Align Fructose PTS system (E-I, HPr, and E-IIA components) (characterized)
to candidate WP_106709795.1 CU102_RS04500 phosphoenolpyruvate--protein phosphotransferase
Query= reanno::azobra:AZOBR_RS32325 (846 letters) >NCBI__GCF_003010955.1:WP_106709795.1 Length = 535 Score = 252 bits (643), Expect = 5e-71 Identities = 181/537 (33%), Positives = 253/537 (47%), Gaps = 28/537 (5%) Query: 283 GIAASPGLAIGPVHVLPRAAVSVPDEPVPLIEGGDRLHEALSLTRQNLKALADDTARRLG 342 G ASPG A G +++ + P E H LS Q A + A R Sbjct: 9 GKGASPGTAFGQIYLAVDVEETFLSPTDPSAE-----HAILSDAVQGSIAALRELAARSS 63 Query: 343 PSEAAIFAAQAEILNDTDLVTLACQLMVEGHGVAWSWHQAVERTAAGLAALDNPVLAARA 402 A+I Q E+L D ++ +A + + G G A +W A++ AG DN + ARA Sbjct: 64 TESASILEFQIEMLLDPEITEMAARRIGTGDGAALAWVTALDNYIAGFEQSDNEAVRARA 123 Query: 403 ADLRDVGQRVLARIDPALRTGGAPDLPDTPCILIAEDLSPSDTAALDMARVIGLATAQGG 462 ADL D+ RVLA A+ D P + + +D+SPS A D + G+ QG Sbjct: 124 ADLFDIKSRVLA----AMTGKPVADFP-VGFVFVGKDISPSVFLAHDWSSGGGIVLFQGS 178 Query: 463 PTSHTAILARTLGLPAMVAGGAALMELANGTPAILDGQSGRLHLSPAAADIADARAWIAR 522 SH ++LAR +P ++ G +A +LDG +G + L P+ ++ A + Sbjct: 179 AASHVSMLARAKSVPMVIETGT--FNIAGEEKLLLDGGTGSVVLHPSDEELRQALSTRLS 236 Query: 523 EEARKAEEEARRGLPARTRDGHEVEIGANVNRPDQVAVALSQGAESVGLMRTEFLFLERG 582 E EA RT DG E+ + NVN + G E +GL+RTEFL Sbjct: 237 MRPIANEAEAPCSTKLRTADGAEISLSINVNDLSDIIGIDHAGIEGIGLLRTEFLMSSAA 296 Query: 583 DAPGEDEQYETYRGMLTALEGRPLIVRALDIGGDKQVPHLQLPHEENPFLGVRGARLLLR 642 D ED QY YR +L +P+ +R LD+GGDK VP + FLG+RG RLLL Sbjct: 297 DIANEDRQYGIYRQVLEWAGQKPVTIRMLDLGGDKPVP----DRDGTSFLGLRGIRLLLA 352 Query: 643 RPELLETQLRALYRAAKDGGAKDGGALSIMFPMITALGEVQ-ALRAACERI----RAELD 697 RPE L Q RAL R+A G L +M PM+T E++ + E + R + Sbjct: 353 RPEFLRIQARALLRSAVHGN------LKVMLPMVTLPSELEKTVTIFREELTLLQRRRIS 406 Query: 698 APAVPLGIMVEVPAAAIQADVLARHVDFFSIGTNDLTQYALAIDRQHPELAAEADSLHPA 757 P+GIMVEVPA AI D +FFS GTNDL QY A R + +A PA Sbjct: 407 HRMPPIGIMVEVPATAIMLDTFGA-AEFFSFGTNDLVQYLTAAARDNAAVADIYTHAAPA 465 Query: 758 VLRLIRLTVEGAERHGRWVGVCGGIAGDPFGAALLTGLGVRELSMTPRDIPAVKDRL 814 + RL+ TV A G V VCG +AG+P L G+R S+ P + ++ ++ Sbjct: 466 IFRLLEHTVHIAATLGAPVSVCGDMAGEPEYIPALLRCGLRHFSLAPAQLAVIRSQI 522 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: 954 Number of extensions: 44 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: 535 Length adjustment: 39 Effective length of query: 807 Effective length of database: 496 Effective search space: 400272 Effective search space used: 400272 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