Align Fructose-specific PTS system, I, HPr, and IIA components (characterized)
to candidate AO353_08465 AO353_08465 phosphoenolpyruvate-protein phosphotransferase
Query= reanno::pseudo3_N2E3:AO353_05485 (953 letters) >FitnessBrowser__pseudo3_N2E3:AO353_08465 Length = 759 Score = 333 bits (853), Expect = 3e-95 Identities = 202/562 (35%), Positives = 318/562 (56%), Gaps = 18/562 (3%) Query: 405 VAAAPGIAIGPAHIQVLQAIDYPLRGESTAIERER----LKTSLADVRRDIEGLIQRSKA 460 V +PG A+G A + +L D + + T + E KT++ VR D+ L + Sbjct: 181 VPGSPGAAVGTA-VVMLPPADLDVVPDKTIADIEAELGLFKTAIEGVRADMRALSAKLAT 239 Query: 461 KAI---REIFITHQEMLDDPELTDEVDTRLKQGESAEAAWMAVIDAAARQQESLQDALLA 517 + R +F + MLDD L EV T +K G+ A+ A V+ + E + DA L Sbjct: 240 QLRPEERALFDVYLMMLDDASLGSEVTTVIKTGQWAQGALRQVVTDHVNRFELMDDAYLR 299 Query: 518 ERAADLRDIGRRVLAQLCGI--ETPSEPDQPYILVMDEVGPSDVARLDPTRVAGILTARG 575 ERA+D++D+GRR+LA L +T PD IL+ +E+ P+ + + ++ G+++ G Sbjct: 300 ERASDVKDLGRRLLAYLQEERQQTLVYPDNT-ILISEELTPAMLGEVPEGKLVGLVSVLG 358 Query: 576 GATAHSAIVARALGIPALVGAGAAVLRLASGTPLLLDGQRGRLHVDADAATLQRAAEERD 635 +H AI+ARA+GIP ++G G +++DG G ++ + ++ A+ + Sbjct: 359 SGNSHVAILARAMGIPTVMGLVDLPYSKVDGIQMIVDGYHGEVYTNPSDVLRKQFADVVE 418 Query: 636 NREQRLQAAAAQRHQPALTTDGHAVEVFANIGESAGVVSAVEQGAEGIGLLRTELIFMAH 695 +Q A R P +T DGH + ++ N G A V A ++GAEG+GL RTE+ FM + Sbjct: 419 EEKQLALGLDALRDLPCVTIDGHRMPLWVNTGLLADVARAQKRGAEGVGLYRTEVPFMIN 478 Query: 696 QQAPDEATQEVEYRRVLDGLAGRPLVVRTLDVGGDKPLPYWPIAKEENPFLGVRGIRLTL 755 Q+ P E Q YR L +P+ +R+LD+GGDK L Y+PI KE+NPFLG RGIR+TL Sbjct: 479 QRFPSEKEQLAIYREQLAAFHPQPVTMRSLDIGGDKSLSYFPI-KEDNPFLGWRGIRVTL 537 Query: 756 QRPQIMEAQLRALLRAADN-RPLRIMFPMVGSVDEWRQARDMTERLRLEI-----PVADL 809 P+I Q RA+L+A++ LRI+ PM+ E +A + R E+ V Sbjct: 538 DHPEIFLVQTRAMLKASEGLNNLRILLPMISGTHELEEALHLIHRAWGEVRDEGTDVPMP 597 Query: 810 QLGIMIEVPSAALLAPVLAKEVDFFSVGTNDLTQYTLAIDRGHPTLSAQADGLHPAVLQL 869 +G+MIE+P+A LA++VDF SVG+NDLTQY LA+DR +P ++ D LHPAVLQ Sbjct: 598 PVGVMIEIPAAVYQTKELARQVDFLSVGSNDLTQYLLAVDRNNPRVADLYDYLHPAVLQA 657 Query: 870 IDITVRAAHAHGKWVGVCGELAADPLAVPVLVGLGVDELSVSARSIGEVKARVRELSLAQ 929 + VR AHA GK V +CGE+A DP A +L+ +G D LS++A ++ +VK +R+++L+ Sbjct: 658 LQTVVRDAHAEGKPVSICGEMAGDPAAAVLLMAMGFDSLSMNATNLPKVKWMLRQINLSW 717 Query: 930 VKHLAQLALAVGSANEVRALVE 951 + L + + + + + ++ Sbjct: 718 ARDLLAELMTIDNPQVIHSSLQ 739 Lambda K H 0.319 0.135 0.383 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: 1389 Number of extensions: 64 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: 953 Length of database: 759 Length adjustment: 42 Effective length of query: 911 Effective length of database: 717 Effective search space: 653187 Effective search space used: 653187 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: 56 (26.2 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