Table 3.
Genes associated with HMM- or IT-predicted Fur boxes
| Prediction | Validation | Fur box | Score (bits) | Distance to ATG (bp) | Gene or Gene cluster | Annotated function (TIGR) | TIGR# | ||
|---|---|---|---|---|---|---|---|---|---|
| METHOD | FURTA | EMSA | ITVA | ||||||
| Iron acquisition | |||||||||
| IT | T | S | R | TGTAATAAGACTCATTCGT | 11.7 | 21 | feoP/feoABC | OprB family porin -Feo FeII uptake transporter | AFE0580 |
| HMM | GTAATAAGACTCATTCGT | 10.56 | 32 | ||||||
| HMM | CTAATATTAGTCATTAGT | 9.69 | 238 | ||||||
| HMM | T | S(36) | TAAACGGGAATCATTCTC | 10.73 | 28 | mntH | Metal ion transporter, NRAMP family | AFE2920 | |
| IT | ATAAACGGGAATCATTCTC | 11.3 | 46 | ||||||
| IT | T | CAATATCGTTATCATCCTT | 6.4 | 35 | tdrA | TonB-dependent receptor | AFE0174 | ||
| IT | TACTATCAGATTTATAATT | 6.2 | 521 | tdrB | TonB-dependent receptor | AFE0173 | |||
| HMM | T | S | R | GATATTATAGTTATTCTT | 11.33 | 161 | gloA | Conserved globin domain protein | AFE1602 |
| IT | TGATATTATAGTTATTCTT | 9.7 | 161 | ||||||
| IT | T | GATATCCAGAATTTTTATC | 8.7 | 55 | abcP1 | ABC iron(lll) dicitrate transport system permease, FecCD family | AFE1594 | ||
| HMM | AAAATGACAATTTTATGA | 9.38 | 109 | exbBDtonB2 | TonB Biopolymer transport system | AFE0827 | |||
| IT | T | TAAATTCATTCCCATTTTC | 13.0 | 1 | tonB4 | TonB family protein | AFE2270 | ||
| IT | T | GAAAATAAAACTTGTGTTC | 5.6 | 113 | tonB4 | TonB family protein | AFE1114 | ||
| IT | TGAAATGAGAATCAAATCT | 9.7 | 20 | exbD4 | Bipolymer transport ExbD protein | AFE0106 | |||
| Iron utilization | |||||||||
| HMM | T | S | AGAATTGTTAATTTGTCT | 11.95 | 255 | hyp/fdx1 | Ferredoxin (4Fe-4S) | AFE1138 | |
| IT | CACAAAGAGAATCAATATC | 10.5 | 304 | fdx2 | Ferredoxin (Fe-S) | AFE2230 | |||
| IT | GAGAATCATATGCAATTTC | 13.0 | −10 | nuoI | NADH-quinone oxidoreductase, I subunit-2(4Fe-4S) | AFE0482 | |||
| IT | AAAAACAATAATATATATT | 7.4 | 273 | noxA | Pyridine nucleotide-disulfide oxidoreductase (Fe-S) | AFE1282 | |||
| IT | T | CGAAACCAGATCCATTTCC | 5.1 | 583 | hemN | O2-indep coproporphyrinogen III DH (4Fe-4S) | AFE2891 | ||
| HMM | T | S | ATATATGTAATTATTCTT | 12.5 | 74 | hppH | MBH NiFe hydrogenase high potential iron-sulfur protein (4Fe-4S) | AFE2333 | |
| T | dsrK | Hup reductase (Fe-S) | AFE3048 | ||||||
| IT | T | GATAACGCGTTTCGTCTTT | 5.3 | 434 | hdrC | Heterosulfide reductase subunit (4Fe-4S) | AFE0551 | ||
| IT | ATCATTGGATAACAATTATC | 10.1 | 26 | nifV | Fe-S cluster assembly accessory protein (Fe-S) | AFE1553 | |||
| IT | TGGAAGGATTGGCATATTC | 5.1 | −20 | nifS | Nitrogenase cofactor synthesis protein | AFE1547 | |||
| IT | GGAAATCGCATTTATCATC | 5.6 | 95 | fdx4 | Ferredoxin (2Fe-2S) | AFE1543 | |||
| IT | GAAAATGGTATTCTTCTGC | 7.5 | −87 | nifX | Nitrogenase cofactor processing protein (Fe-Mo) | AFE1569 | |||
| IT | GAAAAAGCGTTTAATTTTT | 6.7 | 21 | hyp/hyp/fdx7 | Hypothetical in nitrogenase gene cluster | AFE1570 | |||
| Predicted transporters ABC transporters | |||||||||
| HMM | ATAATAATAGCTAGTAAT | 9.53 | −19 | fatC | ABC transporter, permease protein, putative | AFE0990 | |||
| HMM | ATAATAATAGCTAGTAAT | 9.53 | −19 | yvsF | ABC transporter, permease protein | AFE0989 | |||
| IT | TATAATAAGTGTCATTATT | 14.0 | 301 | hyp/cvaA | Hypothetical protein | AFE0932 | |||
| HMM | ATAATAAGTGTCATTATT | 9.98 | 302 | AFE0932 | |||||
| IT | TAAAATGACAATCGATACT | 10.6 | 410 | cvaA | CvaA colicin V exporter MFP family | AFE0931 AFE0931 | |||
| IT | T | TGTTTGTATACTTATTATC | 5.3 | 573 | abcA | ABC transport protein, ATP-binding subunit | AFE0803.1 | ||
| IT | AGTAATGGTAACTGTTCTG | 9.3 | 266 | nikB | Di/oligopeptide/nickel permease | AFE0119 | |||
| HMM | T | S | TACTGGTAACTATTTTTG | 10.59 | 40 | abcS4 | ABC transporter, periplasmic SO4/MoFeIII-binding protein | AFE1586 | |
| Cation diffusion facilitator transporters | |||||||||
| HMM | T | TACTGGTAACTATTTTTG | 10.59 | 40 | cdf1 | CDF family protein* | AFE1588 | ||
| RND efflux transporter | |||||||||
| HMM | TACTGGTAACTATTTTTG | 10.59 | 40 | rnd1 | Heavy metal RND efflux outer membrane protein | AFE1587 | |||
| HMM | T | GAATTGTTAATTTGTCTA | 11.95 | 445 | hyp/omf/mfp/rnd2 | Conserved hypothetical protein TIGR00481 | AFE1140 | ||
| IT | TATAGCGGTATTGCACTTG | 6.5 | 247 | omf/mfp/rnd3 | Heavy metal RND efflux outer membrane protein | AFE1057 | |||
| MFS Transporters | |||||||||
| HMM | GAATGAATAAGTTTTATT | 9.05 | 276 | msfB | Drug resistance transporter, EmrB-QacA family | AFE2984 | |||
| P-type ATPase | |||||||||
| IT | GCAAATGATAAGCATCCTT | 13.1 | 144 | copA | Copper-translocating P-type ATPase | AFE1073 | |||
| HMM | CAAATGATAAGCATCCTT | 9.75 | 143 | AFE0329 | |||||
| HMM | T | S | R | GAAACGATAATTTTATTG | 9.89 | 244 | copB | Copper-translocating P-type ATPase | AFE2222 |
| HMM | ATGATGGTAAATATTCAG | 9.54 | 391 | hat1 | Plasma-membrane proton-efflux P-type ATPase | ||||
| Transcriptional regulators | |||||||||
| HMM | T | ATAAGGGTGAGCATACGG | 10.64 | 272 | iscR | Fe-S cluster assembly | AFE2368 | ||
| HMM | T | ATAACTATAACTAGTTTA | 9.5 | 50 | irr | Transcriptional regulator Fur family | AFE1137 | ||
| HMM | S | R | AAAATGACAATTTTATGA | 9.38 | 109 | phoB | Transcriptional regulator PhoB family | AFE0827 | |
| HMM | TTTTTGGTAATTATAAGC | 9.04 | 31 | arsR | Transcriptional regulator ArsR family | AFE0734 | |||
| HMM | AAAATAGTAAGTATATTT | 10.93 | 56 | marR | Transcriptional regulator MarR family | AFE0507 | |||
| HMM | TCAAAAGTAATTATTTAG | 9.68 | 148 | ntrC | Sigma-54 dependent transcriptional regulator NtrC family | AFE0505 | |||
FURTA, Fur titration assay (T, positive titration); EMSA, Electrophoretic mobility shift assay (S, positive shift); IVTA, in vitro transcription assay (R, transcriptional repression); IT, Information Theory; HMM, Hidden Markov Models.