Query 030500
Match_columns 176
No_of_seqs 130 out of 210
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 14:39:33 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030500.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030500hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG4446 Uncharacterized protei 100.0 1.7E-32 3.8E-37 215.6 3.0 94 63-171 11-104 (141)
2 PF07386 DUF1499: Protein of u 99.9 8.4E-22 1.8E-26 150.7 9.6 81 81-171 3-85 (118)
3 KOG1509 Predicted nucleic acid 61.7 13 0.00028 32.1 4.2 38 89-134 34-71 (209)
4 PF03681 UPF0150: Uncharacteri 49.7 25 0.00053 22.3 3.1 31 81-133 15-45 (48)
5 PF08368 FAST_2: FAST kinase-l 41.9 42 0.00091 24.4 3.7 39 122-171 49-87 (93)
6 COG1598 Predicted nuclease of 40.1 36 0.00077 23.9 3.0 32 81-134 17-48 (73)
7 PF07867 DUF1654: Protein of u 37.3 1.1E+02 0.0023 22.4 5.1 33 119-155 36-68 (73)
8 COG2837 Predicted iron-depende 35.6 48 0.001 30.6 3.8 44 119-166 134-177 (352)
9 KOG3422 Mitochondrial ribosoma 27.4 1E+02 0.0023 26.9 4.3 62 77-145 103-176 (221)
10 PF10369 ALS_ss_C: Small subun 27.1 2.1E+02 0.0046 20.1 5.2 32 121-157 14-45 (75)
11 cd00005 CBM9 Family 9 carbohyd 23.4 97 0.0021 25.1 3.3 26 149-174 52-84 (186)
12 PF08447 PAS_3: PAS fold; Int 23.0 75 0.0016 21.1 2.2 42 119-160 36-78 (91)
13 PF10134 RPA: Replication init 22.6 1E+02 0.0022 26.3 3.3 45 119-169 88-132 (229)
14 PF06240 COXG: Carbon monoxide 21.9 2.6E+02 0.0057 21.1 5.3 37 118-158 8-47 (140)
15 TIGR01413 Dyp_perox_fam Dyp-ty 21.7 1.3E+02 0.0028 26.7 3.9 43 119-164 105-149 (308)
16 COG1566 EmrA Multidrug resista 21.1 34 0.00075 31.3 0.2 54 120-175 193-253 (352)
17 PF01106 NifU: NifU-like domai 20.8 1.8E+02 0.0039 20.2 3.8 35 120-157 2-36 (68)
18 cd04097 mtEFG1_C mtEFG1_C: C-t 20.3 2.1E+02 0.0046 19.6 4.1 42 119-165 11-57 (78)
No 1
>COG4446 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=99.97 E-value=1.7e-32 Score=215.63 Aligned_cols=94 Identities=32% Similarity=0.542 Sum_probs=89.4
Q ss_pred HhcCCCCCCcccccCcccccCCCCCCCeeeeccccCCCCcccCCeeccCCCCCCCCHHHHHHHHHHHHHhcCCCCCCcEE
Q 030500 63 NLSGKKPEYLGVQKNQQALALCPATKNCISTAENISDLTHYAPPWNYNRGRKKPVSREVAMEELLQVIKSTKPDRFTPRL 142 (176)
Q Consensus 63 ~~sg~~P~~LGV~dG~~~La~CP~sPNCVSSqa~~~D~~h~I~Pw~y~g~~~~~~s~e~A~~~L~~vl~~~~~~~f~~~I 142 (176)
.++|+ |.+|||.+|+ |+|||++|||||||+ .|..|.|+|+.|.++ ++.|.++|++++.++|| ++|
T Consensus 11 ~f~~s-~~~lGV~sgr--lapCpn~PNCVssQ~--adt~h~iaPl~f~~~------~~~a~e~l~~il~~lP~----t~i 75 (141)
T COG4446 11 AFSGS-PCNLGVDSGR--LAPCPNSPNCVSSQD--ADTKHAIAPLNFILD------PGVAIEQLERILLSLPG----TVI 75 (141)
T ss_pred hhccC-ccccCcccCc--ccCCCCCCCeeeccc--ccchhcccccccccC------HHHHHHHHHHHHhhCCC----ceE
Confidence 57777 9999999998 999999999999998 799999999999986 88999999999999998 999
Q ss_pred EEecCCEEEEEEEcCCCCcccceEEEeee
Q 030500 143 VEKKDDYVHVEYESPVLGVGLAHHTFVQL 171 (176)
Q Consensus 143 Ve~~~~YL~aef~S~ifGFVDDVEF~~d~ 171 (176)
|+++++||||||+|++||||||||||+++
T Consensus 76 ve~~~nYl~ae~~Srlf~FVDDlEfyl~~ 104 (141)
T COG4446 76 VEKNDNYLRAECTSRLFGFVDDLEFYLPQ 104 (141)
T ss_pred eecCchHHHHHHHHHHhhcccceEEecCC
Confidence 99999999999999999999999999975
No 2
>PF07386 DUF1499: Protein of unknown function (DUF1499); InterPro: IPR010865 This family consists of several hypothetical bacterial and plant proteins of around 125 residues in length. The function of this family is unknown.
Probab=99.87 E-value=8.4e-22 Score=150.70 Aligned_cols=81 Identities=25% Similarity=0.390 Sum_probs=74.4
Q ss_pred ccCCCCCCCeeeeccc-cCCCCcccCCeeccCCCCCCCCHHHHHHHHHHHHHhcCCCCCCcEEE-EecCCEEEEEEEcCC
Q 030500 81 LALCPATKNCISTAEN-ISDLTHYAPPWNYNRGRKKPVSREVAMEELLQVIKSTKPDRFTPRLV-EKKDDYVHVEYESPV 158 (176)
Q Consensus 81 La~CP~sPNCVSSqa~-~~D~~h~I~Pw~y~g~~~~~~s~e~A~~~L~~vl~~~~~~~f~~~IV-e~~~~YL~aef~S~i 158 (176)
|++||++||||||++. ..+..|+|+||.|.++ ++++|++|.++++++++ .+|+ +++++|||++++|++
T Consensus 3 l~~~~~~P~~~ss~~~~~~~~~~~i~P~~~~~~------~~~~~~~l~~~~~~~~~----~~v~~~~~~~~l~a~~~s~~ 72 (118)
T PF07386_consen 3 LSTCPSSPNCVSSAADAPRDAYPDIAPLTYPGS------PEEAFAALEAAVEALPW----TVVVDDQSDGYLEAVARSPL 72 (118)
T ss_pred CCCCCCCCCeeeeccccccccCCCCCCEecCCC------HHHHHHHHHHHHHHCCC----cEEeccCCCCEEEEEEEecc
Confidence 8999999999999864 3489999999999986 89999999999999997 7777 888999999999999
Q ss_pred CCcccceEEEeee
Q 030500 159 LGVGLAHHTFVQL 171 (176)
Q Consensus 159 fGFVDDVEF~~d~ 171 (176)
|||+|||||+++.
T Consensus 73 ~gF~DDv~i~~~~ 85 (118)
T PF07386_consen 73 FGFPDDVEIRVRP 85 (118)
T ss_pred cCCCcEEEEEEeC
Confidence 9999999999975
No 3
>KOG1509 consensus Predicted nucleic acid-binding protein ASMTL [Cell cycle control, cell division, chromosome partitioning]
Probab=61.69 E-value=13 Score=32.06 Aligned_cols=38 Identities=21% Similarity=0.208 Sum_probs=30.4
Q ss_pred CeeeeccccCCCCcccCCeeccCCCCCCCCHHHHHHHHHHHHHhcC
Q 030500 89 NCISTAENISDLTHYAPPWNYNRGRKKPVSREVAMEELLQVIKSTK 134 (176)
Q Consensus 89 NCVSSqa~~~D~~h~I~Pw~y~g~~~~~~s~e~A~~~L~~vl~~~~ 134 (176)
-|||+.++.-+...+.+||.|- .+.|+.+...+++.++
T Consensus 34 ~~~S~feEnl~k~~~~~p~~yv--------~~tA~~KA~~I~erL~ 71 (209)
T KOG1509|consen 34 VVVSTFEENLIKSSFETPEDYV--------VETAKQKAEEIIERLG 71 (209)
T ss_pred EEeccchhhchhhccCCHHHHH--------HHHHHHHHHHHHHHhh
Confidence 4777776545556689999997 5689999999999988
No 4
>PF03681 UPF0150: Uncharacterised protein family (UPF0150); InterPro: IPR005357 This family of small proteins is uncharacterised. In Q9A3L8 from SWISSPROT this domain is found next to a DNA binding helix-turn-helix domain IPR002145 from INTERPRO, which suggests that this is some kind of ligand binding domain.; PDB: 2DSY_C 2YZT_A 3KWR_A.
Probab=49.68 E-value=25 Score=22.33 Aligned_cols=31 Identities=19% Similarity=0.367 Sum_probs=24.3
Q ss_pred ccCCCCCCCeeeeccccCCCCcccCCeeccCCCCCCCCHHHHHHHHHHHHHhc
Q 030500 81 LALCPATKNCISTAENISDLTHYAPPWNYNRGRKKPVSREVAMEELLQVIKST 133 (176)
Q Consensus 81 La~CP~sPNCVSSqa~~~D~~h~I~Pw~y~g~~~~~~s~e~A~~~L~~vl~~~ 133 (176)
..-||+-|.|++.-+ |.++|++.++++|...
T Consensus 15 ~~~~pdlpg~~t~G~----------------------t~eea~~~~~eal~~~ 45 (48)
T PF03681_consen 15 VAYFPDLPGCFTQGD----------------------TLEEALENAKEALELW 45 (48)
T ss_dssp EEEETTCCTCEEEES----------------------SHHHHHHHHHHHHHHH
T ss_pred EEEeCCccChhhcCC----------------------CHHHHHHHHHHHHHHH
Confidence 677999999985432 4789999999998753
No 5
>PF08368 FAST_2: FAST kinase-like protein, subdomain 2; InterPro: IPR013579 This domain represents a conserved region of eukaryotic Fas-activated serine/threonine (FAST) kinases (2.7.1 from EC) that contains several conserved leucine residues. FAST kinase is rapidly activated during Fas-mediated apoptosis, when it phosphorylates TIA-1, a nuclear RNA-binding protein that has been implicated as an effector of apoptosis []. Note that many family members are hypothetical proteins. This subdomain is often found associated with the FAST kinase-like protein, subdomain 2.
Probab=41.94 E-value=42 Score=24.40 Aligned_cols=39 Identities=15% Similarity=0.284 Sum_probs=29.2
Q ss_pred HHHHHHHHHHhcCCCCCCcEEEEecCCEEEEEEEcCCCCcccceEEEeee
Q 030500 122 AMEELLQVIKSTKPDRFTPRLVEKKDDYVHVEYESPVLGVGLAHHTFVQL 171 (176)
Q Consensus 122 A~~~L~~vl~~~~~~~f~~~IVe~~~~YL~aef~S~ifGFVDDVEF~~d~ 171 (176)
....+.++++++=| .++|++....++ +||.=|+|+.+|.
T Consensus 49 ~~~~v~~~L~~lLg----------~~~~~~~~v~tp-~gy~iD~E~~lD~ 87 (93)
T PF08368_consen 49 LQQEVQEALKSLLG----------GENYFRSNVITP-YGYTIDFEIVLDK 87 (93)
T ss_pred HHHHHHHHHHHHhC----------CccceEEccccC-CCceEEEEEEECC
Confidence 45666666666543 457888888888 5998999999985
No 6
>COG1598 Predicted nuclease of the RNAse H fold, HicB family [General function prediction only]
Probab=40.06 E-value=36 Score=23.94 Aligned_cols=32 Identities=25% Similarity=0.330 Sum_probs=24.0
Q ss_pred ccCCCCCCCeeeeccccCCCCcccCCeeccCCCCCCCCHHHHHHHHHHHHHhcC
Q 030500 81 LALCPATKNCISTAENISDLTHYAPPWNYNRGRKKPVSREVAMEELLQVIKSTK 134 (176)
Q Consensus 81 La~CP~sPNCVSSqa~~~D~~h~I~Pw~y~g~~~~~~s~e~A~~~L~~vl~~~~ 134 (176)
...+|+-|+|++.-+ |.++|++.++++|+-.-
T Consensus 17 ~~~~Pdlpgc~s~G~----------------------T~eea~~n~~eai~l~~ 48 (73)
T COG1598 17 VASVPDLPGCHSQGE----------------------TLEEALQNAKEAIELHL 48 (73)
T ss_pred EEEeCCCCCccccCC----------------------CHHHHHHHHHHHHHHHH
Confidence 567899999987432 47888888888877643
No 7
>PF07867 DUF1654: Protein of unknown function (DUF1654); InterPro: IPR012449 This entry is represented by Bacteriophage F116 (Pseudomonas phage F116), Orf28. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of proteins from the Pseudomonadaceae.
Probab=37.31 E-value=1.1e+02 Score=22.40 Aligned_cols=33 Identities=21% Similarity=0.325 Sum_probs=27.2
Q ss_pred HHHHHHHHHHHHHhcCCCCCCcEEEEecCCEEEEEEE
Q 030500 119 REVAMEELLQVIKSTKPDRFTPRLVEKKDDYVHVEYE 155 (176)
Q Consensus 119 ~e~A~~~L~~vl~~~~~~~f~~~IVe~~~~YL~aef~ 155 (176)
.++.|++|++.|..+.+ ..|.-.+++-+++..+
T Consensus 36 ~~~~W~~vl~~i~Eteg----v~v~~~dDGsv~i~W~ 68 (73)
T PF07867_consen 36 SDEDWEQVLEEIAETEG----VEVTFNDDGSVRIRWE 68 (73)
T ss_pred CHHHHHHHHHHHhcCCC----eEEEEcCCCeEEEEEE
Confidence 67899999999999997 7777777777776654
No 8
>COG2837 Predicted iron-dependent peroxidase [Inorganic ion transport and metabolism]
Probab=35.58 E-value=48 Score=30.57 Aligned_cols=44 Identities=14% Similarity=0.174 Sum_probs=36.6
Q ss_pred HHHHHHHHHHHHHhcCCCCCCcEEEEecCCEEEEEEEcCCCCcccceE
Q 030500 119 REVAMEELLQVIKSTKPDRFTPRLVEKKDDYVHVEYESPVLGVGLAHH 166 (176)
Q Consensus 119 ~e~A~~~L~~vl~~~~~~~f~~~IVe~~~~YL~aef~S~ifGFVDDVE 166 (176)
.+..+..+..+++.++. ...|+.+.+++++++-. -+|||+|=.|
T Consensus 134 ~~~~~~~~r~~~~~~~~---~~~V~~~~~GF~~~~~~-nl~GFkDGT~ 177 (352)
T COG2837 134 QDVVFHAARAIIRSLGD---AAEVRWEIHGFRSAEDR-NLLGFKDGTE 177 (352)
T ss_pred HHHHHHHHHHHHHhhcc---ceEEEEeEEeeeecccc-cccccccCCC
Confidence 77889999999999986 57788888888888877 8899998543
No 9
>KOG3422 consensus Mitochondrial ribosomal protein L16 [Translation, ribosomal structure and biogenesis]
Probab=27.41 E-value=1e+02 Score=26.86 Aligned_cols=62 Identities=16% Similarity=0.127 Sum_probs=46.5
Q ss_pred CcccccCCCCCCCeeeecccc-----CCCCcccCCeecc-------CCCCCCCCHHHHHHHHHHHHHhcCCCCCCcEEEE
Q 030500 77 NQQALALCPATKNCISTAENI-----SDLTHYAPPWNYN-------RGRKKPVSREVAMEELLQVIKSTKPDRFTPRLVE 144 (176)
Q Consensus 77 G~~~La~CP~sPNCVSSqa~~-----~D~~h~I~Pw~y~-------g~~~~~~s~e~A~~~L~~vl~~~~~~~f~~~IVe 144 (176)
+.+=-.+||..|-|+-.++.- ...+|+|+|..-. |+ ++.++|-+.|.++...+|. .+++|.
T Consensus 103 ~~iWrr~~p~~Pvt~K~~etRMG~GKGa~d~wva~V~~GrIl~EmgG~----~~~~~Ar~al~~aa~klp~---~~efVs 175 (221)
T KOG3422|consen 103 GKIWRRPAPNLPVTVKGNETRMGGGKGAIDHWVARVKAGRILFEMGGD----VEEEEARQALLQAAHKLPF---KYEFVS 175 (221)
T ss_pred ccEEEEecCCCceeecCcceeccCCCCCcceeEEEecCCcEEEEeCCc----ccHHHHHHHHHHHHhcCCc---cEEEee
Confidence 333346999999999887532 4678999997654 32 5688999999999999984 567765
Q ss_pred e
Q 030500 145 K 145 (176)
Q Consensus 145 ~ 145 (176)
+
T Consensus 176 ~ 176 (221)
T KOG3422|consen 176 E 176 (221)
T ss_pred H
Confidence 4
No 10
>PF10369 ALS_ss_C: Small subunit of acetolactate synthase; InterPro: IPR019455 This entry represents the C-terminal domain of the small subunit of acetolactate synthase (the N-terminal domain being an ACT domain). Acetolactate synthase is a tetrameric enzyme, composed of two large and two small subunits, which catalyses the first step in branched-chain amino acid biosynthesis. This reaction is sensitive to certain herbicides []. ; PDB: 2F1F_B 2FGC_A 2PC6_A.
Probab=27.14 E-value=2.1e+02 Score=20.11 Aligned_cols=32 Identities=22% Similarity=0.342 Sum_probs=26.0
Q ss_pred HHHHHHHHHHHhcCCCCCCcEEEEecCCEEEEEEEcC
Q 030500 121 VAMEELLQVIKSTKPDRFTPRLVEKKDDYVHVEYESP 157 (176)
Q Consensus 121 ~A~~~L~~vl~~~~~~~f~~~IVe~~~~YL~aef~S~ 157 (176)
+...++.++++... ++|++.+++|+-+|++..
T Consensus 14 ~~r~ei~~l~~~f~-----a~ivd~~~~~~iie~tG~ 45 (75)
T PF10369_consen 14 ENRSEILQLAEIFR-----ARIVDVSPDSIIIELTGT 45 (75)
T ss_dssp HHHHHHHHHHHHTT------EEEEEETTEEEEEEEE-
T ss_pred cCHHHHHHHHHHhC-----CEEEEECCCEEEEEEcCC
Confidence 45778888888886 899999999999999853
No 11
>cd00005 CBM9 Family 9 carbohydrate-binding module (CBM), plays a role in microbial degradation of cellulose and hemicellulose found in plants; previously called cellulose-binding domain; the binding sites of the CBMs for which structures have been determined are of two general types: flat surfaces comprising predominantly aromatic residues tryptophan and tyrosine and extended shallow grooves; this domain frequently occurs in tandem.
Probab=23.37 E-value=97 Score=25.13 Aligned_cols=26 Identities=19% Similarity=0.098 Sum_probs=17.4
Q ss_pred EEEEEEEcCC-------CCcccceEEEeeeccc
Q 030500 149 YVHVEYESPV-------LGVGLAHHTFVQLFFH 174 (176)
Q Consensus 149 YL~aef~S~i-------fGFVDDVEF~~d~~~~ 174 (176)
||.++++-+. ..--|.||++||.+-.
T Consensus 52 Yv~~~v~D~~~~~~~~~~~~~D~veifiD~~nd 84 (186)
T cd00005 52 YVLAEVKDPTLNKDSANPWEQDSVEIFIDENNG 84 (186)
T ss_pred EEEEEEECCCccccCCCCccCCeEEEEECCCCC
Confidence 6667766544 2334669999998743
No 12
>PF08447 PAS_3: PAS fold; InterPro: IPR013655 The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs []. The PAS fold appears in archaea, eubacteria and eukarya. The PAS domain contains a sensory box, or S-box domain that occupies the central portion of the PAS domain but is more widely distributed. It is often tandemly repeated. Known prosthetic groups bound in the S-box domain include haem in the oxygen sensor FixL [], FAD in the redox potential sensor NifL [], and a 4-hydroxycinnamyl chromophore in photoactive yellow protein []. Proteins containing the domain often contain other regulatory domains such as response regulator or sensor histidine kinase domains. Other S-box proteins include phytochromes and the aryl hydrocarbon receptor nuclear translocator. This domain has been found in the gene product of the madA gene of the filamentous zygomycete fungus Phycomyces blakesleeanus. It has been shown that MadA encodes a blue-light photoreceptor for phototropism and other light responses. The gene is involved in the phototropic responses associated with sporangiophore growth; they exhibit phototropism by bending toward near-UV and blue wavelengths and away from far-UV wavelengths in a manner that is physiologically similar to plant phototropic responses [].; GO: 0005515 protein binding; PDB: 3NJA_D 3H9W_A 3GDI_B 3ICY_A 3EEH_A 3MR0_B.
Probab=22.97 E-value=75 Score=21.05 Aligned_cols=42 Identities=19% Similarity=0.285 Sum_probs=29.1
Q ss_pred HHHHHHHHHH-HHHhcCCCCCCcEEEEecCCEEEEEEEcCCCC
Q 030500 119 REVAMEELLQ-VIKSTKPDRFTPRLVEKKDDYVHVEYESPVLG 160 (176)
Q Consensus 119 ~e~A~~~L~~-vl~~~~~~~f~~~IVe~~~~YL~aef~S~ifG 160 (176)
.+...+.+.+ .+.....-.++.++..++++|.+++.+..+..
T Consensus 36 ~~~~~~~~~~~~~~~~~~~~~e~R~~~~~G~~~wi~~~~~~~~ 78 (91)
T PF08447_consen 36 RERVRQAIQQAALQNGEPFEIEYRIRRKDGEYRWIEVRGRPIF 78 (91)
T ss_dssp HHHHHHHHHHHHHHTT-EEEEEEEEEGTTSTEEEEEEEEEEEE
T ss_pred HHHHHHHHHHHhhccCcceEEEEEEECCCCCEEEEEEEEEEEE
Confidence 6777777777 45544444445677788899999999876643
No 13
>PF10134 RPA: Replication initiator protein A; InterPro: IPR018777 Members of this family of bacterial proteins are single-stranded DNA binding proteins that are involved in DNA replication, repair and recombination.
Probab=22.60 E-value=1e+02 Score=26.31 Aligned_cols=45 Identities=7% Similarity=0.008 Sum_probs=31.2
Q ss_pred HHHHHHHHHHHHHhcCCCCCCcEEEEecCCEEEEEEEcCCCCcccceEEEe
Q 030500 119 REVAMEELLQVIKSTKPDRFTPRLVEKKDDYVHVEYESPVLGVGLAHHTFV 169 (176)
Q Consensus 119 ~e~A~~~L~~vl~~~~~~~f~~~IVe~~~~YL~aef~S~ifGFVDDVEF~~ 169 (176)
.....++|++.|..+.+ ++|...-. =.-+.++.-||++|++++.-
T Consensus 88 ~G~~Y~~L~~aL~RL~~----T~i~t~~~--~~~~~~~~~F~lI~~~~~~~ 132 (229)
T PF10134_consen 88 GGRYYERLREALDRLQG----TTIETNIR--TGGKWRTEGFGLIDSYRIVS 132 (229)
T ss_pred cHHHHHHHHHHHHHhcC----CEEEEEEc--cCCEEEEEEeeeeeEEEEEE
Confidence 34689999999999996 67743222 11224455589999999874
No 14
>PF06240 COXG: Carbon monoxide dehydrogenase subunit G (CoxG); InterPro: IPR010419 The CO dehydrogenase structural genes coxMSL are flanked by nine accessory genes arranged as the cox gene cluster. The cox genes are specifically and coordinately transcribed under chemolithoautotrophic conditions in the presence of CO as carbon and energy source [].; PDB: 2NS9_A 2PCS_A.
Probab=21.90 E-value=2.6e+02 Score=21.14 Aligned_cols=37 Identities=16% Similarity=0.061 Sum_probs=28.3
Q ss_pred CHHHHHHHHHH---HHHhcCCCCCCcEEEEecCCEEEEEEEcCC
Q 030500 118 SREVAMEELLQ---VIKSTKPDRFTPRLVEKKDDYVHVEYESPV 158 (176)
Q Consensus 118 s~e~A~~~L~~---vl~~~~~~~f~~~IVe~~~~YL~aef~S~i 158 (176)
+++++|+-|.+ +..-+|+ .+.+++.++-..++++-++
T Consensus 8 ~~~~vw~~l~D~~~l~~ciPG----~~~~e~~~~~~~~~~~v~v 47 (140)
T PF06240_consen 8 PPEKVWAFLSDPENLARCIPG----VESIEKVGDEYKGKVKVKV 47 (140)
T ss_dssp -HHHHHHHHT-HHHHHHHSTT----EEEEEEECTEEEEEEEEES
T ss_pred CHHHHHHHhcCHHHHHhhCCC----cEEeeecCcEEEEEEEEEe
Confidence 47888888877 5666887 8888888888888888766
No 15
>TIGR01413 Dyp_perox_fam Dyp-type peroxidase family. dependent signal sequence characteristic of exported proteins with bound redox cofactors.
Probab=21.69 E-value=1.3e+02 Score=26.73 Aligned_cols=43 Identities=9% Similarity=0.129 Sum_probs=29.5
Q ss_pred HHHHHHHHHHHHHhcCCCCCCcEEEEecCCEEEEEEEc--CCCCcccc
Q 030500 119 REVAMEELLQVIKSTKPDRFTPRLVEKKDDYVHVEYES--PVLGVGLA 164 (176)
Q Consensus 119 ~e~A~~~L~~vl~~~~~~~f~~~IVe~~~~YL~aef~S--~ifGFVDD 164 (176)
.+..+.....+...+.+ .++|+.+..+|.|..-+. -+|||+|=
T Consensus 105 ~~~~~~~~~~l~~~~~~---~~~~~~~~~Gf~~~~~~t~R~l~GF~DG 149 (308)
T TIGR01413 105 PDVVFHAARALLRRFGD---AVTVRDEVHGFRYPGAETPRDLLGFKDG 149 (308)
T ss_pred HHHHHHHHHHHHHHhcC---ceEEEEEEeccccCCCCCcccccCcccc
Confidence 56666666666666654 488999888888763311 26999983
No 16
>COG1566 EmrA Multidrug resistance efflux pump [Defense mechanisms]
Probab=21.06 E-value=34 Score=31.32 Aligned_cols=54 Identities=19% Similarity=0.244 Sum_probs=34.3
Q ss_pred HHHHHHHHHHHHhcCC-------CCCCcEEEEecCCEEEEEEEcCCCCcccceEEEeeecccc
Q 030500 120 EVAMEELLQVIKSTKP-------DRFTPRLVEKKDDYVHVEYESPVLGVGLAHHTFVQLFFHQ 175 (176)
Q Consensus 120 e~A~~~L~~vl~~~~~-------~~f~~~IVe~~~~YL~aef~S~ifGFVDDVEF~~d~~~~~ 175 (176)
.+|.+++.++-..+.+ ||+=++.--+.++|+.+- +++|-+|++-.+|++-.|.+
T Consensus 193 ~~a~a~~~~A~l~L~~T~IrAP~dG~V~~~~v~~G~~V~~G--~~l~alVp~~~~yV~AnFkE 253 (352)
T COG1566 193 ASAEAALDQAKLDLERTVIRAPVDGYVTNLSVRVGQYVSAG--TPLMALVPLDSFYVVANFKE 253 (352)
T ss_pred HHHHHHHHHHHHHhhCCEEECCCCceEEeecccCCCeecCC--CceEEEecccceEEEeeeee
Confidence 4455555555555554 322222223345566655 88999999999999988864
No 17
>PF01106 NifU: NifU-like domain; InterPro: IPR001075 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] []. FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins [, ]. It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly []. The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA []. SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA [], acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins []. Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen []. This entry represents the C-terminal of NifU and homologous proteins. NifU contains two domains: an N-terminal (IPR002871 from INTERPRO) and a C-terminal domain []. These domains exist either together or on different polypeptides, both domains being found in organisms that do not fix nitrogen (e.g. yeast), so they have a broader significance in the cell than nitrogen fixation. ; GO: 0005506 iron ion binding, 0051536 iron-sulfur cluster binding, 0016226 iron-sulfur cluster assembly; PDB: 2JNV_A 2Z51_A 1TH5_A 1VEH_A 1XHJ_A.
Probab=20.82 E-value=1.8e+02 Score=20.19 Aligned_cols=35 Identities=26% Similarity=0.303 Sum_probs=28.6
Q ss_pred HHHHHHHHHHHHhcCCCCCCcEEEEecCCEEEEEEEcC
Q 030500 120 EVAMEELLQVIKSTKPDRFTPRLVEKKDDYVHVEYESP 157 (176)
Q Consensus 120 e~A~~~L~~vl~~~~~~~f~~~IVe~~~~YL~aef~S~ 157 (176)
+++++++.-.|+.-+| ..++++-+++.+++.++..
T Consensus 2 ~~~l~~IrP~L~~dGG---dv~lv~v~~~~V~V~l~Ga 36 (68)
T PF01106_consen 2 EEVLEEIRPYLQSDGG---DVELVDVDDGVVYVRLTGA 36 (68)
T ss_dssp HHHHHHCHHHHHHTTE---EEEEEEEETTEEEEEEESS
T ss_pred HHHHHHhChHHHhcCC---cEEEEEecCCEEEEEEEeC
Confidence 5678888888888776 4899999999999988754
No 18
>cd04097 mtEFG1_C mtEFG1_C: C-terminus of mitochondrial Elongation factor G1 (mtEFG1)-like proteins found in eukaryotes. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than that in prokaryotes, with both cytoplasmic and mitochondrial elongation factors and multiple isoforms being expressed in certain species. Eukaryotic EF-2 operates in the cytosolic protein synthesis machinery of eukaryotes, EF-Gs in protein synthesis in bacteria. Eukaryotic mtEFG1 proteins show significant homology to bacterial EF-Gs. Mutants in yeast mtEFG1 have impaired mitochondrial protein synthesis, respiratory defects and a tendency to lose mitochondrial DNA. There are two forms of mtEFG present in mammals (desig
Probab=20.32 E-value=2.1e+02 Score=19.62 Aligned_cols=42 Identities=17% Similarity=0.304 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHHHhcCCCCCCcEEEEec--CCEEEEEEEcCC---CCcccce
Q 030500 119 REVAMEELLQVIKSTKPDRFTPRLVEKK--DDYVHVEYESPV---LGVGLAH 165 (176)
Q Consensus 119 ~e~A~~~L~~vl~~~~~~~f~~~IVe~~--~~YL~aef~S~i---fGFVDDV 165 (176)
+++..-++...|.... ++|++.+ ++..++++.-++ |||-|++
T Consensus 11 p~~~~g~v~~~l~~rr-----g~i~~~~~~~~~~~i~~~~P~~e~~g~~~~L 57 (78)
T cd04097 11 PTEFQGNVIGLLNKRK-----GTIVDTDTGEDEFTLEAEVPLNDMFGYSTEL 57 (78)
T ss_pred cHHHHHHHHHHHHHCC-----CEEeceEecCCeEEEEEEECHHHhhChHHHH
Confidence 4567788888887765 5777544 457777887554 7887764
Done!