Align trehalose-specific PTS system, I, HPr, and IIA components (characterized)
to candidate Pf1N1B4_833 PTS system, glucose-specific IIA component / Phosphotransferase system, phosphocarrier protein HPr / Phosphoenolpyruvate-protein phosphotransferase of PTS system (EC 2.7.3.9)
Query= reanno::pseudo3_N2E3:AO353_15995 (844 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_833 Length = 844 Score = 1272 bits (3292), Expect = 0.0 Identities = 676/846 (79%), Positives = 731/846 (86%), Gaps = 4/846 (0%) Query: 1 MTLTQPLQLLAPLSGVLMPLDHVPDPVFASRVIGDGLCIDPTSQVLCAPLAGVVSNLQHS 60 M Q LQLLAPLSGVLMPLD VPD VF+SRVIGDGLCIDPTSQ LCAPL GV+SN+Q S Sbjct: 1 MATPQQLQLLAPLSGVLMPLDQVPDQVFSSRVIGDGLCIDPTSQTLCAPLTGVISNVQVS 60 Query: 61 GHAISITDDSGVQVLLHIGLDTVNLKGQGFSALVEQGQRVEAGQPLIEFDADYVALHARS 120 GHA+SITDD+GVQVL+HIGLDTVNL G+GF+ LVE+GQRV GQ LIEFDADY+ALHARS Sbjct: 61 GHAVSITDDNGVQVLMHIGLDTVNLAGKGFTRLVEEGQRVIVGQALIEFDADYIALHARS 120 Query: 121 LLTLMLVVSGEPFSLLTPDSGLVACAQPVLRL--SLGDPRTVVAQEEGEALFSKPVHLPN 178 LLTLMLVVSGEPF+ L P++G+V QP+L L S G +AQE GEALFSKPV LPN Sbjct: 121 LLTLMLVVSGEPFTWLAPETGVVESGQPLLSLNPSEGAADEGIAQE-GEALFSKPVTLPN 179 Query: 179 PNGLHARPAAVFAQAAKGFAASICLHKQQDSANAKSLVAIMALQTVHGDALQVSAVGEDA 238 NGLHARPAAVFAQAAKGFAASICLHKQQDSANAKSLVAIMALQT HGD LQVSA G DA Sbjct: 180 TNGLHARPAAVFAQAAKGFAASICLHKQQDSANAKSLVAIMALQTAHGDVLQVSAAGADA 239 Query: 239 ELAISTLAQLLADGCGEAVTPVAVVAPVVEAQEVSTKLLRGVCASAGSAFGYVVQVAERT 298 E+AI TLA+LLA GCGEAVT +A V V AQ S +LRGVCAS G+AFG VVQ+AE+T Sbjct: 240 EVAIKTLAELLAAGCGEAVTLMAEVETVA-AQVSSLTVLRGVCASPGAAFGQVVQIAEQT 298 Query: 299 LEMPEFAADQQLERESLERALMHATQALQRLRDNAAGEAQADIFKAHQELLEDPSLLEQA 358 LE+ E Q+ERE L RAL A ALQ+LRD A G+AQADIFKAHQELLEDP LL+QA Sbjct: 299 LEVSESGVSPQVEREHLSRALAKAVLALQQLRDKATGDAQADIFKAHQELLEDPGLLDQA 358 Query: 359 QALIAEGKSAAFAWNSATEATATLFKSLGSTLLAERALDLMDVGQRVLKLILGVPDGVWE 418 ALI GKSA FAW +ATE+TATLFK LG+ LLAERA DL DVGQRVLKLILGV D E Sbjct: 359 LALIDAGKSAGFAWRAATESTATLFKKLGNALLAERAADLADVGQRVLKLILGVEDRAME 418 Query: 419 LPDQAILIAEQLTPSQTAALDTGKVLGFATVGGGATSHVAILARALGLPAVCGLPLQVLS 478 LPD AILIAEQLTPSQTA LDT KVLGFATVGGGATSHVAILARA GLPA+CGLP+QVL+ Sbjct: 419 LPDGAILIAEQLTPSQTAGLDTRKVLGFATVGGGATSHVAILARASGLPAICGLPVQVLT 478 Query: 479 LASGTRVLLDADKGELHLDPAVSVIEQLHAKRQQQRQRHQHELENAARAAVTRDGHHFEV 538 L +GTRVLLDADKGEL LDP ++ IEQL A RQ Q+QR Q+EL NA AA TRDGHH E+ Sbjct: 479 LINGTRVLLDADKGELQLDPELAAIEQLQANRQLQKQRQQYELANAGLAARTRDGHHVEI 538 Query: 539 TANVASLAETEQAMSLGAEGIGLLRSEFLYQQRSVAPSHDEQAGTYSAIARALGPQRNLV 598 TAN+ASLAE EQAM+LG +G+GLLRSEFLY R+ APSHDEQA TY AIARALGP RNLV Sbjct: 539 TANIASLAEAEQAMALGGDGVGLLRSEFLYLDRNHAPSHDEQASTYGAIARALGPARNLV 598 Query: 599 VRTLDVGGDKPLAYVPMDSEANPFLGMRGIRLCLERPQLLREQFRAILSSAGLARLHIML 658 VRTLDVGGDKPLAYVPMD E NPFLGMRGIRLCLERPQLLR+QF+AILSSAGLARLHIML Sbjct: 599 VRTLDVGGDKPLAYVPMDRETNPFLGMRGIRLCLERPQLLRDQFKAILSSAGLARLHIML 658 Query: 659 PMVSQLSELRLARLMLEEEALALGLRELPKLGIMIEVPAAALMADLFAPEVDFFSIGTND 718 PMV+QLSELRLAR +LEEEALALGL ELPKLGIMIEVPAAALMADLFAPEVDFFSIGTND Sbjct: 659 PMVTQLSELRLARQLLEEEALALGLTELPKLGIMIEVPAAALMADLFAPEVDFFSIGTND 718 Query: 719 LTQYTLAMDRDHPRLASQADSFHPSVLRLIASTVKAAHAHGKWVGVCGALASETLAVPLL 778 LTQYTLAMDRDHPRLASQADSFHPSVLRLIA+TVKAAHAHGKWVGVCGALASE LAVPLL Sbjct: 719 LTQYTLAMDRDHPRLASQADSFHPSVLRLIATTVKAAHAHGKWVGVCGALASEKLAVPLL 778 Query: 779 LGLGVDELSVSVPLIPAIKAAIREVELSDCQAIAHQVLGLESAEQVREALSVQQQAMVET 838 LGLGVDELSVSVPLIPAIKAA+REV+L DCQAIA QVLGLESAEQVREAL +A V+T Sbjct: 779 LGLGVDELSVSVPLIPAIKAAVREVDLLDCQAIAQQVLGLESAEQVREALRRHHEATVDT 838 Query: 839 SQVLES 844 S VLE+ Sbjct: 839 SLVLEN 844 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: 1858 Number of extensions: 81 Number of successful extensions: 4 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: 844 Length adjustment: 42 Effective length of query: 802 Effective length of database: 802 Effective search space: 643204 Effective search space used: 643204 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: 56 (26.2 bits)
This GapMind analysis is from Apr 09 2024. 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