Align trehalose-specific PTS system, I, HPr, and IIA components (characterized)
to candidate Ga0059261_2514 Ga0059261_2514 phosphoenolpyruvate-protein phosphotransferase
Query= reanno::pseudo3_N2E3:AO353_15995 (844 letters) >FitnessBrowser__Korea:Ga0059261_2514 Length = 759 Score = 251 bits (642), Expect = 9e-71 Identities = 188/608 (30%), Positives = 288/608 (47%), Gaps = 30/608 (4%) Query: 216 VAIMALQTVHGDALQVSAVGEDAELAISTLAQLLADGCGEAVTPVAVVAPV-----VEAQ 270 V ++A+Q H D + V +A + T+A +L+ E + ++ P Q Sbjct: 128 VGVLAVQ--HADPRKYDEVEIEA---LQTVAMVLS----ELIANAGLIDPAGGGGTTRLQ 178 Query: 271 EVSTKLLRGVCASAGSAFGYVVQVAERTLEMPEFAADQQLERESLERALMHATQALQRLR 330 T + G G A G V R + A D + ER + A + + R+ Sbjct: 179 STGTARVPGFKLVEGMAAGAAVFHQPRIIIEHTVAEDIEAERHRVYAAFDKMREQIDRMT 238 Query: 331 DNA---AGEAQADIFKAHQELLEDPSLLEQAQALIAEGKSAAFAWNSATEATATLFKSLG 387 A G ++ + ++ D + I G +A A + T + + Sbjct: 239 SQAEFGGGGEHEEVLETYKMFAYDEGWSRRINEAIDSGLTAEAAIERVQQRTRMRMRQID 298 Query: 388 STLLAERALDLMDVGQRVLKLILGVPDGVWELP--DQAILIAEQLTPSQTAALDTGKVLG 445 LL +R DL D+ R+L+++ G +L +ILIA L P++ D ++ G Sbjct: 299 DPLLRDRMHDLEDLSNRLLRIVSGQLGTAAQLGLRQDSILIARNLGPAELLEYDRRRLKG 358 Query: 446 FATVGGGATSHVAILARALGLPAVCGLPLQVLSLASGTRVLLDADKGELHLDPAVSVIEQ 505 G T+HV I+ARA+G+P + + +A G R+L+D + L + P ++ E Sbjct: 359 VVLEEGSLTAHVTIVARAMGVPVLGRVKDIRRLIAEGDRLLVDVTEDTLIIRPTAAMDEA 418 Query: 506 LHAKRQQQRQRHQHELENAARAAVTRDGHHFEVTANVASLAETEQAMSL-GAEGIGLLRS 564 AK ++R A VT DGH V N A L + A+ L GA+GIGL R+ Sbjct: 419 FEAKLLVTQKRRAAFAALKNEAPVTTDGHRLTVMVN-AGLRDDVAALDLTGADGIGLFRT 477 Query: 565 EFLYQQRSVAPSHDEQAGTYSAIARALGPQRNLVVRTLDVGGDKPLAYVPMDS---EANP 621 EF + + P D Q Y + A G R + RT+D+GGDK L Y+ D E NP Sbjct: 478 EFQFLVSATLPQRDSQRRLYKDVLDAAG-DRPVTFRTVDIGGDKALPYLDHDENGEEENP 536 Query: 622 FLGMRGIRLCLERPQLLREQFRAILSSAGLARLHIMLPMVSQLSELRLARLMLEEEALAL 681 +G R +RL L+R L++ Q RA+L +A L++M PMVS+ E AR + E + L Sbjct: 537 AMGWRALRLALDREGLMKVQARALLEAAAGRTLNVMFPMVSEPWEFDEARTLFETQRAWL 596 Query: 682 GLR--ELP---KLGIMIEVPAAALMADLFAPEVDFFSIGTNDLTQYTLAMDRDHPRLASQ 736 R +LP + G M+EVPA A + DL P +DF S+GTNDLTQ+ A DR HP+LA + Sbjct: 597 ESRGHKLPLHIRYGAMLEVPALAEVLDLLLPRLDFLSVGTNDLTQFLFAADRAHPKLAVR 656 Query: 737 ADSFHPSVLRLIASTVKAAHAHGKWVGVCGALASETLAVPLLLGLGVDELSVSVPLIPAI 796 D PS+LR + A + VCG + L L+GLG+D LS++ + I Sbjct: 657 YDWLSPSILRFLRRVTAEAAEADVPLAVCGEMGGRPLEAMALIGLGIDRLSITPAAVGPI 716 Query: 797 KAAIREVE 804 KA +R ++ Sbjct: 717 KAMVRSLD 724 Lambda K H 0.318 0.132 0.370 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 1236 Number of extensions: 53 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 844 Length of database: 759 Length adjustment: 41 Effective length of query: 803 Effective length of database: 718 Effective search space: 576554 Effective search space used: 576554 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 55 (25.8 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory