Align Fructose-specific PTS system, I, HPr, and IIA components (characterized)
to candidate PfGW456L13_953 FIG001592: Phosphocarrier protein kinase/phosphorylase, nitrogen regulation associated
Query= reanno::pseudo3_N2E3:AO353_05485 (953 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_953 Length = 759 Score = 338 bits (867), Expect = 8e-97 Identities = 207/561 (36%), Positives = 320/561 (57%), Gaps = 16/561 (2%) Query: 405 VAAAPGIAIGPAHIQVLQA-IDYPLRGESTAIERER--LKTSLADVRRDIEGLIQRSKAK 461 V +PG A+G A + + A +D T I+ E KT++ VR D+ L + + Sbjct: 181 VPGSPGAAVGTAVVMLPPADLDVVPDKTITDIDAELGLFKTAIEGVRADMRTLSAKLATQ 240 Query: 462 AI---REIFITHQEMLDDPELTDEVDTRLKQGESAEAAWMAVIDAAARQQESLQDALLAE 518 R +F + MLDD L EV T +K G+ A+ A V+ + E + DA L E Sbjct: 241 LRPEERALFDVYLMMLDDAALGSEVTTVIKTGQWAQGALRQVVTDHVNRFELMDDAYLRE 300 Query: 519 RAADLRDIGRRVLAQLCGI--ETPSEPDQPYILVMDEVGPSDVARLDPTRVAGILTARGG 576 RA+D++D+GRR+LA L +T PD ILV +E+ P+ + + ++AG+++ G Sbjct: 301 RASDVKDLGRRLLAYLQEERQQTLVYPDNT-ILVSEELTPAMLGEVPEGKLAGLVSVLGS 359 Query: 577 ATAHSAIVARALGIPALVGAGAAVLRLASGTPLLLDGQRGRLHVDADAATLQRAAEERDN 636 +H AI+ARA+GIP ++G G +++DG G ++ + ++ AE + Sbjct: 360 GNSHVAILARAMGIPTVMGLVDLPYSKVDGIQMIVDGYHGEVYTNPSEVLRKQFAEVVEE 419 Query: 637 REQRLQAAAAQRHQPALTTDGHAVEVFANIGESAGVVSAVEQGAEGIGLLRTELIFMAHQ 696 +Q A R P +T DGH + ++ N G A V A ++GAEG+GL RTE+ FM +Q Sbjct: 420 EKQLALGLDALRDLPCVTVDGHRMPLWVNTGLLADVARAQKRGAEGVGLYRTEVPFMINQ 479 Query: 697 QAPDEATQEVEYRRVLDGLAGRPLVVRTLDVGGDKPLPYWPIAKEENPFLGVRGIRLTLQ 756 + P E Q YR L +P+ +RTLD+GGDK L Y+PI KE+NPFLG RGIR+TL Sbjct: 480 RFPSEKEQLAIYREQLSAFHPQPVTMRTLDIGGDKSLSYFPI-KEDNPFLGWRGIRVTLD 538 Query: 757 RPQIMEAQLRALLRAADN-RPLRIMFPMVGSVDEWRQARDMTERLRLEI-----PVADLQ 810 P+I Q RA+L+A++ LRI+ PM+ E +A + R E+ V Sbjct: 539 HPEIFLVQTRAMLKASEGLNNLRILLPMISGTHELEEALHLIHRAWGEVRDEGCDVPMPP 598 Query: 811 LGIMIEVPSAALLAPVLAKEVDFFSVGTNDLTQYTLAIDRGHPTLSAQADGLHPAVLQLI 870 +G+MIE+P+A LA++VDF SVG+NDLTQY LA+DR +P ++ D LHPAVLQ + Sbjct: 599 IGVMIEIPAAVYQTKELARQVDFLSVGSNDLTQYLLAVDRNNPRVADLYDYLHPAVLQAL 658 Query: 871 DITVRAAHAHGKWVGVCGELAADPLAVPVLVGLGVDELSVSARSIGEVKARVRELSLAQV 930 VR AHA GK V +CGE+A DP A +L+ +G D LS++A ++ +VK +R+++L++ Sbjct: 659 QNVVRDAHAEGKPVSICGEMAGDPAAAVLLMAMGFDSLSMNATNLPKVKWMLRQINLSKA 718 Query: 931 KHLAQLALAVGSANEVRALVE 951 + L + + + + + ++ Sbjct: 719 RELLAELMTIDNPQVIHSSLQ 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: 1377 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