983 88 EKGSDCVHPFVALQNCIKAN 107 (149)
Q Consensus 88 ~KGsDC~e~F~amq~Cm~~~ 107 (149)
.||+.|-+.|++|..|...+
T Consensus 9 MkgG~Cke~F~awe~C~~ea 28 (76)
T PF07802_consen 9 MKGGGCKESFTAWEDCVDEA 28 (76)
T ss_pred hcCCChhHHHHHHHHHHHHH
Confidence 37999999999999999543
No 5
>PF12225 MTHFR_C: Methylene-tetrahydrofolate reductase C terminal; InterPro: IPR022026 This family is found in bacteria and archaea, and is approximately 100 amino acids in length. There is a conserved NGPCGG sequence motif. This family is the C-terminal of methylene-tetrahydrofolate reductase. This protein reduces FAD using the reducing equivalents from reduced FAD, subsequently reduces tetrahydrofolate. The C-terminal of MTHFR contains the FAD binding site and is the catalytic portion of the enzyme.
Probab=55.26 E-value=5.4 Score=29.91 Aligned_cols=32 Identities=31% Similarity=0.842 Sum_probs=23.4
Q ss_pred CCC---cccCCCCCCchHHHHhhhhcccccCCCcCCCCChHh
Q 031983 58 ECP---CIADLRSGPCGAQFSEAFLCFLKSTSEEKGSDCVHP 96 (149)
Q Consensus 58 dCP---CLggMa~GPCG~eFkeAFSCF~~S~eE~KGsDC~e~ 96 (149)
-|| |-.+|.+||||.. ++- .|=++. ..+|+=.
T Consensus 37 iCP~~~CpK~l~NGPCGG~-~~G-~CEV~~-----~~~C~w~ 71 (97)
T PF12225_consen 37 ICPMSRCPKSLLNGPCGGS-QDG-KCEVDP-----DRPCAWV 71 (97)
T ss_pred cCccccCcCccccCCCCCC-CCC-ceecCC-----CCcccHH
Confidence 464 8899999999999 444 786554 3778643
No 6
>PF05051 COX17: Cytochrome C oxidase copper chaperone (COX17); InterPro: IPR007745 Cox17p is essential for the assembly of functional cytochrome c oxidase (CCO) and for delivery of copper ions to the mitochondrion for insertion into the enzyme in Saccharomyces cerevisiae [].; GO: 0005507 copper ion binding, 0016531 copper chaperone activity, 0006825 copper ion transport, 0005758 mitochondrial intermembrane space; PDB: 1U97_A 1U96_A 1Z2G_A 2RNB_A 2RN9_A 2LGQ_A 2L0Y_B.
Probab=47.15 E-value=13 Score=25.25 Aligned_cols=34 Identities=21% Similarity=0.443 Sum_probs=25.3
Q ss_pred chHHHHhhhhcccccCCCcCCCCChHhHHHHHHHHHhC
Q 031983 70 CGAQFSEAFLCFLKSTSEEKGSDCVHPFVALQNCIKAN 107 (149)
Q Consensus 70 CG~eFkeAFSCF~~S~eE~KGsDC~e~F~amq~Cm~~~ 107 (149)
|-++=+.==-|++.+.++. |.+.+.+...||+.|
T Consensus 12 CpetK~aRDeC~l~~g~e~----C~~~Ieahk~Cmr~~ 45 (49)
T PF05051_consen 12 CPETKKARDECILFNGEED----CKELIEAHKACMRGE 45 (49)
T ss_dssp SHHHHHHHHHHHHHC-CCC----CHHHHHHHHHHHHHH
T ss_pred ChhHHHHhHhhHHhcChHH----HHHHHHHHHHHHHHc
Confidence 4444444457888888754 999999999999975
No 7
>KOG0568 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=45.94 E-value=16 Score=32.59 Aligned_cols=38 Identities=34% Similarity=0.446 Sum_probs=28.7
Q ss_pred HHHHHHHHHhcCCCCcchhhHH--HhhhcCCCcccCCCCC
Q 031983 31 IESLIAEAAAYGDDENESLDEK--AQKALECPCIADLRSG 68 (149)
Q Consensus 31 ~e~~~aea~a~g~~~~es~e~~--~~iNwdCPCLggMa~G 68 (149)
+|.||.|||+.|++++=++..+ -..--+||-|.-|.+-
T Consensus 205 vedliqeamakgdfdnlngkgkplkk~qsd~~yid~~th~ 244 (342)
T KOG0568|consen 205 VEDLIQEAMAKGDFDNLNGKGKPLKKAQSDCPYIDFMTHK 244 (342)
T ss_pred HHHHHHHHHhcCCccccCCCCCcchhhccCCCccchhhhh
Confidence 6899999999999998443322 2445799999887663
No 8
>PF11326 DUF3128: Protein of unknown function (DUF3128); InterPro: IPR021475 This eukaryotic family of proteins has no known function.
Probab=44.00 E-value=29 Score=24.43 Aligned_cols=40 Identities=18% Similarity=0.478 Sum_probs=29.0
Q ss_pred CchHHHHhhhhcccccC------CCcCCCCChHhHHHHHHHHHhCc
Q 031983 69 PCGAQFSEAFLCFLKST------SEEKGSDCVHPFVALQNCIKANP 108 (149)
Q Consensus 69 PCG~eFkeAFSCF~~S~------eE~KGsDC~e~F~amq~Cm~~~P 108 (149)
.|-.-|.+++.|+=-.. -=....+|-.++..+..||+.--
T Consensus 6 sC~~~fd~~~~C~S~~~q~~~yYryG~~~~C~~~~~df~~C~~~k~ 51 (84)
T PF11326_consen 6 SCMDAFDELWFCYSPGGQFRNYYRYGEFDDCSQWWEDFKFCLRWKS 51 (84)
T ss_pred cHHHHHHHHHHcCCchHhheeeeecCCCccHHHHHHHHHHHHHhcc
Confidence 38899999999961110 01235789999999999997543
No 9
>cd00307 RuBisCO_small_like Ribulose bisphosphate carboxylase/oxygenase (Rubisco), small subunit and related proteins. Rubisco is a bifunctional enzyme catalyzes the initial steps of two opposing metabolic pathways: photosynthetic carbon fixation and the competing process of photorespiration. Rubisco Form I, present in plants and green algae, is composed of eight large and eight small subunits. The nearly identical small subunits are encoded by a family of nuclear genes. After translation, the small subunits are translocated across the chloroplast membrane, where an N-terminal signal peptide is cleaved off. While the large subunits contain the catalytic activities, it has been shown that the small subunits are important for catalysis by enhancing the catalytic rate through inducing conformational changes in the large subunits. This superfamily also contains specific proteins from cyanobacteria. CcmM plays a role in a CO2 concentrating mechanism, which cyanobacteria need to to overcome t
Probab=36.19 E-value=26 Score=25.59 Aligned_cols=21 Identities=19% Similarity=0.577 Sum_probs=17.4
Q ss_pred ChHhHHHHHHHHHhCccchhh
Q 031983 93 CVHPFVALQNCIKANPSAFSK 113 (149)
Q Consensus 93 C~e~F~amq~Cm~~~Pd~y~~ 113 (149)
=..-+..+++|++.||+.|-.
T Consensus 44 ~~~Vl~el~~c~~~~p~~YVR 64 (84)
T cd00307 44 EAQVLAALEACLAEHPGEYVR 64 (84)
T ss_pred HHHHHHHHHHHHHHCCCCeEE
Confidence 346788999999999998853
No 10
>PF08583 Cmc1: Cytochrome c oxidase biogenesis protein Cmc1 like; InterPro: IPR013892 Cmc1 is a metallo-chaperone like protein which is known to localise to the inner mitochondrial membrane in Saccharomyces cerevisiae. It is essential for full expression of cytochrome c oxidase and respiration []. Cmc1 contains two Cx9C motifs and is able to bind copper(I). Cmc1 is thought to play a role in mitochondrial copper trafficking and transfer to cytochrome c oxidase.
Probab=35.73 E-value=22 Score=23.21 Aligned_cols=40 Identities=18% Similarity=0.338 Sum_probs=30.1
Q ss_pred CCCchHHHHhhhhcccccCCCcC-CCCChHhHHHHHHHHHhCc
Q 031983 67 SGPCGAQFSEAFLCFLKSTSEEK-GSDCVHPFVALQNCIKANP 108 (149)
Q Consensus 67 ~GPCG~eFkeAFSCF~~S~eE~K-GsDC~e~F~amq~Cm~~~P 108 (149)
.-.|......-.-|... .-.+ -..|-+...+|..||+.|-
T Consensus 10 ~~~C~~~i~~~~~C~~~--~~~~~~~~C~~~~~~m~~Cl~~~~ 50 (69)
T PF08583_consen 10 HKKCADEIEAFAECHKD--RTFKFVGKCREEKKAMNECLKEER 50 (69)
T ss_pred HHHhHHHHHHHHHHHhc--chHHHHHhhhHHHHHHHHHHHHHH
Confidence 34688888888888544 2222 4679999999999999884
No 11
>PF05254 UPF0203: Uncharacterised protein family (UPF0203); InterPro: IPR007918 This is a family of small highly conserved proteins. In Saccharomyces cerevisiae (Baker's yeast) the gene YKL053C-A (MDM35) O60200 from SWISSPROT is one of the genes essential for maintenance of normal mitochondrial distribution and morphology (MDM) []; wherease in Homo sapiens (Human), p53CSV, O43715 from SWISSPROT is a direct transcriptional target for p53 and appears to be a cell-survival mediator in response to genotoxic stress including low-levels of DNA damage. It is suggested that p53CSV modulates the apoptotic pathway through interaction with HSP70 and Apaf-1 thereby inhibiting activation of procaspase-3 and procaspase-9 [].
Probab=34.88 E-value=42 Score=23.53 Aligned_cols=20 Identities=20% Similarity=0.532 Sum_probs=17.1
Q ss_pred CCCCChHhHHHHHHHHHhCc
Q 031983 89 KGSDCVHPFVALQNCIKANP 108 (149)
Q Consensus 89 KGsDC~e~F~amq~Cm~~~P 108 (149)
.+..|.+.|..-|.|++++=
T Consensus 34 ~~~~C~~~~~~Y~~Cv~~al 53 (68)
T PF05254_consen 34 SDNECGELFKEYQQCVQKAL 53 (68)
T ss_pred CCCcHHHHHHHHHHHHHHHH
Confidence 34799999999999998764
No 12
>KOG0983 consensus Mitogen-activated protein kinase (MAPK) kinase MKK7/JNKK2 [Signal transduction mechanisms]
Probab=28.00 E-value=66 Score=29.58 Aligned_cols=52 Identities=25% Similarity=0.313 Sum_probs=31.8
Q ss_pred CCCCccccccHHHHHHHHHhcCCCCc------c-hhhHHHhhhcCCCcccCCCCCCchHH
Q 031983 21 SPDSSQRAASIESLIAEAAAYGDDEN------E-SLDEKAQKALECPCIADLRSGPCGAQ 73 (149)
Q Consensus 21 ~~~~~~~~~s~e~~~aea~a~g~~~~------e-s~e~~~~iNwdCPCLggMa~GPCG~e 73 (149)
.|+++....++++|.-+|.+.+-.-. . ...-.+.|| +=.-||.|.+|.||.-
T Consensus 50 ~pS~s~~d~~~~al~~~~~e~~~~~~tg~lti~~g~r~~~din-dl~~l~dlGsGtcG~V 108 (391)
T KOG0983|consen 50 LPSTSSTDRSMEALEIDAKEQEIMKQTGYLTIGGGQRYQADIN-DLENLGDLGSGTCGQV 108 (391)
T ss_pred CCCCCCCcchHHHHHHHhhhccccCCceeEEecCCcccccChH-HhhhHHhhcCCCccce
Confidence 34444457788999888887755211 0 111123343 3356899999999974
No 13
>PF09350 DUF1992: Domain of unknown function (DUF1992); InterPro: IPR018961 This entry represents a family of proteins that may have a role in protein folding or as a chaperone. DnaJ is a member of the J-protein family, which are defined by the presence of a J domain that can regulate the activity of 70kDa heat-shock proteins []. Some of the proteins in this entry contain a J domain.
Probab=26.56 E-value=56 Score=22.72 Aligned_cols=16 Identities=44% Similarity=0.439 Sum_probs=14.3
Q ss_pred HHHHHHHHHhcCCCCc
Q 031983 31 IESLIAEAAAYGDDEN 46 (149)
Q Consensus 31 ~e~~~aea~a~g~~~~ 46 (149)
++..|.+|++.|++++
T Consensus 2 ~e~~I~~A~~~GeFdn 17 (71)
T PF09350_consen 2 AERRIREAMARGEFDN 17 (71)
T ss_pred HHHHHHHHHHcCCccC
Confidence 4788999999999997
No 14
>COG4802 FtrB Ferredoxin-thioredoxin reductase, catalytic subunit [Energy production and conversion]
Probab=24.20 E-value=81 Score=24.61 Aligned_cols=11 Identities=36% Similarity=1.096 Sum_probs=8.7
Q ss_pred HhhhcCCCccc
Q 031983 53 AQKALECPCIA 63 (149)
Q Consensus 53 ~~iNwdCPCLg 63 (149)
...+|.|||+-
T Consensus 61 edk~ivCPCvy 71 (110)
T COG4802 61 EDKDIVCPCVY 71 (110)
T ss_pred HhhceeccCcC
Confidence 34779999986
No 15
>KOG4477 consensus RING1 interactor RYBP and related Zn-finger-containing proteins [Transcription]
Probab=23.99 E-value=60 Score=27.91 Aligned_cols=33 Identities=27% Similarity=0.433 Sum_probs=25.0
Q ss_pred hhhhcccccCCC---cCCCCChHhHHHHHHHHHhCc
Q 031983 76 EAFLCFLKSTSE---EKGSDCVHPFVALQNCIKANP 108 (149)
Q Consensus 76 eAFSCF~~S~eE---~KGsDC~e~F~amq~Cm~~~P 108 (149)
+||-||+-..-- -+-..|..++++||-=.+-.+
T Consensus 37 eAfkC~vCdvRKGTSTRkpr~nsqlVaqQvtqq~~~ 72 (228)
T KOG4477|consen 37 EAFKCFVCDVRKGTSTRKPRCNSQLVAQQVTQQTMV 72 (228)
T ss_pred hhhheeeecccccccccCCcchHHHHHHHHhhhhcC
Confidence 789999765542 356889999999998766554
No 16
>PF00101 RuBisCO_small: Ribulose bisphosphate carboxylase, small chain; InterPro: IPR000894 RuBisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase) is a bifunctional enzyme that catalyses both the carboxylation and oxygenation of ribulose-1,5-bisphosphate (RuBP) [], thus fixing carbon dioxide as the first step of the Calvin cycle. RuBisCO is the major protein in the stroma of chloroplasts, and in higher plants exists as a complex of 8 large and 8 small subunits. The function of the small subunit is unknown []. While the large subunit is coded for by a single gene, the small subunit is coded for by several different genes, which are distributed in a tissue specific manner. They are transcriptionally regulated by light receptor phytochrome [], which results in RuBisCO being more abundant during the day when it is required. The RuBisCo small subunit consists of a central four-stranded beta-sheet, with two helices packed against it [].; PDB: 1BWV_W 1IWA_P 3AXM_X 1WDD_S 3AXK_T 1IR2_K 1RBL_N 1UZH_J 1RSC_P 1UW9_C ....
Probab=23.83 E-value=55 Score=24.43 Aligned_cols=20 Identities=15% Similarity=0.615 Sum_probs=16.8
Q ss_pred hHhHHHHHHHHHhCccchhh
Q 031983 94 VHPFVALQNCIKANPSAFSK 113 (149)
Q Consensus 94 ~e~F~amq~Cm~~~Pd~y~~ 113 (149)
..-+..+..|++.||+.|-.
T Consensus 59 ~~Vl~el~~c~~~~p~~yVR 78 (99)
T PF00101_consen 59 AQVLAELEACLAEHPGEYVR 78 (99)
T ss_dssp HHHHHHHHHHHHHSTTSEEE
T ss_pred HHHHHHHHHHHHhCCCceEE
Confidence 35788899999999999854
No 17
>cd03527 RuBisCO_small Ribulose bisphosphate carboxylase/oxygenase (Rubisco), small subunit. Rubisco is a bifunctional enzyme catalyzes the initial steps of two opposing metabolic pathways: photosynthetic carbon fixation and the competing process of photorespiration. Rubisco Form I, present in plants and green algae, is composed of eight large and eight small subunits. The nearly identical small subunits are encoded by a family of nuclear genes. After translation, the small subunits are translocated across the chloroplast membrane, where an N-terminal signal peptide is cleaved off. While the large subunits contain the catalytic activities, it has been shown that the small subunits are important for catalysis by enhancing the catalytic rate through inducing conformational changes in the large subunits.
Probab=22.48 E-value=61 Score=24.33 Aligned_cols=20 Identities=20% Similarity=0.519 Sum_probs=16.6
Q ss_pred hHhHHHHHHHHHhCccchhh
Q 031983 94 VHPFVALQNCIKANPSAFSK 113 (149)
Q Consensus 94 ~e~F~amq~Cm~~~Pd~y~~ 113 (149)
..-...+++|.+.||+.|-.
T Consensus 60 ~~Vl~ei~~C~~~~p~~YVR 79 (99)
T cd03527 60 AQVLREIEACRKAYPDHYVR 79 (99)
T ss_pred HHHHHHHHHHHHHCCCCeEE
Confidence 46688889999999998853
No 18
>COG0723 QcrA Rieske Fe-S protein [Energy production and conversion]
Probab=21.95 E-value=36 Score=26.42 Aligned_cols=10 Identities=30% Similarity=0.896 Sum_probs=8.1
Q ss_pred hhcCCCcccC
Q 031983 55 KALECPCIAD 64 (149)
Q Consensus 55 iNwdCPCLgg 64 (149)
.=|.|||-|+
T Consensus 124 ~~~~CPCHGS 133 (177)
T COG0723 124 GGFFCPCHGS 133 (177)
T ss_pred CeEEccCCCC
Confidence 4589999887
No 19
>PF10200 Ndufs5: NADH:ubiquinone oxidoreductase, NDUFS5-15kDa; InterPro: IPR019342 Proteins in this entry form part of the NADH:ubiquinone oxidoreductase complex I. Complex I is the first multisubunit inner membrane protein complex of the mitochondrial electron transport chain and it transfers two electrons from NADH to ubiquinone. The mammalian complex I is composed of 45 different subunits. The proteins in this entry represent a component of the iron-sulphur (IP) fragment of the enzyme, that is not involved in catalysis. These proteins carry four highly conserved cysteine residues, but these do not appear to be in a configuration which would favour metal binding, so the exact function of the protein is uncertain [].
Probab=20.55 E-value=96 Score=23.36 Aligned_cols=48 Identities=10% Similarity=0.160 Sum_probs=37.3
Q ss_pred CCCCchHHHHhhhhcccccCCCcCCCCChHhHHHHHHHHHhCccchhh
Q 031983 66 RSGPCGAQFSEAFLCFLKSTSEEKGSDCVHPFVALQNCIKANPSAFSK 113 (149)
Q Consensus 66 a~GPCG~eFkeAFSCF~~S~eE~KGsDC~e~F~amq~Cm~~~Pd~y~~ 113 (149)
..+.|+...++-+.|.+-....---..|.-.|.-+.+|+--.-++-+-
T Consensus 29 ~~~RC~~FE~e~i~C~~~~G~~r~kKeC~~e~EDy~EClh~~Ke~~R~ 76 (96)
T PF10200_consen 29 QPSRCHPFEKEWIECAEAYGQTRGKKECKLELEDYYECLHHTKEMKRM 76 (96)
T ss_pred CCCchHHHHHHHHHHHHHHcccchhhhchhHHhHHHHHHhhHHHHHHH
Confidence 356799999999999765544444578999999999999877665543
Done!