Align Fructose PTS system (E-I, HPr, and E-IIA components) (characterized)
to candidate WP_057508246.1 ABB28_RS08640 phosphoenolpyruvate--protein phosphotransferase
Query= reanno::azobra:AZOBR_RS32325 (846 letters) >NCBI__GCF_001431535.1:WP_057508246.1 Length = 585 Score = 300 bits (769), Expect = 1e-85 Identities = 206/566 (36%), Positives = 299/566 (52%), Gaps = 22/566 (3%) Query: 277 PLPAVPGIAASPGLAIGPVHVLPRAAVSVPDE---PVPLIEGGDRLHEALSLTRQNLKAL 333 P+ + G AS G A+G V A+ V ++ P + + RLH AL R + L Sbjct: 15 PVQLLSGHGASRGTALGRARVRLAHALEVAEQRVAPQQVDKELKRLHVALDAARNEMHDL 74 Query: 334 ADDTARRLGPSEAAIFAAQAEILNDTDLVTLACQLMVEG-HGVAWSWHQAVERTAAGLAA 392 L A +L+D +L+ +L+ G + ++ +R A Sbjct: 75 RQRLQGALNQEAGEFLDLHALLLDDPELLFGLDELIRSGPYSAGYALRLQRDRLAKVFDG 134 Query: 393 LDNPVLAARAADLRDVGQRVLARIDPALRTGGAPDLPDTPCILIAEDLSPSDTAALDMAR 452 +D+ L +R DL V R+ A + P L + IL+ ++++PS+ A L Sbjct: 135 MDDAYLKSRMDDLDHVIGRIHAFLQPVLPPAVKGLAGE---ILVCDNIAPSEMAQLQSQG 191 Query: 453 VIGLATAQGGPTSHTAILARTLGLPAMVAGGAALMELANGTPAILDGQSGRLHLSPAAAD 512 V+ + T G SH+AILAR+L LP +V L ++++G I+DG G + ++P A + Sbjct: 192 VVAIVTTAGSALSHSAILARSLHLPLIVNVPGLLHKVSDGDVLIVDGSDGSITVNPQAEN 251 Query: 513 IADARAWIAREEARKAEEEAR-RGLPARTRDGHEVEIGANVNRPDQVAVALSQGAESVGL 571 + D R + +E AR+ E R R P+RTRD ++ + AN + V A + GA+ +GL Sbjct: 252 LRDYRVRL-KEHAREQRELGRLRSKPSRTRDQVDIALLANAESLEDVTQAHAFGAQGLGL 310 Query: 572 MRTEFLFLERGDAPGEDEQYETYRGMLTALEGRPLIVRALDIGGDK-QVPHLQLPHEENP 630 RTEFLFL+R + P E+EQ+ TYR + GR + +R LD+G DK L L +EENP Sbjct: 311 YRTEFLFLQRNELPDEEEQFHTYRDAALGMAGRLVTIRTLDLGADKADRTGLTLSNEENP 370 Query: 631 FLGVRGARLLLRRPELLETQLRALYRAAKDGGAKDGGALSIMFPMITALGEVQALRAACE 690 LG+RG RL L RP + +TQLRA+ RA+ G + I+ PM++ E+ A+R Sbjct: 371 ALGLRGVRLSLARPLVADTQLRAILRASAYGKVR------ILIPMVSTREELLAVRRRMT 424 Query: 691 RIRAELDAPA------VPLGIMVEVPAAAIQADVLARHVDFFSIGTNDLTQYALAIDRQH 744 R+ A+L A VPLG M+EVPAAA + VDF SIGTNDL QY LA DR + Sbjct: 425 RLTAQLRAEGHAVSERVPLGAMIEVPAAAFALESFIDLVDFLSIGTNDLVQYLLAADRNN 484 Query: 745 PELAAEADSLHPAVLRLIRLTVEGAERHGRWVGVCGGIAGDPFGAALLTGLGVRELSMTP 804 L LHPAVLRL++L +E +RH V VCG IAGD A LL LG+ E S+ P Sbjct: 485 EALGELYSPLHPAVLRLLKLVIETGQRHQIPVAVCGEIAGDARLAPLLLALGLTEFSLHP 544 Query: 805 RDIPAVKDRLRGSDLSALKDAAQRAL 830 + V+ +R SDL L+ A + L Sbjct: 545 GTLLEVRRAIRESDLGELRARAPKLL 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: 1047 Number of extensions: 43 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: 846 Length of database: 585 Length adjustment: 39 Effective length of query: 807 Effective length of database: 546 Effective search space: 440622 Effective search space used: 440622 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 Sep 24 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