Align trehalose-specific PTS system, I, HPr, and IIA components (characterized)
to candidate WP_008507649.1 BIBO1_RS12560 phosphoenolpyruvate--protein phosphotransferase
Query= reanno::pseudo3_N2E3:AO353_15995 (844 letters) >NCBI__GCF_000182725.1:WP_008507649.1 Length = 756 Score = 262 bits (670), Expect = 5e-74 Identities = 194/607 (31%), Positives = 295/607 (48%), Gaps = 22/607 (3%) Query: 236 EDAELAISTLAQLLADGCGEAVTPVAVVAPVVEAQEVSTKLLRGVCASAGSAFGYVVQVA 295 E E LA+++A G G + + P +E + G + G G+VV Sbjct: 147 EALETTAMVLAEIIATGDG-----LRLARPGIELDLGRPMNVTGHGFNDGIGLGHVVLHE 201 Query: 296 ERTLEMPEFAADQQLERESLERALMHATQALQRL---RDNAAGEAQADIFKAHQELLEDP 352 R + F D Q E L+ AL ++ + RD A ++ +A++ D Sbjct: 202 PRIVVTNLFNEDSQAELNRLDEALGSLRISIDDMLSRRDVAVEGEHREVLEAYRMFAHDR 261 Query: 353 SLLEQAQALIAEGKSAAFAWNSATEATATLFKSLGSTLLAERALDLMDVGQRVLKLILG- 411 + + + + G +A A T L + ER D D+ R+L+ ++G Sbjct: 262 GWVRRLEEAVHNGLTAEAAVEKVQSDTRARMVHLTDPYMRERLSDFDDLANRLLRQLMGR 321 Query: 412 -VPDGVWELPDQAILIAEQLTPSQTAALDTGKVLGFATVGGGATSHVAILARALGLPAVC 470 V L AI++A + ++ ++ G G ATSHV I+ARA+G+P V Sbjct: 322 DVKTIAESLAKDAIIVARSMGAAELLDYPRERLRGVVLEDGAATSHVVIVARAMGIPVV- 380 Query: 471 GLPLQVLSLASGT-RVLLDADKGELHLDPAVSVIEQLHAKRQQQRQRHQ-HELENAARAA 528 G V+S+A +++D D+G +HL P V E +A++ + R R Q H E + A Sbjct: 381 GQAKGVVSMAENNDAIIVDGDEGIVHLRPQADV-ESAYAEKVRFRARRQAHYRELRDKPA 439 Query: 529 VTRDGHHFEVTANVASLAETEQAMSLGAEGIGLLRSEFLYQQRSVAPSHDEQAGTYSAIA 588 +T+DG + N L + Q + GA GIGL R+E + S P ++Q Y ++ Sbjct: 440 ITKDGVDIALLMNAGLLVDLPQLSASGAAGIGLFRTELQFMVASTFPRSEQQERLYRSVI 499 Query: 589 RALGPQRNLVVRTLDVGGDKPLAYVPMDS-EANPFLGMRGIRLCLERPQLLREQFRAILS 647 A G + + RTLD+GGDK L Y + E NP LG R IRL L+RP LLR Q RA+L Sbjct: 500 DAAG-DKPVTFRTLDIGGDKVLPYFRATAQEENPALGWRAIRLTLDRPGLLRTQLRALLK 558 Query: 648 SAGLARLHIMLPMVSQLSELRLARLMLEEEALALG--LRELP---KLGIMIEVPAAALMA 702 +AG L +MLPMV+++SE++ AR ++E E L LP KLG M+EVPA Sbjct: 559 AAGGRELKLMLPMVTEVSEVKAAREIIEREVRHLSRFAHSLPLCLKLGAMVEVPALLWQL 618 Query: 703 DLFAPEVDFFSIGTNDLTQYTLAMDRDHPRLASQADSFHPSVLRLIASTVKAAHAHGKWV 762 D VDF S+G+NDL Q+ +A DR + ++ + D PS LR + VKA H K V Sbjct: 619 DELMTAVDFVSVGSNDLFQFLMAADRGNSLISDRFDQLSPSFLRALRHIVKAGARHDKPV 678 Query: 763 GVCGALASETLAVPLLLGLGVDELSVSVPLIPAIKAAIREVELSDCQAIAHQVLGL-ESA 821 +CG +A L L+GLG +S+S I +KA + ++ A+ + L +A Sbjct: 679 TLCGEMAGRPLTAMTLIGLGFRSISMSAAAIGPVKAMLGALDAGKLNALLLEELNKPNNA 738 Query: 822 EQVREAL 828 +RE L Sbjct: 739 HSLRELL 745 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: 1224 Number of extensions: 47 Number of successful extensions: 6 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: 756 Length adjustment: 41 Effective length of query: 803 Effective length of database: 715 Effective search space: 574145 Effective search space used: 574145 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 24 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