Align Fructose PTS system (E-I, HPr, and E-IIA components) (characterized)
to candidate WP_058858173.1 AS188_RS06525 phosphoenolpyruvate--protein phosphotransferase
Query= reanno::azobra:AZOBR_RS32325 (846 letters) >NCBI__GCF_001482365.1:WP_058858173.1 Length = 566 Score = 313 bits (802), Expect = 2e-89 Identities = 227/574 (39%), Positives = 310/574 (54%), Gaps = 39/574 (6%) Query: 283 GIAASPGLAIGPVHVLPRAAVSVPDEPVPLIEGGD-----RLHEALSLTRQNLKALADDT 337 G+ G IG + +P A V+ P + L + RL EA + + LK A+ Sbjct: 6 GVGVCAGRVIGELVSMP-APVAEPAAGLALRDEAPEDAVARLQEAAAEVKAELKRRAEAA 64 Query: 338 ARRLGPSEAAIFAAQAEILNDTDLVTLACQLMVE-GHGVAWSWHQAVERTAAGLAALDNP 396 + A + + A + D L+ A +L+ + G + +A A + AL Sbjct: 65 TEK---DAADVLKSTALMAGDRALLKNAGKLITDRGLAPERALWEAASAYAEQMRALGG- 120 Query: 397 VLAARAADLRDVGQRVLARIDPALRTGGAPDLPDTPCILIAEDLSPSDTAALDMARVIGL 456 +A RAAD+ DV R++AR+ L G P+ +TP +L AEDL+P+DTA LD A+V+ L Sbjct: 121 YMAERAADIEDVRARLVARLR-GLPMPGIPER-ETPFVLTAEDLAPADTATLDPAKVLAL 178 Query: 457 ATAQGGPTSHTAILARTLGLPAMVAGGAALMELANGTPAILDGQSGRLHLSPAAADIADA 516 T+ GGP SHTAILAR LGLPA+VA + ELA+GT +DG +G + P A + Sbjct: 179 VTSAGGPQSHTAILARNLGLPAIVAA-RGVEELADGTEVFVDGATGEVRTEPGAEERELV 237 Query: 517 RAWIAREEARKAEEEARRGLPARTRDGHEVEIGANVNRPDQVAVALSQGAESVGLMRTEF 576 +W R A +++ + R L DG EV + ANV + A + GA+ VGL+RTEF Sbjct: 238 ASW-ERAAAARSDFDGRGVLA----DGTEVPLYANVGTAEDARTAAAAGAQGVGLLRTEF 292 Query: 577 LFLERGDAPGEDEQYETYRGMLTALEGRPLIVRALDIGGDKQVPHLQLPHEENPFLGVRG 636 FL RG+ P +EQ E Y + A E + ++VR LD G DK +P L E NP LGVRG Sbjct: 293 CFLGRGEEPSVEEQVEQYTAIFAAFEEKKVVVRTLDAGADKPLPFLTDTAEPNPALGVRG 352 Query: 637 ARLLLRRPELLETQLRALYRAAKDGGAKDGGALSIMFPMITALGEVQALRAACERIRAEL 696 R P +L QL A+ RA + A+ + +M PMI+A E + A A L Sbjct: 353 YRTDRSVPGVLARQLEAIARADEATAAE----VWVMAPMISAAEEARDFAAMA--ATAGL 406 Query: 697 DAPAVPLGIMVEVPAAAIQADVLARHVDFFSIGTNDLTQYALAIDRQHPELAAEADSLHP 756 P G+MVE P+AA+ AD + RHV+F S+GTNDLTQY +A DR LA + P Sbjct: 407 RVP----GVMVETPSAAVTADQILRHVEFVSLGTNDLTQYTMAADRMLGSLAELNNPWQP 462 Query: 757 AVLRLIRLTVEGAER------HGRWVGVCGGIAGDPFGAALLTGLGVRELSMTPRDIPAV 810 AVLR++RLTVEGA R R VGVCG A DP A +L GLGV LSM+PR + V Sbjct: 463 AVLRMVRLTVEGARRAEAEGAGRRNVGVCGEAAADPALAVVLVGLGVHTLSMSPRALSPV 522 Query: 811 KDRLRGSDLSALKDAAQRALD----CETADAVRA 840 LR DL+ + A+ A++ E A AVRA Sbjct: 523 AAVLRSVDLATARSLAELAVEQATAAEAAAAVRA 556 Lambda K H 0.319 0.134 0.387 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: 1072 Number of extensions: 54 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: 846 Length of database: 566 Length adjustment: 39 Effective length of query: 807 Effective length of database: 527 Effective search space: 425289 Effective search space used: 425289 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 54 (25.4 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