Query 034816
Match_columns 82
No_of_seqs 116 out of 709
Neff 7.2
Searched_HMMs 46136
Date Fri Mar 29 06:42:45 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034816.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034816hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF07876 Dabb: Stress responsi 99.9 6.4E-22 1.4E-26 119.0 8.4 74 2-76 18-96 (97)
2 PF03992 ABM: Antibiotic biosy 96.7 0.02 4.3E-07 31.8 7.2 46 10-61 31-77 (78)
3 PF07045 DUF1330: Protein of u 95.5 0.031 6.7E-07 31.3 3.8 34 26-60 32-65 (65)
4 COG1359 Uncharacterized conser 94.7 0.44 9.6E-06 28.6 7.6 58 6-69 28-86 (100)
5 PRK10486 autoinducer-2 (AI-2) 94.0 0.46 1E-05 28.3 6.6 56 15-76 36-91 (96)
6 PF01037 AsnC_trans_reg: AsnC 91.8 0.92 2E-05 24.9 5.3 42 2-52 12-54 (74)
7 COG5470 Uncharacterized conser 90.2 1.2 2.5E-05 27.4 4.9 41 34-74 53-94 (96)
8 PF13826 DUF4188: Domain of un 89.5 1 2.2E-05 28.4 4.5 36 32-67 50-85 (117)
9 TIGR02118 conserved hypothetic 88.8 3.5 7.5E-05 24.5 8.0 39 31-69 50-88 (100)
10 COG3224 Uncharacterized protei 88.2 1.4 2.9E-05 30.2 4.6 49 28-76 53-101 (195)
11 PF07110 EthD: EthD domain; I 86.7 4.2 9.1E-05 23.2 5.9 35 28-62 52-87 (95)
12 PRK13314 heme-degrading monoox 85.5 4.1 9E-05 25.2 5.5 48 10-61 29-77 (107)
13 COG2329 Uncharacterized enzyme 82.9 8.3 0.00018 23.5 6.6 34 33-66 51-84 (105)
14 PRK13315 heme-degrading monoox 81.9 6.2 0.00013 24.4 5.2 46 12-62 31-78 (107)
15 PRK13312 heme-degrading monoox 80.9 7.7 0.00017 24.1 5.3 48 9-61 29-78 (107)
16 PRK13313 heme-degrading monoox 77.2 11 0.00024 23.4 5.3 49 9-62 28-78 (108)
17 PF02410 Oligomerisation: Olig 71.5 19 0.00042 21.5 5.6 46 1-50 1-46 (100)
18 PRK11179 DNA-binding transcrip 70.6 18 0.0004 23.0 5.3 24 29-52 102-125 (153)
19 PRK11169 leucine-responsive tr 67.3 19 0.00041 23.3 4.9 24 29-52 109-132 (164)
20 PRK13316 heme-degrading monoox 64.3 34 0.00074 21.7 7.2 51 8-62 34-86 (121)
21 PHA00650 hypothetical protein 62.7 7.6 0.00016 22.3 2.0 28 41-68 6-33 (82)
22 PF13816 Dehydratase_hem: Haem 62.5 16 0.00034 26.7 4.1 59 5-67 204-274 (310)
23 PF14114 DUF4286: Domain of un 56.6 41 0.00089 20.1 7.8 31 30-60 48-80 (98)
24 PHA02085 hypothetical protein 54.7 17 0.00036 21.7 2.6 28 38-65 2-30 (87)
25 PRK12866 YciI-like protein; Re 42.9 73 0.0016 19.0 4.6 49 4-58 23-74 (97)
26 PRK12864 YciI-like protein; Re 41.8 72 0.0016 18.6 4.2 47 5-58 25-74 (89)
27 PHA02087 hypothetical protein 37.1 64 0.0014 18.7 3.1 25 36-60 3-27 (83)
28 PRK06524 biotin carboxylase-li 36.6 23 0.0005 27.5 1.6 27 39-65 78-105 (493)
29 PF07978 NIPSNAP: NIPSNAP ; I 35.2 84 0.0018 17.9 3.6 35 32-66 46-84 (102)
30 PRK12865 YciI-like protein; Re 34.0 1E+02 0.0022 18.1 4.2 50 5-58 24-77 (97)
31 PF07626 PSD3: Protein of unkn 33.8 38 0.00082 19.0 1.8 48 4-52 7-54 (67)
32 PRK11370 YciI-like protein; Re 33.2 1.1E+02 0.0023 18.1 5.1 23 36-58 60-83 (99)
33 PF01106 NifU: NifU-like domai 29.5 82 0.0018 17.6 2.8 25 58-82 3-31 (68)
34 PF11813 DUF3334: Protein of u 28.3 59 0.0013 22.8 2.4 24 29-52 56-79 (229)
35 COG5256 TEF1 Translation elong 24.9 1.2E+02 0.0025 23.5 3.5 74 5-79 38-122 (428)
36 PRK11118 putative monooxygenas 24.5 1.2E+02 0.0025 18.8 2.9 19 38-58 53-71 (100)
37 PF09128 RGS-like: Regulator o 24.3 34 0.00074 23.3 0.6 22 41-65 5-27 (188)
38 PF14799 FAM195: FAM195 family 24.0 52 0.0011 20.0 1.3 18 53-70 31-48 (99)
39 PF11695 DUF3291: Domain of un 22.5 1.6E+02 0.0035 19.0 3.5 35 34-68 60-94 (140)
40 TIGR00125 cyt_tran_rel cytidyl 21.0 1.4E+02 0.0031 15.5 2.7 17 53-69 12-28 (66)
No 1
>PF07876 Dabb: Stress responsive A/B Barrel Domain; InterPro: IPR013097 The stress-response A/B barrel domain is found in a class of stress-response proteins in plants. It is also found in some bacterial fructose-bisphosphate aldolase such as at the C terminus of a fructose 1,6-bisphosphate aldolase from Hydrogenophilus thermoluteolus (Q9ZA13 from SWISSPROT) []. Q93NG5 from SWISSPROT is found in the pA01 plasmid, which encodes genes for molybdopterin uptake and degradation of plant alkaloid nicotine. The stress-response A/B barrel domain forms a very stable dimer. This dimer belongs to the superfamily of dimeric alpha+beta barrels in which the two beta-sheets form a beta-barrel. The two molecules in the dimer are related by a 2-fold axis parallel to helix H1 and beta-strands B3 and B4. C-terminal residues extending from the beta4 strand of each monomer wrap around and connect with the beta2 strand and alpha1 helix of the opposing monomer to form the dimer interface [, , ].The outer surface of the beta-sheets of the two molecules forms a beta-barrel-like structure defining a central pore. The function of the stress-response A/B barrel domain is unknown [, , ], but it is upregulated in response to salt stress in Populus balsamifera (balsam poplar) []. Some proteins known to contain a stress response A/B barrel domain are listed below: - Arabidopsis thaliana At3g17210 - Arabidopsis thaliana At5g22580 -Populus tremula stable protein 1 (SP-1)(Populus species), a thermostable stress-responsive protein. - Pseudomonas hydrogenothermophila fructose 1,6-bisphosphate aldolase (cbbA). The structure of one of these proteins has been solved (Q9LUV2 from SWISSPROT) and the domain forms an alpha-beta barrel dimer [].; PDB: 3BB5_E 3FMB_A 3BDE_B 2QYC_A 1Q53_B 2Q3P_A 1Q4R_A 3BN7_A 3BGU_B 1RJJ_B ....
Probab=99.87 E-value=6.4e-22 Score=118.96 Aligned_cols=74 Identities=34% Similarity=0.608 Sum_probs=66.2
Q ss_pred HHHHHHHhhcccc-----cceEEeceeCCccccCCCeeEEEEEEECCHhhHHhhhcChhHHHHHHHHhhhhhceEEEEee
Q 034816 2 IAELIRSCCGLEL-----LAVKYKGKNVSIENLHQGFTHIFESTFESTEGVAEYVAHPAHVEYANLFLANLEKVLVIDYK 76 (82)
Q Consensus 2 i~~~~~~l~~L~~-----~~~~~~G~~~~~e~~~~gy~~~l~~~F~s~e~l~~Y~~hP~H~~~~~~~~~~~~~~~v~D~~ 76 (82)
++++++.+++|++ +++++ |+|.++++.++|||++++++|+|.+++++|+.||.|+++++.++|++++++++||+
T Consensus 18 ~~~~~~~l~~l~~~ip~i~~~~~-G~~~~~~~~~~~~~~~~~~~F~s~~~l~~Y~~hp~H~~~~~~~~p~~~~~~~~D~~ 96 (97)
T PF07876_consen 18 IEEVLEALRALKDKIPGIVSFEV-GRNFSPEDLAKGYDHALVSTFESEEDLDAYQTHPAHQAFVEFLKPILEDRIVFDFE 96 (97)
T ss_dssp HHHHHHHHHHHHHHSTTECEEEE-EEESSTSSTSTT-SEEEEEEESSHHHHHHHHTSHHHHHHHHHHHGGEEEEEEEEEE
T ss_pred HHHHHHHHHhcccCCCceEEEEE-EcccCcccccCCCcEEEEEEECCHHHHHHHHcCHHHHHHHHHHHHHhCceEEEEEE
Confidence 4566777777755 89999 99999866679999999999999999999999999999999999999999999997
No 2
>PF03992 ABM: Antibiotic biosynthesis monooxygenase; InterPro: IPR007138 This domain is found in monooxygenases involved in the biosynthesis of several antibiotics by Streptomyces species, which can carry out oxygenation without the assistance of any of the prosthetic groups, metal ions or cofactors normally associated with activation of molecular oxygen. The structure of ActVA-Orf6 monooxygenase from Streptomyces coelicolor (Q53908 from SWISSPROT), which is involved in actinorhodin biosynthesis, reveals a dimeric alpha+beta barrel topology []. There is also a conserved histidine that is likely to be an active site residue. In S. coelicolor SCO1909 (Q9X9W3 from SWISSPROT) this domain occurs as a repeat. This domain is also found in protein LsrG, involved in the degradation of quorum-sensing molecule autoinducer-2 [], and in several uncharacterised proteins.; PDB: 1X7V_A 3F44_A 4DN9_B 1N5T_B 1LQ9_A 1N5Q_B 1N5V_A 1N5S_A 2GFF_B 3BM7_A ....
Probab=96.74 E-value=0.02 Score=31.83 Aligned_cols=46 Identities=11% Similarity=0.106 Sum_probs=36.4
Q ss_pred hcccc-cceEEeceeCCccccCCCeeEEEEEEECCHhhHHhhhcChhHHHHHH
Q 034816 10 CGLEL-LAVKYKGKNVSIENLHQGFTHIFESTFESTEGVAEYVAHPAHVEYAN 61 (82)
Q Consensus 10 ~~L~~-~~~~~~G~~~~~e~~~~gy~~~l~~~F~s~e~l~~Y~~hP~H~~~~~ 61 (82)
++-++ +++.+ .++.. ++-.+.++..++|.++++.+..+|.|+++.+
T Consensus 31 ~~~~G~~~~~~-~~~~~-----~~~~~~~~~~W~s~~a~~~~~~s~~~~~~~~ 77 (78)
T PF03992_consen 31 RKEPGCLSYEL-YRSLD-----DPNRYVIVERWESEEAFQAHFKSPEFKAFQE 77 (78)
T ss_dssp HTSTTEEEEEE-EEESS-----STTEEEEEEEESSHHHHHHHHTSHHHHHHHH
T ss_pred hcCCCcEEEEE-EEecC-----CCCEEEEEEEECCHHHHHHHHcCHHHHHHHh
Confidence 44555 78887 66542 2345999999999999999999999999875
No 3
>PF07045 DUF1330: Protein of unknown function (DUF1330); InterPro: IPR010753 This family consists of several hypothetical bacterial proteins of around 90 residues in length. The function of this family is unknown.; PDB: 2FIU_B 3HHL_A 3DCA_D 3LO3_I.
Probab=95.50 E-value=0.031 Score=31.30 Aligned_cols=34 Identities=15% Similarity=0.177 Sum_probs=28.9
Q ss_pred ccccCCCeeEEEEEEECCHhhHHhhhcChhHHHHH
Q 034816 26 IENLHQGFTHIFESTFESTEGVAEYVAHPAHVEYA 60 (82)
Q Consensus 26 ~e~~~~gy~~~l~~~F~s~e~l~~Y~~hP~H~~~~ 60 (82)
.+| ...++.++++.|.|.++...+-++|+.|+++
T Consensus 32 leG-~~~~~~~viieFPs~~aa~~~~~speYq~~~ 65 (65)
T PF07045_consen 32 LEG-DWDPDRVVIIEFPSMEAAKAWYNSPEYQALK 65 (65)
T ss_dssp EES-T-SSSEEEEEEESSHHHHHHHHCSHHHHHHH
T ss_pred Eec-CCCCCeEEEEECCCHHHHHHHHCCHhHHhhC
Confidence 345 4567999999999999999999999999874
No 4
>COG1359 Uncharacterized conserved protein [Function unknown]
Probab=94.69 E-value=0.44 Score=28.63 Aligned_cols=58 Identities=9% Similarity=0.120 Sum_probs=46.1
Q ss_pred HHHhhcccc-cceEEeceeCCccccCCCeeEEEEEEECCHhhHHhhhcChhHHHHHHHHhhhhhc
Q 034816 6 IRSCCGLEL-LAVKYKGKNVSIENLHQGFTHIFESTFESTEGVAEYVAHPAHVEYANLFLANLEK 69 (82)
Q Consensus 6 ~~~l~~L~~-~~~~~~G~~~~~e~~~~gy~~~l~~~F~s~e~l~~Y~~hP~H~~~~~~~~~~~~~ 69 (82)
++.-++-.+ +++.+ .++.. ..=.+.++-.++|.++++.....|.-+++.+.+.+++.+
T Consensus 28 v~~sr~EeGcl~Y~l-~~d~~-----~~~~~~~~E~w~d~~A~~~H~~s~h~~~~~~~~~~l~~~ 86 (100)
T COG1359 28 VEASRAEEGCLSYEL-HRDPD-----NPGRFVLIEVWEDEAALDAHLQSPHFQAFVAALPPLLAG 86 (100)
T ss_pred HHHhccCCCceEEEE-EEeCC-----CCCEEEEEEEECCHHHHHHHhCCHHHHHHHHhChHhhcC
Confidence 333333444 78888 66653 334689999999999999999999999999999999987
No 5
>PRK10486 autoinducer-2 (AI-2) modifying protein LsrG; Provisional
Probab=94.02 E-value=0.46 Score=28.33 Aligned_cols=56 Identities=7% Similarity=-0.075 Sum_probs=44.5
Q ss_pred cceEEeceeCCccccCCCeeEEEEEEECCHhhHHhhhcChhHHHHHHHHhhhhhceEEEEee
Q 034816 15 LAVKYKGKNVSIENLHQGFTHIFESTFESTEGVAEYVAHPAHVEYANLFLANLEKVLVIDYK 76 (82)
Q Consensus 15 ~~~~~~G~~~~~e~~~~gy~~~l~~~F~s~e~l~~Y~~hP~H~~~~~~~~~~~~~~~v~D~~ 76 (82)
+.+.+ ..+. ++.-.+.++=.++|.++++.....|.-++|.+.+.+++++-..+-..
T Consensus 36 l~y~~-~~~~-----~~p~~~~~~E~w~d~~Al~~H~~tph~k~f~~~~~~ll~~~~~i~~~ 91 (96)
T PRK10486 36 LRFDV-LQDP-----EVPTRFYIYEAYKDEAAVAFHKTTPHYKTCVEKLEPLMTGPRKKRLF 91 (96)
T ss_pred eEEEE-EeCC-----CCCCEEEEEEEeCCHHHHHHHhcCHHHHHHHHHHHHHHhCCccccee
Confidence 66666 5543 33567899999999999999999999999999999999875544443
No 6
>PF01037 AsnC_trans_reg: AsnC family; InterPro: IPR019887 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One such family is the AsnC/Lrp subfamily []. The Lrp family of transcriptional regulators appears to be widely distributed among bacteria and archaea, as an important regulatory system of the amino acid metabolism and related processes []. Members of the Lrp family are small DNA-binding proteins with molecular masses of around 15 kDa. Target promoters often contain a number of binding sites that typically lack obvious inverted repeat elements, and to which binding is usually co-operative. LrpA from Pyrococcus furiosus is the first Lrp-like protein to date of which a three-dimensional structure has been solved. In the crystal structure LrpA forms an octamer consisting of four dimers. The structure revealed that the N-terminal part of the protein consists of a helix-turn-helix (HTH) domain, a fold generally involved in DNA binding. The C terminus of Lrp-like proteins has a beta-fold, where the two alpha-helices are located at one side of the four-stranded antiparallel beta-sheet. LrpA forms a homodimer mainly through interactions between the beta-strands of this C-terminal domain, and an octamer through further interactions between the second alpha-helix and fourth beta-strand of the motif. Hence, the C-terminal domain of Lrp-like proteins appears to be involved in ligand-response and activation [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2DJW_F 2GQQ_A 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2CG4_B 2DBB_B 1I1G_A ....
Probab=91.76 E-value=0.92 Score=24.91 Aligned_cols=42 Identities=10% Similarity=0.188 Sum_probs=31.7
Q ss_pred HHHHHHHhhcccc-cceEEeceeCCccccCCCeeEEEEEEECCHhhHHhhhc
Q 034816 2 IAELIRSCCGLEL-LAVKYKGKNVSIENLHQGFTHIFESTFESTEGVAEYVA 52 (82)
Q Consensus 2 i~~~~~~l~~L~~-~~~~~~G~~~~~e~~~~gy~~~l~~~F~s~e~l~~Y~~ 52 (82)
.+++.+.+.+++. .++.. .+++||+.+.+.++|.++++.+..
T Consensus 12 ~~~~~~~l~~~p~V~~~~~---------vtG~~d~~~~v~~~d~~~l~~~i~ 54 (74)
T PF01037_consen 12 YDEFAEALAEIPEVVECYS---------VTGEYDLILKVRARDMEELEEFIR 54 (74)
T ss_dssp HHHHHHHHHTSTTEEEEEE---------ESSSSSEEEEEEESSHHHHHHHHH
T ss_pred HHHHHHHHHcCCCEEEEEE---------EeCCCCEEEEEEECCHHHHHHHHH
Confidence 3567777777777 33333 456899999999999999998753
No 7
>COG5470 Uncharacterized conserved protein [Function unknown]
Probab=90.18 E-value=1.2 Score=27.37 Aligned_cols=41 Identities=17% Similarity=0.222 Sum_probs=32.7
Q ss_pred eEEEEEEECCHhhHHhhhcChhHHHHHHHHhhhh-hceEEEE
Q 034816 34 THIFESTFESTEGVAEYVAHPAHVEYANLFLANL-EKVLVID 74 (82)
Q Consensus 34 ~~~l~~~F~s~e~l~~Y~~hP~H~~~~~~~~~~~-~~~~v~D 74 (82)
+-.++++|+|.++....=++|+.|++.+.-.... ...+++|
T Consensus 53 tr~vviEFps~~~ar~~y~SpeYq~a~~~Rq~~ad~~~iiVe 94 (96)
T COG5470 53 TRNVVIEFPSLEAARDCYNSPEYQAAAAIRQAAADSEIIIVE 94 (96)
T ss_pred ccEEEEEcCCHHHHHHHhcCHHHHHHHHHHhhcccccEEEEe
Confidence 6789999999999999999999999998443333 3465555
No 8
>PF13826 DUF4188: Domain of unknown function (DUF4188)
Probab=89.49 E-value=1 Score=28.41 Aligned_cols=36 Identities=17% Similarity=0.198 Sum_probs=30.3
Q ss_pred CeeEEEEEEECCHhhHHhhhcChhHHHHHHHHhhhh
Q 034816 32 GFTHIFESTFESTEGVAEYVAHPAHVEYANLFLANL 67 (82)
Q Consensus 32 gy~~~l~~~F~s~e~l~~Y~~hP~H~~~~~~~~~~~ 67 (82)
+=+.+++.-|+|.|+|.+|..+|.|.+.-+.+....
T Consensus 50 ~~~~~~v~YwRs~e~L~~fA~~~~H~~aW~~fn~~~ 85 (117)
T PF13826_consen 50 PRTIMLVQYWRSFEDLHRFAHDPPHRPAWRWFNKRV 85 (117)
T ss_pred CCceEEEEEECCHHHHHHHHCCChHHHHHHHHHHHh
Confidence 356899999999999999999999999888655443
No 9
>TIGR02118 conserved hypothetical protein. This model represents a small family of proteins of unknown function, each about 105 amino acids in length. Conserved sites in the multiple alignment include a pair of aromatic residues, a histidine, and an aspartate.
Probab=88.77 E-value=3.5 Score=24.50 Aligned_cols=39 Identities=15% Similarity=0.090 Sum_probs=32.5
Q ss_pred CCeeEEEEEEECCHhhHHhhhcChhHHHHHHHHhhhhhc
Q 034816 31 QGFTHIFESTFESTEGVAEYVAHPAHVEYANLFLANLEK 69 (82)
Q Consensus 31 ~gy~~~l~~~F~s~e~l~~Y~~hP~H~~~~~~~~~~~~~ 69 (82)
..||.+..+.|+|.++++.-...|.=+++.+-...+.+.
T Consensus 50 ~~~d~i~el~Fds~e~~~~a~~sp~~~~~~~D~~nF~d~ 88 (100)
T TIGR02118 50 SPYYGMCELYFDSIEDFQAAFDSPEGKAAAADVANFADG 88 (100)
T ss_pred CCeeEEEEEEECCHHHHHHHHcCHHHHHHHHHHHhhcCC
Confidence 349999999999999999999999888887766655544
No 10
>COG3224 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=88.16 E-value=1.4 Score=30.16 Aligned_cols=49 Identities=12% Similarity=0.101 Sum_probs=39.9
Q ss_pred ccCCCeeEEEEEEECCHhhHHhhhcChhHHHHHHHHhhhhhceEEEEee
Q 034816 28 NLHQGFTHIFESTFESTEGVAEYVAHPAHVEYANLFLANLEKVLVIDYK 76 (82)
Q Consensus 28 ~~~~gy~~~l~~~F~s~e~l~~Y~~hP~H~~~~~~~~~~~~~~~v~D~~ 76 (82)
+....+.+..+..|++.|-+.++..+|.-++.++.-..+.+.-......
T Consensus 53 ~~G~~~e~~~ifRFD~~enl~aW~~SpeR~~wl~~~e~~~ee~~~~~~~ 101 (195)
T COG3224 53 QAGDRFEYETIFRFDNLENLAAWIHSPERRAWLERGENLVEEFVGKQRT 101 (195)
T ss_pred CCCCceeEEEEEEecCHHHHHHhhcCHHHHHHHHHhhccccccchhhcc
Confidence 4556689999999999999999999999999999877777665444333
No 11
>PF07110 EthD: EthD domain; InterPro: IPR009799 This family consists of several bacterial sequences which are related to the EthD protein of Rhodococcus ruber (Q93EX2 from SWISSPROT). R. ruber (formerly Gordonia terrae) IFP 2001 is one of a few bacterial strains able to degrade ethyl tert-butyl ether (ETBE), which is a major pollutant from gasoline. This strain was found to undergo a spontaneous 14.3-kbp chromosomal deletion, which results in the loss of the ability to degrade ETBE. Sequence analysis of the region corresponding to the deletion revealed the presence of a gene cluster, ethABCD, encoding a ferredoxin reductase (EthA), a cytochrome P-450 (EthB), a ferredoxin (EthC), and a 10kDa protein of unknown function (EthD), respectively. Upstream of ethABCD lies ethR, which codes for a putative positive transcriptional regulator of the AraC/XylS family. Transformation of the ETBE-negative mutant by a plasmid carrying the ethRABCD genes restored the ability to degrade ETBE. Complementation was abolished if the plasmid carried ethRABC only demonstrating that EthD is essential for the ETBE degradation system [].; PDB: 3BF4_B 2FTR_A.
Probab=86.66 E-value=4.2 Score=23.17 Aligned_cols=35 Identities=20% Similarity=0.141 Sum_probs=29.0
Q ss_pred ccCCCeeEEEEEEECCHhhHHhhhcChhHHH-HHHH
Q 034816 28 NLHQGFTHIFESTFESTEGVAEYVAHPAHVE-YANL 62 (82)
Q Consensus 28 ~~~~gy~~~l~~~F~s~e~l~~Y~~hP~H~~-~~~~ 62 (82)
.....||-+..+.|+|.+++.....+|..++ +.+-
T Consensus 52 ~~~~~~Dgi~e~~f~~~e~~~~~~~~p~~~~~l~~D 87 (95)
T PF07110_consen 52 GDPPDYDGIAELWFDSLEALQAAFADPEYQAALRAD 87 (95)
T ss_dssp TC--SEEEEEEEEECCHHHHHHHHCSHHCHHHHHHH
T ss_pred CCCCCEeEEEEEEECCHHHHHHHHCCHHHHHHHhcc
Confidence 3456899999999999999999999999998 5443
No 12
>PRK13314 heme-degrading monooxygenase IsdG; Provisional
Probab=85.52 E-value=4.1 Score=25.20 Aligned_cols=48 Identities=8% Similarity=0.007 Sum_probs=34.5
Q ss_pred hcccc-cceEEeceeCCccccCCCeeEEEEEEECCHhhHHhhhcChhHHHHHH
Q 034816 10 CGLEL-LAVKYKGKNVSIENLHQGFTHIFESTFESTEGVAEYVAHPAHVEYAN 61 (82)
Q Consensus 10 ~~L~~-~~~~~~G~~~~~e~~~~gy~~~l~~~F~s~e~l~~Y~~hP~H~~~~~ 61 (82)
+.+++ +++++ -++.. ..+.-.+...+..+|.++++++..+++|++..+
T Consensus 29 e~~pGF~~~~v-Lr~~~---~~~~~~y~v~T~Wes~eaF~aW~~S~aFr~AH~ 77 (107)
T PRK13314 29 ETMPGFLGLEV-LLTQN---TVDYDEVTISTRWNAKEDFQGWTKSPAFKAAHS 77 (107)
T ss_pred ccCCCcEEEEE-ecCCC---CCCCceEEEEEEECCHHHHHHHHcCHHHHHHHh
Confidence 34445 77776 54433 122336777899999999999999998888775
No 13
>COG2329 Uncharacterized enzyme involved in biosynthesis of extracellular polysaccharides [General function prediction only]
Probab=82.93 E-value=8.3 Score=23.45 Aligned_cols=34 Identities=15% Similarity=0.057 Sum_probs=29.5
Q ss_pred eeEEEEEEECCHhhHHhhhcChhHHHHHHHHhhh
Q 034816 33 FTHIFESTFESTEGVAEYVAHPAHVEYANLFLAN 66 (82)
Q Consensus 33 y~~~l~~~F~s~e~l~~Y~~hP~H~~~~~~~~~~ 66 (82)
-.++.++..+|.+|..+..+++.|++..+.-+..
T Consensus 51 ~~~~vvt~WeS~eaf~~W~~s~~~~~ah~~~~~~ 84 (105)
T COG2329 51 DEYVVVTRWESEEAFKAWRKSDEFKEAHKAGRSN 84 (105)
T ss_pred ceEEEEEEECCHHHHHhHhcCHHHHHHHHhcccc
Confidence 3499999999999999999999999988866554
No 14
>PRK13315 heme-degrading monooxygenase IsdG; Provisional
Probab=81.87 E-value=6.2 Score=24.42 Aligned_cols=46 Identities=15% Similarity=0.048 Sum_probs=33.5
Q ss_pred ccc-cceEEeceeCCccccCCCee-EEEEEEECCHhhHHhhhcChhHHHHHHH
Q 034816 12 LEL-LAVKYKGKNVSIENLHQGFT-HIFESTFESTEGVAEYVAHPAHVEYANL 62 (82)
Q Consensus 12 L~~-~~~~~~G~~~~~e~~~~gy~-~~l~~~F~s~e~l~~Y~~hP~H~~~~~~ 62 (82)
+++ +.+++ -++.. ..+++ +...+..+|.++.+++..+++|++..+.
T Consensus 31 ~pGFv~~~l-Lr~~~----~~~~~~~~v~T~Wes~eaF~aW~~S~aF~~AH~~ 78 (107)
T PRK13315 31 LEGFHKVEV-WLIDN----DDEYDEMYVNMWWETEEDFEAWRNSDAFKEAHKR 78 (107)
T ss_pred CCCeEEEEE-eccCC----CCCCceEEEEEEECCHHHHHHHhcCHHHHHHhhc
Confidence 444 77776 44432 23554 5568999999999999999999888864
No 15
>PRK13312 heme-degrading monooxygenase IsdG; Provisional
Probab=80.93 E-value=7.7 Score=24.08 Aligned_cols=48 Identities=8% Similarity=0.075 Sum_probs=36.0
Q ss_pred hhcccc-cceEEeceeCCccccCCCe-eEEEEEEECCHhhHHhhhcChhHHHHHH
Q 034816 9 CCGLEL-LAVKYKGKNVSIENLHQGF-THIFESTFESTEGVAEYVAHPAHVEYAN 61 (82)
Q Consensus 9 l~~L~~-~~~~~~G~~~~~e~~~~gy-~~~l~~~F~s~e~l~~Y~~hP~H~~~~~ 61 (82)
++.+++ +.+++ -++..+ .+| .+...+..+|.++.+++..++++.+..+
T Consensus 29 ie~~pGF~~~~v-Lr~~~~----~~~d~y~v~T~WeseeaFeaW~~SdaFr~AH~ 78 (107)
T PRK13312 29 IETLEGFDGMFV-TQTLEQ----EDFDEVKILTVWKSKQAFTDWLKSDVFKAAHK 78 (107)
T ss_pred cccCCCeEEEEE-eecCCC----CCceEEEEEEEECCHHHHHHHhcCHHHHHHHh
Confidence 344555 77777 555432 345 4788889999999999999998888775
No 16
>PRK13313 heme-degrading monooxygenase IsdI; Provisional
Probab=77.22 E-value=11 Score=23.39 Aligned_cols=49 Identities=10% Similarity=0.045 Sum_probs=36.0
Q ss_pred hhcccc-cceEEeceeCCccccCCCee-EEEEEEECCHhhHHhhhcChhHHHHHHH
Q 034816 9 CCGLEL-LAVKYKGKNVSIENLHQGFT-HIFESTFESTEGVAEYVAHPAHVEYANL 62 (82)
Q Consensus 9 l~~L~~-~~~~~~G~~~~~e~~~~gy~-~~l~~~F~s~e~l~~Y~~hP~H~~~~~~ 62 (82)
++.+++ +.+++ -++.. ..+|| +...+..+|.++.+++..++++++..+.
T Consensus 28 ie~~pGF~~~~v-Lr~~~----~~~~~~~~V~T~Wesee~F~~Wt~SdaF~~AH~~ 78 (108)
T PRK13313 28 IETIEGFQQMFV-TKTLN----TEDTDEVKILTIWESEDSFNNWLNSDVFKEAHKN 78 (108)
T ss_pred cccCCCeEEEEE-ecCCC----CCCceEEEEEEEECCHHHHHHHhcCHHHHHHHhc
Confidence 344555 77777 55432 34674 6778889999999999999988887763
No 17
>PF02410 Oligomerisation: Oligomerisation domain; InterPro: IPR004394 The gene iojap is a pattern-striping gene in maize, reflecting a chloroplast development defect in some cells. Maize has two RNA polymerases in plastids, but the plastid-encoded one, similar to bacterial RNA polymerases, is missing in iojap mutants. The role of iojap in chloroplast development, and the role of its bacterial orthologs modeled here, is unclear [, ]. This entry contains the bacterial protein YbeB (P0AAT6 from SWISSPROT), which has been shown to comigrate with the mature 50S ribosome subunit. Therefore it either represents a novel ribosome-associated protein or it is associated with a different oligomeric complex that comigrates with ribosomal particles [].; PDB: 2O5A_A 2ID1_B 3UPS_A.
Probab=71.54 E-value=19 Score=21.53 Aligned_cols=46 Identities=13% Similarity=0.029 Sum_probs=33.1
Q ss_pred CHHHHHHHhhcccccceEEeceeCCccccCCCeeEEEEEEECCHhhHHhh
Q 034816 1 MIAELIRSCCGLELLAVKYKGKNVSIENLHQGFTHIFESTFESTEGVAEY 50 (82)
Q Consensus 1 ~i~~~~~~l~~L~~~~~~~~G~~~~~e~~~~gy~~~l~~~F~s~e~l~~Y 50 (82)
|++++.+.+...++.++.+ .|++ +.+.-.|+.++++-.|.-.+.+=
T Consensus 1 ~~~~i~~~l~~~k~~dI~v--~dv~--~~~~~~dy~II~T~~S~rh~~ai 46 (100)
T PF02410_consen 1 MLEEIVEALEDKKAEDIVV--LDVR--EKSSWADYFIIATGRSERHVRAI 46 (100)
T ss_dssp -HHHHHHHHHHTT-EEEEE--EEGC--TTBSS-SEEEEEEESSHHHHHHH
T ss_pred CHHHHHHHHHHcCCCCeEE--EECC--CCCcccCEEEEEEcCCHHHHHHH
Confidence 7899999999999877655 5665 34455799999999997766554
No 18
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=70.56 E-value=18 Score=23.02 Aligned_cols=24 Identities=4% Similarity=0.117 Sum_probs=20.7
Q ss_pred cCCCeeEEEEEEECCHhhHHhhhc
Q 034816 29 LHQGFTHIFESTFESTEGVAEYVA 52 (82)
Q Consensus 29 ~~~gy~~~l~~~F~s~e~l~~Y~~ 52 (82)
.+++||+.+.+.+.|.++++.+..
T Consensus 102 ~tG~~dl~~~v~~~d~~~l~~~~~ 125 (153)
T PRK11179 102 TTGHYSIFIKVMCRSIDALQHVLI 125 (153)
T ss_pred cccCCCEEEEEEECCHHHHHHHHH
Confidence 456899999999999999998753
No 19
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=67.30 E-value=19 Score=23.26 Aligned_cols=24 Identities=4% Similarity=0.207 Sum_probs=20.5
Q ss_pred cCCCeeEEEEEEECCHhhHHhhhc
Q 034816 29 LHQGFTHIFESTFESTEGVAEYVA 52 (82)
Q Consensus 29 ~~~gy~~~l~~~F~s~e~l~~Y~~ 52 (82)
.+++||+.+.+.+.|.++++.+..
T Consensus 109 vtG~~d~~l~v~~~~~~~l~~~l~ 132 (164)
T PRK11169 109 VSGDFDYLLKTRVPDMSAYRKLLG 132 (164)
T ss_pred ecCCCCEEEEEEECCHHHHHHHHH
Confidence 456899999999999999988763
No 20
>PRK13316 heme-degrading monooxygenase IsdG; Provisional
Probab=64.35 E-value=34 Score=21.71 Aligned_cols=51 Identities=14% Similarity=0.158 Sum_probs=36.1
Q ss_pred Hhhcccc-cceEEeceeCCccccCCCe-eEEEEEEECCHhhHHhhhcChhHHHHHHH
Q 034816 8 SCCGLEL-LAVKYKGKNVSIENLHQGF-THIFESTFESTEGVAEYVAHPAHVEYANL 62 (82)
Q Consensus 8 ~l~~L~~-~~~~~~G~~~~~e~~~~gy-~~~l~~~F~s~e~l~~Y~~hP~H~~~~~~ 62 (82)
.++.+++ +++++ =.+.. ...+| .+...+.-+|.++.+++..+++|++..+.
T Consensus 34 ~ie~~pGFv~f~l-L~~~~---~~~~~~e~~V~T~WeSeeaF~aW~~SdaFr~AH~~ 86 (121)
T PRK13316 34 DIAEVEGFLGFEL-WHSKP---EDKDYEEVVVTSKWESEEAQRNWVKSDSFKKAHGR 86 (121)
T ss_pred chhcCCCceEEEE-eeccC---CCCCceEEEEEEEECCHHHHHHHhcCHHHHHHHhc
Confidence 3555555 77776 33321 23456 46778899999999999999988887763
No 21
>PHA00650 hypothetical protein
Probab=62.75 E-value=7.6 Score=22.32 Aligned_cols=28 Identities=18% Similarity=0.418 Sum_probs=23.7
Q ss_pred ECCHhhHHhhhcChhHHHHHHHHhhhhh
Q 034816 41 FESTEGVAEYVAHPAHVEYANLFLANLE 68 (82)
Q Consensus 41 F~s~e~l~~Y~~hP~H~~~~~~~~~~~~ 68 (82)
....||+++-..-|+|-+|..++...+.
T Consensus 6 intredldalagtpahgefldylrgsit 33 (82)
T PHA00650 6 INTREDLDALAGTPAHGEFLDYLRGSIT 33 (82)
T ss_pred cccHHHHHHhcCCCcchhHHHHHhhhcc
Confidence 4578999999999999999998876554
No 22
>PF13816 Dehydratase_hem: Haem-containing dehydratase; PDB: 3A18_C 3A17_F 3A15_C 3A16_D.
Probab=62.50 E-value=16 Score=26.67 Aligned_cols=59 Identities=19% Similarity=0.301 Sum_probs=37.1
Q ss_pred HHHHhhcccc-------cceEEeceeCCcc--c--cCCCeeEEEEEEECCHhhHHhhhc-ChhHHHHHHHHhhhh
Q 034816 5 LIRSCCGLEL-------LAVKYKGKNVSIE--N--LHQGFTHIFESTFESTEGVAEYVA-HPAHVEYANLFLANL 67 (82)
Q Consensus 5 ~~~~l~~L~~-------~~~~~~G~~~~~e--~--~~~gy~~~l~~~F~s~e~l~~Y~~-hP~H~~~~~~~~~~~ 67 (82)
+.+++..|.+ .+..+ -.+...+ . ..+.|.+ .-|.|.++|+.... ||.|+++-..+....
T Consensus 204 L~~gm~~L~d~~~e~Gc~s~R~-~~~~d~~~~~~~~~~t~~l---~yf~~L~~LE~Wa~~H~tHl~If~~fm~~~ 274 (310)
T PF13816_consen 204 LREGMDFLRDNGDETGCYSLRF-MRNLDPDSGNLDLDRTCGL---GYFRSLSSLERWARSHPTHLAIFRGFMKHY 274 (310)
T ss_dssp HHHHHHHHHHSHHHHTEEEEEE-EEEE-TT-S-E-EEEEEEE---EEES-HHHHHHHHHHSHHHHHHHHHHHHHG
T ss_pred HHHHHHHHHhCCcccceEEEEe-EeccCccccchhhhcccch---hhhhhHHHHHHHHhcCchHHHHHHHHHHHh
Confidence 4455555555 66776 6666543 1 2333333 46999999999997 999999987544433
No 23
>PF14114 DUF4286: Domain of unknown function (DUF4286)
Probab=56.57 E-value=41 Score=20.09 Aligned_cols=31 Identities=29% Similarity=0.320 Sum_probs=25.4
Q ss_pred CCCeeEEEEEEECCHhhHHhhhc-C-hhHHHHH
Q 034816 30 HQGFTHIFESTFESTEGVAEYVA-H-PAHVEYA 60 (82)
Q Consensus 30 ~~gy~~~l~~~F~s~e~l~~Y~~-h-P~H~~~~ 60 (82)
..|-++++.-.++|.++++.|.. | |..++-.
T Consensus 48 ~~g~tysvQy~~~s~e~l~~y~~~~~~~l~~e~ 80 (98)
T PF14114_consen 48 EGGKTYSVQYEVESMEDLERYYEEHAPKLREEG 80 (98)
T ss_pred CCCeEEEEEEEECCHHHHHHHHHHHHHHHHHHH
Confidence 34899999999999999999997 3 6655544
No 24
>PHA02085 hypothetical protein
Probab=54.74 E-value=17 Score=21.65 Aligned_cols=28 Identities=21% Similarity=0.190 Sum_probs=24.0
Q ss_pred EEEECCHhhHHhhhc-ChhHHHHHHHHhh
Q 034816 38 ESTFESTEGVAEYVA-HPAHVEYANLFLA 65 (82)
Q Consensus 38 ~~~F~s~e~l~~Y~~-hP~H~~~~~~~~~ 65 (82)
.++|+|++++..|.. ||.-+.+.+.+.-
T Consensus 2 kIrFKS~e~R~~Fa~~~~~N~~IAe~mGm 30 (87)
T PHA02085 2 KIRFKSEEHKAMFARRHDCNQWIADKMGT 30 (87)
T ss_pred ceeecCHhHHHHHHhhchhhHHHHHHhcC
Confidence 368999999999996 8999999887753
No 25
>PRK12866 YciI-like protein; Reviewed
Probab=42.90 E-value=73 Score=19.00 Aligned_cols=49 Identities=10% Similarity=0.030 Sum_probs=31.1
Q ss_pred HHHHHhhcccc--cceEEeceeCCccccCCCeeEEEEEEECCHhhHHhhhc-ChhHHH
Q 034816 4 ELIRSCCGLEL--LAVKYKGKNVSIENLHQGFTHIFESTFESTEGVAEYVA-HPAHVE 58 (82)
Q Consensus 4 ~~~~~l~~L~~--~~~~~~G~~~~~e~~~~gy~~~l~~~F~s~e~l~~Y~~-hP~H~~ 58 (82)
+.++-|+.+.. +-+.. |+-..+ .. | -.+++.++|.++.+.... +|-+++
T Consensus 23 ~H~~~L~~~~~~G~ll~a-Gp~~~~--~~-G--~~ii~~a~s~~e~~~~l~~DPf~~~ 74 (97)
T PRK12866 23 EHLALAQAATERGELLLA-GALADP--AD-G--AVLVFEGDSPAAAEAFARADPYVRN 74 (97)
T ss_pred HHHHHHHHHHhCCEEEEe-CCCCCC--CC-c--EEEEEEeCCHHHHHHHHHcCChhhc
Confidence 34455555554 44444 664432 11 2 456779999999999996 797764
No 26
>PRK12864 YciI-like protein; Reviewed
Probab=41.77 E-value=72 Score=18.60 Aligned_cols=47 Identities=13% Similarity=0.099 Sum_probs=29.5
Q ss_pred HHHHhhcccc--cceEEeceeCCccccCCCeeEEEEEEECCHhhHHhhhc-ChhHHH
Q 034816 5 LIRSCCGLEL--LAVKYKGKNVSIENLHQGFTHIFESTFESTEGVAEYVA-HPAHVE 58 (82)
Q Consensus 5 ~~~~l~~L~~--~~~~~~G~~~~~e~~~~gy~~~l~~~F~s~e~l~~Y~~-hP~H~~ 58 (82)
.++-++.|.. .-+.. |+-..+ + | ...+..++|.++.+.+.. +|..++
T Consensus 25 H~~~l~~~~~~G~~~~~-Gp~~~~---~-g--~~~i~~a~s~eea~~~~~~DPy~~a 74 (89)
T PRK12864 25 HLDRLAKLKEQGILITL-GPTKDL---T-Y--VFGIFEAEDEETVRQLIEADPYWQN 74 (89)
T ss_pred HHHHHHHHHhCCeEEEe-cCCCCC---C-C--EEEEEEeCCHHHHHHHHHcCCchhc
Confidence 3444555544 34455 755432 2 2 234779999999999986 798764
No 27
>PHA02087 hypothetical protein
Probab=37.07 E-value=64 Score=18.75 Aligned_cols=25 Identities=20% Similarity=0.122 Sum_probs=18.6
Q ss_pred EEEEEECCHhhHHhhhcChhHHHHH
Q 034816 36 IFESTFESTEGVAEYVAHPAHVEYA 60 (82)
Q Consensus 36 ~l~~~F~s~e~l~~Y~~hP~H~~~~ 60 (82)
+..+.|+|.|.+++|..+.-.-+=-
T Consensus 3 i~rvkfks~ehrk~fa~s~~yn~~f 27 (83)
T PHA02087 3 IVRVKFKSPEHRKAFAESEWYNEEF 27 (83)
T ss_pred eEEEEcCCHHHHHHHHhhhHHHHHH
Confidence 3467899999999999875444333
No 28
>PRK06524 biotin carboxylase-like protein; Validated
Probab=36.55 E-value=23 Score=27.54 Aligned_cols=27 Identities=26% Similarity=0.501 Sum_probs=22.9
Q ss_pred EEECCHhhHHhhhc-ChhHHHHHHHHhh
Q 034816 39 STFESTEGVAEYVA-HPAHVEYANLFLA 65 (82)
Q Consensus 39 ~~F~s~e~l~~Y~~-hP~H~~~~~~~~~ 65 (82)
-+|+|.||...|+- ||.-+++++.-.|
T Consensus 78 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 105 (493)
T PRK06524 78 RDFDGMEDVCNYLLRHPETLEFIKRRGP 105 (493)
T ss_pred hhhhhhHHHhhhhhcCHHHHHHHHhhCC
Confidence 47999999999996 9999999886544
No 29
>PF07978 NIPSNAP: NIPSNAP ; InterPro: IPR012577 Members of this family include many hypothetical proteins. It also includes members of the NIPSNAP family, which have putative roles in vesicular transport []. This domain is often found in duplicate.; PDB: 1VQY_D 2AP6_H.
Probab=35.18 E-value=84 Score=17.91 Aligned_cols=35 Identities=9% Similarity=-0.027 Sum_probs=25.1
Q ss_pred CeeEEEEEEECCHhhHHhhhc----ChhHHHHHHHHhhh
Q 034816 32 GFTHIFESTFESTEGVAEYVA----HPAHVEYANLFLAN 66 (82)
Q Consensus 32 gy~~~l~~~F~s~e~l~~Y~~----hP~H~~~~~~~~~~ 66 (82)
.-++..+-.|+|.++++.... ||..++......+.
T Consensus 46 ~~~~~~l~~y~~~~~r~~~~~a~~~d~~w~~~~~~~~~~ 84 (102)
T PF07978_consen 46 LNQVVHLWSYDDLAAREEAREALYADPEWKAYVAEARPL 84 (102)
T ss_dssp SSEEEEEEEES-HHHHHHHHHHHHH-HHHHHHHHHCCTT
T ss_pred CceEEEEEEcCCHHHHHHHHHHHHcCchHHHHHHhcccc
Confidence 346788889999999887765 88887777766554
No 30
>PRK12865 YciI-like protein; Reviewed
Probab=34.03 E-value=1e+02 Score=18.12 Aligned_cols=50 Identities=10% Similarity=-0.019 Sum_probs=30.8
Q ss_pred HHHHhhcccc--cceEEeceeCCccccCCCee-EEEEEEECCHhhHHhhhc-ChhHHH
Q 034816 5 LIRSCCGLEL--LAVKYKGKNVSIENLHQGFT-HIFESTFESTEGVAEYVA-HPAHVE 58 (82)
Q Consensus 5 ~~~~l~~L~~--~~~~~~G~~~~~e~~~~gy~-~~l~~~F~s~e~l~~Y~~-hP~H~~ 58 (82)
.++-+..+.. .-+.. |+-..++ ..+. -.++...+|.++.+.... +|.+++
T Consensus 24 H~~~l~~~~~~G~l~~~-Gp~~~~~---g~~~G~~~i~~a~s~e~a~~~~~~DP~~~~ 77 (97)
T PRK12865 24 HLEYLNKLNAEGTLKIA-GPFLDDD---GKPCGSLVIVKAETKEAAKALADADPYAKA 77 (97)
T ss_pred HHHHHHHHHhCCeEEEe-cCCcCCC---CCceeEEEEEEcCCHHHHHHHHHcCCchhc
Confidence 3444444444 33334 6665432 2233 355679999999999996 798875
No 31
>PF07626 PSD3: Protein of unknown function (DUF1587); InterPro: IPR013036 A region of similarity shared by several Rhodopirellula baltica cytochrome-like proteins that are predicted to be secreted. These proteins also contain IPR011478 from INTERPRO, IPR013039 from INTERPRO, IPR013042 from INTERPRO and IPR013043 from INTERPRO.
Probab=33.80 E-value=38 Score=19.02 Aligned_cols=48 Identities=17% Similarity=0.113 Sum_probs=32.4
Q ss_pred HHHHHhhcccccceEEeceeCCccccCCCeeEEEEEEECCHhhHHhhhc
Q 034816 4 ELIRSCCGLELLAVKYKGKNVSIENLHQGFTHIFESTFESTEGVAEYVA 52 (82)
Q Consensus 4 ~~~~~l~~L~~~~~~~~G~~~~~e~~~~gy~~~l~~~F~s~e~l~~Y~~ 52 (82)
|.-..++.|-++.+.. +..+.++....|||-.-..-+=|...++.|..
T Consensus 7 EY~nTvrDLlg~~~~~-~~~lP~D~~~~GFdn~~~~l~~s~~~~e~Y~~ 54 (67)
T PF07626_consen 7 EYQNTVRDLLGVDVDP-ADGLPADPGSEGFDNNGEALSVSPLLLEQYLE 54 (67)
T ss_pred HHHHHHHHHhCCCCch-hccCCCCCCcCCCCCcccccccCHHHHHHHHH
Confidence 4445566666655555 44454456778998876666778888888875
No 32
>PRK11370 YciI-like protein; Reviewed
Probab=33.19 E-value=1.1e+02 Score=18.08 Aligned_cols=23 Identities=22% Similarity=0.307 Sum_probs=17.9
Q ss_pred EEEEEECCHhhHHhhhc-ChhHHH
Q 034816 36 IFESTFESTEGVAEYVA-HPAHVE 58 (82)
Q Consensus 36 ~l~~~F~s~e~l~~Y~~-hP~H~~ 58 (82)
.+++.|+|.++.+.... +|-+++
T Consensus 60 ~ii~ea~s~~~a~~~~~~DPy~~a 83 (99)
T PRK11370 60 TVIAEFESLEAAQAWADADPYVAA 83 (99)
T ss_pred EEEEEECCHHHHHHHHHCCchhhc
Confidence 67779999999888876 576653
No 33
>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=29.45 E-value=82 Score=17.56 Aligned_cols=25 Identities=24% Similarity=0.216 Sum_probs=19.0
Q ss_pred HHHHHHhhhhh----ceEEEEeecceeeC
Q 034816 58 EYANLFLANLE----KVLVIDYKPTTVRV 82 (82)
Q Consensus 58 ~~~~~~~~~~~----~~~v~D~~~~~~~~ 82 (82)
++++.+.|.+. ++..+|++.+.++|
T Consensus 3 ~~l~~IrP~L~~dGGdv~lv~v~~~~V~V 31 (68)
T PF01106_consen 3 EVLEEIRPYLQSDGGDVELVDVDDGVVYV 31 (68)
T ss_dssp HHHHHCHHHHHHTTEEEEEEEEETTEEEE
T ss_pred HHHHHhChHHHhcCCcEEEEEecCCEEEE
Confidence 45556888885 48889999888764
No 34
>PF11813 DUF3334: Protein of unknown function (DUF3334); InterPro: IPR024513 This family of proteins are functionally uncharacterised. This family is only found in bacteria. Proteins in this family are typically between 227 to 238 amino acids in length.
Probab=28.31 E-value=59 Score=22.81 Aligned_cols=24 Identities=17% Similarity=0.409 Sum_probs=21.8
Q ss_pred cCCCeeEEEEEEECCHhhHHhhhc
Q 034816 29 LHQGFTHIFESTFESTEGVAEYVA 52 (82)
Q Consensus 29 ~~~gy~~~l~~~F~s~e~l~~Y~~ 52 (82)
-++||+--.++-|...+|++.|..
T Consensus 56 FDGGFsGLVviNFsa~AAmEiY~~ 79 (229)
T PF11813_consen 56 FDGGFSGLVVINFSAQAAMEIYRS 79 (229)
T ss_pred ecCCcceEEEEecChHHHHHHHHH
Confidence 467999999999999999999975
No 35
>COG5256 TEF1 Translation elongation factor EF-1alpha (GTPase) [Translation, ribosomal structure and biogenesis]
Probab=24.87 E-value=1.2e+02 Score=23.45 Aligned_cols=74 Identities=16% Similarity=0.214 Sum_probs=44.9
Q ss_pred HHHHhhcccc------cceEEeceeCCccccCCCeeEEE-EEEECCHhhHHhhhcChhHHHHHH-HHhhhhh---ceEEE
Q 034816 5 LIRSCCGLEL------LAVKYKGKNVSIENLHQGFTHIF-ESTFESTEGVAEYVAHPAHVEYAN-LFLANLE---KVLVI 73 (82)
Q Consensus 5 ~~~~l~~L~~------~~~~~~G~~~~~e~~~~gy~~~l-~~~F~s~e~l~~Y~~hP~H~~~~~-~~~~~~~---~~~v~ 73 (82)
.++.++.+.. -+|.| =.+...|.|.+|.|.-. .+.|++..-.=.-...|.|+.|++ .+..... .++|+
T Consensus 38 tmeK~~~ea~~~gK~sf~faw-vlD~tkeERerGvTi~~~~~~fet~k~~~tIiDaPGHrdFvknmItGasqAD~aVLVV 116 (428)
T COG5256 38 TMEKLEKEAKELGKESFKFAW-VLDKTKEERERGVTIDVAHSKFETDKYNFTIIDAPGHRDFVKNMITGASQADVAVLVV 116 (428)
T ss_pred HHHHHHHHHHhcCCCceEEEE-EecCChhHHhcceEEEEEEEEeecCCceEEEeeCCchHHHHHHhhcchhhccEEEEEE
Confidence 4455555532 36777 66665677888876533 456766543111224699999997 4443332 38888
Q ss_pred Eeecce
Q 034816 74 DYKPTT 79 (82)
Q Consensus 74 D~~~~~ 79 (82)
|-..|.
T Consensus 117 ~a~~~e 122 (428)
T COG5256 117 DARDGE 122 (428)
T ss_pred ECCCCc
Confidence 876664
No 36
>PRK11118 putative monooxygenase; Provisional
Probab=24.54 E-value=1.2e+02 Score=18.77 Aligned_cols=19 Identities=21% Similarity=0.361 Sum_probs=15.1
Q ss_pred EEEECCHhhHHhhhcChhHHH
Q 034816 38 ESTFESTEGVAEYVAHPAHVE 58 (82)
Q Consensus 38 ~~~F~s~e~l~~Y~~hP~H~~ 58 (82)
+=-|+|+++.++|.. -|.+
T Consensus 53 iYlF~~e~~a~aYl~--mH~a 71 (100)
T PRK11118 53 IYLFEDEASAEAYLE--MHTA 71 (100)
T ss_pred EEEECCHHHHHHHHH--HHHH
Confidence 446999999999998 3554
No 37
>PF09128 RGS-like: Regulator of G protein signalling-like domain; InterPro: IPR015212 This entry represents a domain consisting of twelve helices that fold into a compact structure that contains the overall structural scaffold observed in other regulator of G protein signalling (RGS) proteins and three additional helical elements that pack closely to it. Helices 1-9 comprise the RGS fold, in which helices 4-7 form a classic antiparallel bundle adjacent to the other helices. Like other RGS structures, helices 7 and 8 span the length of the folded domain and form essentially one continuous helix with a kink in the middle. Helices 10-12 form an apparently stable C-terminal extension of the structural domain, and although other RGS proteins lack this structure, these elements are intimately associated with the rest of the structural framework by hydrophobic interactions. This domain binds to active G-alpha proteins, promoting GTP hydrolysis by the alpha subunit of heterotrimeric G proteins, thereby inactivating the G protein and rapidly switching off G protein-coupled receptor signalling pathways []. ; GO: 0005089 Rho guanyl-nucleotide exchange factor activity, 0005737 cytoplasm; PDB: 3CX6_B 3CX8_B 3CX7_B 1HTJ_F 1SHZ_C 3AB3_D 1IAP_A.
Probab=24.27 E-value=34 Score=23.27 Aligned_cols=22 Identities=36% Similarity=0.516 Sum_probs=13.4
Q ss_pred ECCHhhHHhhhcChhHHHHH-HHHhh
Q 034816 41 FESTEGVAEYVAHPAHVEYA-NLFLA 65 (82)
Q Consensus 41 F~s~e~l~~Y~~hP~H~~~~-~~~~~ 65 (82)
|.|.+.| ..||+|.++- .++..
T Consensus 5 F~sl~~L---k~rPaHlaVFl~yv~s 27 (188)
T PF09128_consen 5 FQSLELL---KSRPAHLAVFLNYVLS 27 (188)
T ss_dssp HHSHHHH---HC-HHHHHHHHHHHHH
T ss_pred ccCHHHH---hcCcHHHHHHHHHHHh
Confidence 5555555 6799999864 45443
No 38
>PF14799 FAM195: FAM195 family
Probab=24.03 E-value=52 Score=20.03 Aligned_cols=18 Identities=28% Similarity=0.480 Sum_probs=15.4
Q ss_pred ChhHHHHHHHHhhhhhce
Q 034816 53 HPAHVEYANLFLANLEKV 70 (82)
Q Consensus 53 hP~H~~~~~~~~~~~~~~ 70 (82)
.|.|.+++.+|-..|..+
T Consensus 31 tpqHEElVrfI~esW~~V 48 (99)
T PF14799_consen 31 TPQHEELVRFIYESWNKV 48 (99)
T ss_pred chhHHHHHHHHHHHHHHH
Confidence 599999999999888753
No 39
>PF11695 DUF3291: Domain of unknown function (DUF3291); InterPro: IPR021708 This bacterial family of proteins has no known function.
Probab=22.46 E-value=1.6e+02 Score=19.01 Aligned_cols=35 Identities=23% Similarity=0.158 Sum_probs=28.4
Q ss_pred eEEEEEEECCHhhHHhhhcChhHHHHHHHHhhhhh
Q 034816 34 THIFESTFESTEGVAEYVAHPAHVEYANLFLANLE 68 (82)
Q Consensus 34 ~~~l~~~F~s~e~l~~Y~~hP~H~~~~~~~~~~~~ 68 (82)
...=.+.-+|.++|..|.-.-.|.++.+..+.-.+
T Consensus 60 ~~~nlSvWes~eaL~~Fvy~~~H~~~l~rrreWF~ 94 (140)
T PF11695_consen 60 VIVNLSVWESVEALRAFVYRGPHREALRRRREWFE 94 (140)
T ss_pred eEEEEeeeCCHHHHHHHHhcChHHHHHHHHHHHhh
Confidence 46677899999999999977669999987665443
No 40
>TIGR00125 cyt_tran_rel cytidyltransferase-related domain. Protein families that contain at least one copy of this domain include citrate lyase ligase, pantoate-beta-alanine ligase, glycerol-3-phosphate cytidyltransferase, ADP-heptose synthase, phosphocholine cytidylyltransferase, lipopolysaccharide core biosynthesis protein KdtB, the bifunctional protein NadR, and a number whose function is unknown. Many of these proteins are known to use CTP or ATP and release pyrophosphate.
Probab=21.02 E-value=1.4e+02 Score=15.49 Aligned_cols=17 Identities=12% Similarity=0.212 Sum_probs=14.3
Q ss_pred ChhHHHHHHHHhhhhhc
Q 034816 53 HPAHVEYANLFLANLEK 69 (82)
Q Consensus 53 hP~H~~~~~~~~~~~~~ 69 (82)
|.-|+.+.+........
T Consensus 12 H~GH~~~l~~a~~~~~~ 28 (66)
T TIGR00125 12 HLGHLDLLERAKELFDE 28 (66)
T ss_pred CHHHHHHHHHHHHhCCE
Confidence 89999999988777763
Done!