Align Fructose PTS system (E-I, HPr, and E-IIA components) (characterized)
to candidate N515DRAFT_3957 N515DRAFT_3957 phosphotransferase system, enzyme I, PtsI
Query= reanno::azobra:AZOBR_RS32325 (846 letters) >FitnessBrowser__Dyella79:N515DRAFT_3957 Length = 576 Score = 300 bits (768), Expect = 2e-85 Identities = 210/579 (36%), Positives = 296/579 (51%), Gaps = 31/579 (5%) Query: 281 VPGIAASPGLAIGPVHVLPRAAVSVPDEPVPLIEGG---DRLHEALSLTRQNLKALADDT 337 +PG AS G+A+G ++ + V P+ E ++LH AL RQ L+ L Sbjct: 5 LPGSNASRGMALGRARLVQPSRYLVDTRPLGEDEVDVELEKLHRALDTARQELRELRGKL 64 Query: 338 ARRLGPSEAAIFAAQAEILNDTDLVTLACQLMVEGH---GVAWSWHQAVERTAAGLAALD 394 L A + +L+D +L+ L+ GH G A + +R AA A+D Sbjct: 65 HGALAREVNEFIDAHSLLLDDQELLRGLDDLVRIGHYRPGAALKKQR--DRLAAVFEAMD 122 Query: 395 NPVLAARAADLRDVGQRVLARIDPALRTGGAPDLPDTPCILIAEDLSPSDTAALDMARVI 454 +P L +R D+ V RV++ + ILIA+ ++P+D A L ++ Sbjct: 123 DPYLRSRKEDVDQVINRVISALQRQTSREERKLAARVGEILIADTIAPADMAHLAGNGLL 182 Query: 455 GLATAQGGPTSHTAILARTLGLPAMVAGGAALMELANGTPAILDGQSGRLHLSPAAADIA 514 G+ + G P SH+AILAR+L LP +V AL + + +LD + G + P A D+A Sbjct: 183 GVVASSGSPYSHSAILARSLDLPMLVGVRDALATIHDDDLILLDAERGEAVVHPTAQDLA 242 Query: 515 DARAWIAREEARKAEEEARR-----GLPARTRDGHEVEIGANVNRPDQVAVALSQGAESV 569 RAW R+A++E RR P RTRDG ++ + AN +A+A ++GA+ V Sbjct: 243 RYRAW-----QREAQQEGRRLASLANAPTRTRDGTDIRLLANAETTTDIAMARARGADGV 297 Query: 570 GLMRTEFLFLERGDAPGEDEQYETYRGMLTALEGRPLIVRALDIGGDK-QVPHLQLPHEE 628 GL RTEFLFL P EDEQ+ YR ++ + G P+ +R LD+G DK L L EE Sbjct: 298 GLYRTEFLFLRHKGLPSEDEQFIAYRDLVLGMGGLPVTIRTLDLGADKADAAGLALRGEE 357 Query: 629 NPFLGVRGARLLLRRPELLETQLRALYRAAKDGGAKDGGALSIMFPMITALGEVQALRAA 688 NP LGVRG RL LR P + TQ+RA+ RAA G + ++ PMIT E+ A+R Sbjct: 358 NPALGVRGVRLSLRYPAVFTTQIRAILRAACYGPVR------VLVPMITQPDELIAVRTL 411 Query: 689 CERIRAEL-----DAP-AVPLGIMVEVPAAAIQADVLARHVDFFSIGTNDLTQYALAIDR 742 + R +L D P + LG M+EVPAAAI L H DF +IGTNDL QY LA DR Sbjct: 412 FKLARQDLKRENVDLPEKLQLGAMIEVPAAAINVRSLLEHADFLAIGTNDLAQYVLASDR 471 Query: 743 QHPELAAEADSLHPAVLRLIRLTVEGAERHGRWVGVCGGIAGDPFGAALLTGLGVRELSM 802 + L + L PA+LRLI + R G+ V +CG I GD ALL LG+ E SM Sbjct: 472 GNDALDNIYNPLQPALLRLISYVITSGRRAGKPVSLCGEIGGDTKFTALLLALGLCEFSM 531 Query: 803 TPRDIPAVKDRLRGSDLSALKDAAQRALDCETADAVRAL 841 + V+DR+ + L+ A L C T + L Sbjct: 532 HSSQLLHVRDRIASLNHKGLRRLAPAILRCRTHEEAEDL 570 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: 1094 Number of extensions: 58 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: 846 Length of database: 576 Length adjustment: 39 Effective length of query: 807 Effective length of database: 537 Effective search space: 433359 Effective search space used: 433359 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 Apr 09 2024. 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