Align Fructose PTS system (E-I, HPr, and E-IIA components) (characterized)
to candidate WP_011386738.1 AMB_RS22220 phosphoenolpyruvate--protein phosphotransferase
Query= reanno::azobra:AZOBR_RS32325 (846 letters) >NCBI__GCF_000009985.1:WP_011386738.1 Length = 596 Score = 340 bits (872), Expect = 1e-97 Identities = 213/577 (36%), Positives = 322/577 (55%), Gaps = 25/577 (4%) Query: 283 GIAASPGLAIGPVHVLPRAAVSVPDEPVP---LIEGGDRLHEALSLTRQNLKALADDTAR 339 G+ S G+AIG +++ ++VP+ +P L R +EA + + ++ L D R Sbjct: 25 GLGVSRGIAIGTLYLHDAGTITVPELRIPAARLDAECARFNEASANAGRQVEQLQDKAGR 84 Query: 340 ---RLGPSEAAIFAAQAEILNDTDLVT-LACQLMVEGHGVAWSWHQAVERTAAGLAALDN 395 G + A ++L+ + L+ + ++ + + Q + G A+++ Sbjct: 85 LGGAAGEELGYLLDAYRQMLHGSRLLRGVEARIRNDRINAEAAVQQEINEIVRGFEAMED 144 Query: 396 PVLAARAADLRDVGQRVL-ARIDPALRTGGAPDLPDTPCILIAEDLSPSDTAALDMARVI 454 P LAAR AD++D+G+R+L A + A R A LP +++AE+++P+DTA LD +V Sbjct: 145 PYLAARVADIKDIGRRLLRALTNTAYRPFTA--LPRN-AVIVAEEMTPADTALLDPNQVA 201 Query: 455 GLATAQGGPTSHTAILARTLGLPAMVAGGAALMELANGTPAILDGQSGRLHLSPAAADIA 514 GLAT GG HTAI+AR+LGLP+++ L + G I+DG +G + ++P +A Sbjct: 202 GLATVMGGSEGHTAIMARSLGLPSVLGIADLLTGVKGGEQVIIDGTNGLVVINPGPETLA 261 Query: 515 DARAWIAREEARKAEEEARRGLPARTRDGHEVEIGANVNRPDQVAVALSQGAESVGLMRT 574 R A + + +PA TRDG + + AN+ P++V L GAE +GL+R+ Sbjct: 262 FYRRERAAFLKARRVLSRLKDVPAVTRDGGRITLQANMELPNEVGAVLDSGAEGIGLLRS 321 Query: 575 EFLFLERGDAPGEDEQYETYRGMLTALEGRPLIVRALDIGGDKQVPHLQLPHEENPFLGV 634 EFL++ R D P EDEQY + ++ + GR + VR D GGDK P L NP LG+ Sbjct: 322 EFLYMNRDDVPSEDEQYAILKDVVERMGGRTVTVRTFDAGGDKLAPALGCTIGPNPSLGL 381 Query: 635 RGARLLLRRPELLETQLRALYRAAKDGGAKDGGALSIMFPMITALGEVQALRAACERI-- 692 R RL L R +LLE QL A+ RA+ G + I+ PMI +GE++A R R+ Sbjct: 382 RAIRLGLARQDLLEAQLAAILRASAHGPVR------ILIPMIATVGELRATREVMNRVIR 435 Query: 693 -----RAELDAPAVPLGIMVEVPAAAIQADVLARHVDFFSIGTNDLTQYALAIDRQHPEL 747 L P LG M+E+P AA+ AD +A H DFF+IGTNDL QY LAIDR + Sbjct: 436 RLRKAGVSLPDPLPRLGAMIEIPGAALSADSIAWHADFFAIGTNDLVQYTLAIDRSDEAV 495 Query: 748 AAEADSLHPAVLRLIRLTVEGAERHGRWVGVCGGIAGDPFGAALLTGLGVRELSMTPRDI 807 A + LHPAVLRLI+ T + A+R V VCG +AGDP A LL GLG+R+LSM+ ++ Sbjct: 496 AHLYNPLHPAVLRLIQFTTQAAQRANIPVSVCGEMAGDPRYAPLLLGLGLRDLSMSTSNL 555 Query: 808 PAVKDRLRGSDLSALKDAAQRALD-CETADAVRALDG 843 P VK+R+R DL+A + A+ ++ ++ + LDG Sbjct: 556 PVVKNRIRSLDLAAAETLARTVMEQTDSGKIGQLLDG 592 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: 1265 Number of extensions: 82 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: 596 Length adjustment: 39 Effective length of query: 807 Effective length of database: 557 Effective search space: 449499 Effective search space used: 449499 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: 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