Align D-trehalose PTS system, I, HPr, and IIA components (characterized)
to candidate SMc02437 SMc02437 phosphoenolpyruvate phosphotransferase PTSP (enzyme I-Ntr) protein
Query= reanno::WCS417:GFF4500 (838 letters) >FitnessBrowser__Smeli:SMc02437 Length = 755 Score = 235 bits (599), Expect = 8e-66 Identities = 180/613 (29%), Positives = 294/613 (47%), Gaps = 23/613 (3%) Query: 234 EDAEAAIKALVALLAE--GCGEAVVNVAEP--VATQSSATLLRGVCASPGSAFGQVVQVT 289 ED A++ +LAE GE + + +P S + G G G VV + Sbjct: 143 EDEVEALETTAMVLAEMVATGE-LKKITKPGLELDLSRPVTIEGNSYGEGIGLGYVV-LH 200 Query: 290 DPELVITE---QGTGGATERAALTRGLLAAN-EALQVLQDKAAGSAQAEIFRAHQELLED 345 +P +V+T + T +R A G L + + + +D + + ++ D Sbjct: 201 EPRIVVTNLLNEDTEHELQRLAEALGSLRISIDDMLSRRDVSMEGEHRAVLETYRMFAHD 260 Query: 346 PTLLEHAHRLLGEGKSAAFAWNSATLATVTLFQGLGNALIAERAADLADVGQRVLKLI-- 403 + + G +A A T L + + ER D D+ R+L+ + Sbjct: 261 RGWVRKLEEAIRNGLTAEAAVERVQSETKARMIRLTDPYLRERMHDFDDLANRLLRQLSG 320 Query: 404 LGIQDSAWDLPERAILIAEQLTPSQTASLDTRKVLGFVTVAGGATSHVAILARALGLPAI 463 G + SA D P AI++A + ++ V G V G TSHV I+ARA+G+P + Sbjct: 321 YGAKLSAADFPNDAIVVARAMGAAELLDYPRENVRGLVLEEGAVTSHVVIVARAMGIPVV 380 Query: 464 CGVPAQVLALA-NGKQVLLDADKGELHLEPNLAEIEQ-LEAARKHQVLRHQRDVAQASLP 521 G A +ALA N +++D D ++HL P +A++++ E + + R + A + Sbjct: 381 -GQAAGAVALAENRDAIIVDGDDAKVHLRP-MADLQRAYEEKVRFRARRQAQFRALRDVE 438 Query: 522 ATTRDGHHVEVTANVASLQEVEHALTLGGEGVGLLRSEFLYLDRNRAPSPEEQAGTYTAI 581 T+DG + + N L ++ H G EG+GL R+E ++ + P EEQ Y + Sbjct: 439 PLTKDGKRITLQMNAGLLVDLPHLNEAGAEGIGLFRTELQFMIASTMPKAEEQEAFYRNV 498 Query: 582 ARALGTERNLVVRTLDVGGDKPLAYVPMDAETNPFLGLRGIRLCLERPQLLREQFRAILA 641 + + + RTLD+GGDK + Y E NP LG R IRL L+RP LLR QFRA+L Sbjct: 499 MKQT-AGKPVTFRTLDIGGDKVVPYFRAAEEENPALGWRAIRLSLDRPGLLRTQFRAMLR 557 Query: 642 SAGFARLHIMLPMVSLLSELHLARKILEEE-----ALALGLTELPKLGIMIEVPSAALMA 696 + A L +MLPMV+ ++EL AR++L++E L L + G M+EVP+ Sbjct: 558 ATAGAELKMMLPMVTEVAELKSARELLQKEIERQSKLGEQLPRKLQFGAMLEVPALLWQL 617 Query: 697 DVFAPHVDFFSIGTNDLTQYTLAMDRDHPRLANQADSFHPAVLRLIATTVKAAHAHGKWV 756 D VDF S+G+NDL Q+ +A+DR + R++ + D LR++ V+A + V Sbjct: 618 DELMAEVDFVSVGSNDLFQFAMAVDRGNARVSERFDILGRPFLRILREIVRAGERNNTPV 677 Query: 757 GVCGALASEALAVPVLIGLGVDELSVSVPLIPTIKATVRELDLADCQIIARQVL-GLEEA 815 +CG +AS+ L+ L+GLG +S+S + +KA + LD + L ++ Sbjct: 678 TLCGEMASKPLSAMALLGLGFRSVSMSPTAVGPVKAMLLALDAGRLNELLEAALDDVKSD 737 Query: 816 AEVREALRQYHAA 828 +R+ L + AA Sbjct: 738 TSIRQLLVDFAAA 750 Lambda K H 0.318 0.133 0.371 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: 1136 Number of extensions: 44 Number of successful extensions: 3 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: 838 Length of database: 755 Length adjustment: 41 Effective length of query: 797 Effective length of database: 714 Effective search space: 569058 Effective search space used: 569058 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 55 (25.8 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