Align N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized)
to candidate 16515 b2416 PEP-protein phosphotransferase of PTS system (enzyme I) (NCBI)
Query= reanno::BFirm:BPHYT_RS02740 (854 letters) >FitnessBrowser__Keio:16515 Length = 575 Score = 355 bits (912), Expect = e-102 Identities = 207/556 (37%), Positives = 314/556 (56%), Gaps = 15/556 (2%) Query: 293 LAGVCAAPGVAVGK--LVRWDDADIDPPEKANGTSAAESRLLDKAIATVDADLDTTVRDA 350 ++G+ A+PG+A GK L++ D+ ID + + E A A L+T A Sbjct: 2 ISGILASPGIAFGKALLLKEDEIVIDRKKISADQVDQEVERFLSGRAKASAQLETIKTKA 61 Query: 351 SQRGAVGEAGIFSVHRVLLEDPTLLDAARDLISLGK----SAGFAWREAIRAQIAILTNI 406 + + IF H +LLED L +++I+L K +A A E I Q + L + Sbjct: 62 GETFGEEKEAIFEGHIMLLEDEEL---EQEIIALIKDKHMTADAAAHEVIEGQASALEEL 118 Query: 407 EDALLAERAADLRDIEKRVLR-ALGYTSATARTLPEEAVLAAEEFTPSDLSTLDRSRVTA 465 +D L ERAAD+RDI KR+LR LG + +E +L A + TPS+ + L+ +V Sbjct: 119 DDEYLKERAADVRDIGKRLLRNILGLKIIDLSAIQDEVILVAADLTPSETAQLNLKKVLG 178 Query: 466 LVMARGGATSHAAILARQAGIPALVAVGDALHAIPEGTQVVVNATTGRLEFAPTELDVER 525 + GG TSH +I+AR +PA+V G + ++++A ++ PT +++ Sbjct: 179 FITDAGGRTSHTSIMARSLELPAIVGTGSVTSQVKNDDYLILDAVNNQVYVNPTNEVIDK 238 Query: 526 ARLERTRLADVREANRRTSQQAAVTSDGRAIEVAANIATLDDAKTAVENGADSVGLLRTE 585 R + ++A + + A+T DG +EV ANI T+ D + A NGA+ VGL RTE Sbjct: 239 MRAVQEQVASEKAELAKLKDLPAITLDGHQVEVCANIGTVRDVEGAERNGAEGVGLYRTE 298 Query: 586 LLFIHRAAAPTTDEHRQSYQAIVDALSGRTAIIRTLDVGADKEVDYLTLPPEPNPALGLR 645 LF+ R A PT +E +Y+A+ +A + I+RT+D+G DKE+ Y+ P E NP LG R Sbjct: 299 FLFMDRDALPTEEEQFAAYKAVAEACGSQAVIVRTMDIGGDKELPYMNFPKEENPFLGWR 358 Query: 646 GIRLAQVRPDLLDDQLRGLLAVQPLGAVRILLPMVTDVGELIRIRKRIDEFAREL---GR 702 IR+A R ++L DQLR +L G +RI+ PM+ V E+ +RK I+ + +EL G+ Sbjct: 359 AIRIAMDRREILRDQLRAILRASAFGKLRIMFPMIISVEEVRALRKEIEIYKQELRDEGK 418 Query: 703 T--EPIEVGVMIEVPSAALLADQLAQHADFLSIGTNDLTQYTLAMDRCQADLAAQADGLH 760 E IE+GVM+E P+AA +A LA+ DF SIGTNDLTQYTLA+DR ++ + Sbjct: 419 AFDESIEIGVMVETPAAATIARHLAKEVDFFSIGTNDLTQYTLAVDRGNDMISHLYQPMS 478 Query: 761 PAVLRLIAATVQGADKHGKWVGVCGALAGDPLAMPLLVGLGVTELSVDPVSVPGIKARVR 820 P+VL LI + + GKW G+CG LAGD A LL+G+G+ E S+ +S+P IK +R Sbjct: 479 PSVLNLIKQVIDASHAEGKWTGMCGELAGDERATLLLLGMGLDEFSMSAISIPRIKKIIR 538 Query: 821 NLDYQLCRQRAQDALA 836 N +++ + A+ ALA Sbjct: 539 NTNFEDAKVLAEQALA 554 Lambda K H 0.317 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: 891 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: 854 Length of database: 575 Length adjustment: 39 Effective length of query: 815 Effective length of database: 536 Effective search space: 436840 Effective search space used: 436840 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: 54 (25.4 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