Table 3. Genomic structure of phage KLPN1.
| KLPN1 genome | Start | Stop | Ribosome-binding site | Start | Strand | Predicted product* | Representative ORF in phage (% amino acid identity) | |||
|---|---|---|---|---|---|---|---|---|---|---|
| KP36 | F20 | 1513 | phiKO2 | |||||||
| KLPN1_01 | 516 | 1079 | AAGGAG | ATG | + | Unknown | – | – | – | – |
| KLPN1_02 | 1069 | 1290 | AGGAGG | ATG | + | HP | – | – | – | – |
| KLPN1_03 | 1395 | 1547 | GAGGAA | ATG | + | HP pSf1_0028 (Shigella phage pSf-1) | – | – | 39 (94) | – |
| KLPN1_04 | 1752 | 1997 | GAAGAtAG | TTG | + | HP (Escherichia phage e4/1c) | – | – | 38 (98.36) | – |
| KLPN1_05 | 2186 | 2416 | AGGAGGA | ATG | + | HP KP36_04 KP36 | 04 (74.65) | 76 (63.38) | 37 (92.11) | – |
| KLPN1_06 | 2487 | 2699 | AGAGGA | ATG | + | HP KP36_06 KP36 | 06 (82.86) | – | 36 (90) | – |
| KLPN1_07 | 2710 | 3030 | AAGGAGAA | ATG | + | HP KP36_11 KP36 | 11 (78.3) | 70 (65.09) | 35 (82.08) | – |
| KLPN1_08 | 3100 | 3471 | GGAGA | ATG | + | HP (Enterobacteria phage F20) | – | 69 (83.74) | – | – |
| KLPN1_09 | 3481 | 3783 | GAGGtGGccG | ATG | + | HP KP36_15 KP36 | 15 (91) | 68 (56) | 33 (85) | – |
| KLPN1_10 | 3783 | 4028 | AAcGGGA | ATG | + | HP KP36_16 KP36 | 16 (97.53) | 67 (83.95) | 32 (92.59) | – |
| KLPN1_11 | 4025 | 4210 | GAGGtAAAAG | ATG | + | HP KP36_17 KP36 (signal peptide) | 17 (85.25) | 66 (78.69) | 31 (58.18) | – |
| KLPN1_12 | 4291 | 4500 | AAtcAGGAG | ATG | + | HP (Enterobacteria phage F20) | – | 65 (73.91) | – | – |
| KLPN1_13 | 4500 | 4934 | GAGGAGA | ATG | + | HP (Enterobacteria phage F20) | 19 (33.93) | 64 (32.54) | 29 (35.58) | – |
| KLPN1_14 | 5004 | 5750 | AAGAGGAA | ATG | + | HP (Enterobacteria phage F20) | 20 (50.94) | 63 (54.55) | 28 (34.84) | – |
| KLPN1_15 | 5827 | 6099 | AGGAG | ATG | + | HP KP36_22 KP36 | 22 (65.56) | 61 (66.67) | – | – |
| KLPN1_16 | 6096 | 6668 | AAGGtGAtcGAA | ATG | + | HP KP36_23 KP36 | 23 (96.32) | 60 (78.53) | 25 (76.44) | – |
| KLPN1_17 | 6738 | 6974 | AAGGAG | ATG | + | HP KP36_24 KP36 | 24 (92.31) | 59a (86.3) | 24 (96.15) | – |
| KLPN1_18 | 6962 | 7195 | GGAGAAGG | ATG | + | HP KP36_25 KP36 | 25 (100) | 59 (87.01) | 23 (95.45) | – |
| KLPN1_19 | 7324 | 7518 | AAAGGG | ATG | + | HP KP36_26 KP36 | 26 (96.67) | 57 (93.65) | 22 (96.88) | – |
| KLPN1_20 | 7512 | 7718 | AAGGGAA | ATG | + | HP KP36_27 KP36 (signal peptide) | 27 (96.2) | 56 (64.81) | 21 (100) | – |
| KLPN1_21 | 7773 | 8378 | GAAGcGGcGtAA | ATG | + | terminase small subunit KP36 | 28(92.53) | 55 (91.95) | 20 (90.8) | – |
| KLPN1_22 | 8388 | 9992 | AAGGGccGA | ATG | + | terminase large subunit KP36 (terminase-like family: PF03237) | 29 (99.25) | 54 (98.13) | 19 (99.44) | – |
| KLPN1_23 | 10038 | 11348 | AAAcAAGGttGA | ATG | + | portal protein KP36 (phage portal protein, SPP1 Gp6-like: PF05133) | 30 (98.62) | 53 (91.78) | 18 (99.31) | – |
| KLPN1_24 | 11335 | 12102 | GGAGGcGGA | ATG | + | capsid morphogenesis protein KP36 (phage head morphogenesis domain: IPR006528) | 31 (96.44) | 52 (90.12) | 17 (95.22) | – |
| KLPN1_25 | 12104 | 12589 | GAGGttAG | ATG | + | HP gp40 (Escherichia phage phiEB49) HNH endonuclease (HNH endonuclease: PF13392) | – | – | – | – |
| KLPN1_26 | 12586 | 13716 | GGAGA | ATG | + | capsid protein KP36 | 32 (99.47) | 51 (93.09) | 16 (99.47) | – |
| KLPN1_27 | 13768 | 14286 | AGGAGA | ATG | + | HP KP36_33 KP36 | 33 (96.2) | 50 (50.87) | 15 (96.84) | – |
| KLPN1_28 | 14400 | 15359 | AGGAG | ATG | + | major capsid protein KP36_34 KP36 | 34 (98.75) | 49 (94.36) | 14 (98.43) | – |
| KLPN1_29 | 15451 | 15756 | GGAGcA | ATG | + | HP KP36_35 KP36 | 35 (100) | 48 (86.15) | 13 (98.77) | – |
| KLPN1_30 | 15753 | 16226 | AAAAGcGcGGA | ATG | + | HP KP36_36 KP36 | 36 (100) | 47 (92.75) | 12 (97.83) | – |
| KLPN1_31 | 16232 | 16609 | GGtAGGtGA | ATG | + | HP KP36_37 KP36 | 37 (99.2) | 46 (94.4) | 11 (98.4) | – |
| KLPN1_32 | 16602 | 17039 | AGGGtGGcGA | ATG | + | HP KP36_38 KP36 | 38 (100) | 45 (92.41) | 10 (99.05) | – |
| KLPN1_33 | 17029 | 17463 | GAGcGAGG | ATG | + | HP (Enterobacteria phage F20) Tail protein (phage tail protein: PF13554) | 39 (76.39) | 44 (88.19) | 09 (74.19) | – |
| KLPN1_34 | 17450 | 18136 | GGAGGcGA | ATG | + | HP (Enterobacteria phage F20) Tail protein (phage tail protein: PF08813) | – | 43/42 (68.26/42.04) | 08 (43.36) | – |
| KLPN1_35 | 18189 | 18845 | AGGAG | ATG | + | HP (Enterobacteria phage F20) Tail protein (phage tail protein: PF08813) | 40 (91.67) | 42 (82.87) | 08 (96.33) | – |
| KLPN1_36 | 18922 | 19248 | AGGAG | ATG | + | Tape measure chaperone protein (domain of unknown function DUF1789: PF08748) | 41 (98.15) | 41 (57.01) | 07 (98.15) | – |
| KLPN1_36.1 | 19239 | 19562 | – | – | + | Tape measure chaperone protein (phage-related hypothetical protein DUF1799: PF08809) | – | 40 (92.73) | 06 (96.36) | – |
| KLPN1_38 | 19620 | 22565 | GAtAAAGtAG | TTG | + | tail length tape-measure protein KP36 (λ phage tail tape-measure protein: PF09718) | 43 (91.63) | 39 (80.22/68.85) | 05 (91.04) | – |
| KLPN1_39 | 22568 | 22912 | AAcGAGGG | GTG | + | minor tail protein KP36 (minor tail protein: PF05939) | 44 (88.6) | 38 (87.72) | 04 (86.84) | 16 (28.32) |
| KLPN1_40 | 22949 | 23734 | – | + | minor tail protein KP36 (minor tail protein L: TIGR01600) | 45 (93.17) | 37 (91.27) | 03 (92.77) | 17 (36.78) | |
| KLPN1_41 | 23736 | 24473 | GAAAAGcGGAcGG | ATG | + | minor tail protein KP36 (endopeptidase, NlpC/P60 family: PF00877) | 46 (93.47) | 36 (96.33) | 02 (94.69) | 18 (42.62) |
| KLPN1_42 | 24448 | 25050 | AAGGA | ATG | + | tail assembly protein KP36 (λ tail assembly protein I: PF06805) | 47 (94.5) | 35 (98) | 01 (95.03) | – |
| KLPN1_43 | 25138 | 28839 | AGGAGG | ATG | + | tail fiber protein KP36 (putative phage tail protein: PF13550) | 48 (95.86) | 34 (88.6) | 01a (95.06) | 21 (39.75) |
| KLPN1_44 | 29027 | 31297 | AAGAGG | ATG | – | HP L418_01651 (Klebsiellapneumoniae UCICRE 7) (galactose-binding domain-like: IPR008979) | 49 (66.79) | 32 (83.49) | 71 (70.15) | – |
| KLPN1_45 | 31392 | 31853 | AGGAAcGA | ATG | – | single-stranded DNA binding protein KP36 (nucleic-acid binding proteins: SSF50249) | 50 (98.04) | 31 (82.35) | 70 (96.08) | – |
| KLPN1_46 | 31890 | 32546 | AAGGAAA | ATG | – | putative recombination protein KP36 (signal peptide) | 51 (99.54) | 30 (93.12) | 69 (98.62) | – |
| KLPN1_47 | 32606 | 33652 | GGAGcAA | ATG | – | exodeoxyribonuclease VIII KP36 (PD-(D/E)XK nuclease superfamily: PF12705) | 52 (97.7) | 29 (93.39) | 68 (97.99) | – |
| KLPN1_48 | 34148 | 35107 | GGAGGtAA | GTG | – | DNA primase KP36 (bacteriophage T7, Gp4, DNA primase/helicase, N-terminal: IPR013237) | 53 (98.7) | 28 (88.64) | 67 (99.35) | – |
| KLPN1_49 | 35183 | 35584 | GAGGGttAA | ATG | – | putative transcriptional regulator KP36 (λ repressor-like, DNA-binding domain: IPR010982) | 54 (98.5) | 27 (95.49) | 66 (99.25) | – |
| KLPN1_50 | 35676 | 37712 | AGGAttG | ATG | + | DNA helicase KP36 (helicase, C-terminal: IPR001650) | 55 (98.52) | 26 (94.25) | 65 (98.82) | – |
| KLPN1_51 | 37709 | 38116 | GGAGGcGAGG | GTG | + | HP KP36_56 KP36 (VRR-NUC domain: IPR014883) | 56 (99.08) | 25 (86.61) | 64 (100) | – |
| KLPN1_52 | 38181 | 38468 | GAAGAAcGGA | ATG | + | HP KP36_57 KP36 (signal peptide) | 57 (95.65) | – | 63 (94.87) | – |
| KLPN1_53 | 38471 | 39202 | GcGAGGttAA | ATG | + | DNA adenine methyltransferase KP36 (phage N-6-adenine-methyltransferase: TIGR01712) | 58 (97.53) | 23 (92.59) | 62 (97.94) | – |
| KLPN1_54 | 39204 | 39440 | GcGtAtGcGAA | ATG | + | HP KP36_59 KP36 | 59 (88.46) | 22 (79.49) | 61 (89.74) | – |
| KLPN1_55 | 39451 | 39741 | – | ATG | + | HP (Enterobacteria phage F20) | 60 (98.72) | 21 (83.33) | 60 (98.72) | – |
| KLPN1_56 | 39741 | 39989 | GGtGAcGA | ATG | + | HP KP36_61 KP36 | 61 (95.18) | 20 (89.02) | 59 (96.39) | – |
| KLPN1_57 | 40085 | 41215 | AAttGGGAtAA | ATG | + | HP KP36_62 KP36 (metallo-dependent phosphatase-like: IPR029052) | 62 (99.2) | 19 (94.15) | 58 (99.2) | – |
| KLPN1_58 | 41254 | 41745 | AAGGAAA | ATG | + | 3’-phosphatase, 5’-polynucleotide kinase KP36 (HAD superfamily, subfamily IIIB (acid phosphatase): PF03767) | 63 (93.87) | 18 (75.46) | 57 (95.09) | – |
| KLPN1_59 | 41742 | 42323 | GGAGtAGA | ATG | + | HP KP36_64 KP36 (P-loop containing nucleoside triphosphate hydrolase: IPR027417) | 64 (99.48) | 17 (88.17) | 56 (99.48) | – |
| KLPN1_60 | 42450 | 42665 | AGAGG | ATG | + | holin KP36 | 65 (83.1) | 16 (80.28) | 55 (83.1) | – |
| KLPN1_61 | 42667 | 43149 | AGGAGcAAG | ATG | + | endolysin KP36 (lysozyme-like domain: IPR023346) | 66 (86.23) | 15 (90.57) | 54 (98.12) | – |
| KLPN1_62 | 43146 | 43571 | AAGGA | ATG | + | Rz1A protein KP36 | 67 (96.45) | 14 (89.36) | 53 (99.29) | – |
| KLPN1_63 | 43641 | 44102 | GAGGtAA | ATG | – | HP KP36_68 KP36 | 68 (98.69) | 13 (88.89) | 52 (98.69) | – |
| KLPN1_64 | 44106 | 45674 | AGGAGcAAGG | ATG | – | HP KP36_69 KP36 (protein of unknown function DUF3987: PF13148) | 69 (99.81) | 12 (95.79) | 51 (99.81) | – |
| KLPN1_65 | 45800 | 46237 | GGAGAAAG | ATG | – | HP KP36_70 KP36 | 70 (97.93) | 11 (91.03) | 50 (98.62) | – |
| KLPN1_66 | 46238 | 46420 | GAAGAAA | ATG | – | HP KP36_71 KP36 | 71 (93.33) | 10 (86.44) | 49 (93.33) | – |
| KLPN1_67 | 46417 | 46620 | GGAGtAAAcGGA | ATG | – | HP KP36_72 KP36 | 72 (97.01) | 09 (65.67) | 48 (92.54) | – |
| KLPN1_68 | 46693 | 47385 | AAAtGGtGGA | ATG | – | HP KP36_73 KP36 | 73 (97.83) | 08 (90) | 47 (96.96) | 42 (56.83) |
| KLPN1_69 | 47382 | 47681 | GGcAtAG | TTG | – | HP KP36_74 KP36 | 74 (100) | 06 (55.41) | 46 (52.7) | – |
| KLPN1_70 | 47688 | 48065 | GAAAcGAGG | ATG | – | HP KP36_75 KP36 | 75 (96) | 05 (66.13) | 45 (70) | – |
| KLPN1_71 | 48065 | 48304 | GAGAAGGG | ATG | – | HP KP36_76 KP36 | 76 (96.2) | 04 (93.1) | 44 (97.47) | – |
| KLPN1_72 | 48301 | 48495 | AGGAGAA | ATG | – | HP KP36_77 KP36 | 77 (93.75) | 03 (84.81) | 43 (95.31) | – |
| KLPN1_73 | 48568 | 48849 | AGAGGG | ATG | – | HP KP36_78 KP36 | 78 (97.47) | 02 (84.81) | 42 (96.2) | – |
Notes.
*
HP, hypothetical protein. Underlined predicted products are from InterProScan (http://www.ebi.ac.uk/interpro/) searches that returned results with the amino acid sequence encoded by each ORF (Table S2).