Align N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized)
to candidate PP_0793 PP_0793 Phosphotransferase system, fructose-specific EI/HPr/EIIA components
Query= reanno::BFirm:BPHYT_RS02740 (854 letters) >FitnessBrowser__Putida:PP_0793 Length = 950 Score = 453 bits (1166), Expect = e-131 Identities = 282/672 (41%), Positives = 389/672 (57%), Gaps = 19/672 (2%) Query: 181 QVTLVHAGGLHARPAARAREAARGFDARVEVRYEGRK---AAIESVVGLLGLGAGEGATV 237 +V L + GLHARPA + A+GF+ + VR +++S+ LL LGA G + Sbjct: 286 RVVLANPHGLHARPAKVLAQLAKGFEGEIRVRLVDSAQPAVSVKSLSKLLSLGARRGQAL 345 Query: 238 ELLGMGPQAAAAVAAIANELTREAHGEVEEKP---ARQSSPAPQAVARPAGETLAPNTLA 294 EL+ AA A+ + + + EVE P A + P+ + PA A + + Sbjct: 346 ELVAEPSIAADALPVLLAAIEQGLGEEVEPLPQSVAPIADDVPEVLQAPA----AGSRIQ 401 Query: 295 GVCAAPGVAVGKLVRWDDADIDPPEKANGTSAAESRLLDKAIATVDADLDTTVRDASQRG 354 GV AAPG+A G + + D P + + A E + L +A+ATV+ +L V + + Sbjct: 402 GVGAAPGIASGPAHVCVEREFDYPLRGE-SCALERQKLREALATVNGELQALVLRSDK-- 458 Query: 355 AVGEAGIFSVHRVLLEDPTLLDAARDLISLGKSAGFAWREAIRAQIAILTNIEDALLAER 414 A+GE IF H+ +L DP L D ++ G+SA AW I A + DALLAER Sbjct: 459 AIGE--IFVTHQEMLADPALTDDVEQRLAQGESAAAAWMAVIEAAARQQEALHDALLAER 516 Query: 415 AADLRDIEKRVLRALGYTSATARTLPEEA-VLAAEEFTPSDLSTLDRSRVTALVMARGGA 473 AADLRDI +RVL L A+ PE+ VL E PSD++ LD +RV +V A+GGA Sbjct: 517 AADLRDIGRRVLAQL--CGVQAQVEPEQPYVLVMTEVGPSDVARLDPNRVAGIVTAQGGA 574 Query: 474 TSHAAILARQAGIPALVAVGDALHAIPEGTQVVVNATTGRLEFAPTELDVERARLERTRL 533 T+H+AI+AR GIPA+V G ++ + GT ++++ G + AP +++RA ER Sbjct: 575 TAHSAIVARALGIPAVVGAGASILLLESGTPLLLDGQRGVVSVAPPADELQRALAERDLR 634 Query: 534 ADVREANRRTSQQAAVTSDGRAIEVAANIATLDDAKTAVENGADSVGLLRTELLFIHRAA 593 +A + A+T DG A+EV ANI + VE GA+ VGLLRTEL+F+ Sbjct: 635 EQRLQAAWANRFEPAITRDGHAVEVFANIGDSNGIAKVVEQGAEGVGLLRTELIFMAHPQ 694 Query: 594 APTTDEHRQSYQAIVDALSGRTAIIRTLDVGADKEVDYLTLPPEPNPALGLRGIRLAQVR 653 AP Y+ ++D L GR ++RTLDVG DK + Y + E NP LG+RG+RL R Sbjct: 695 APDVATQEAEYRRVLDGLDGRPLVVRTLDVGGDKPLPYWPIAAEENPFLGVRGVRLTLQR 754 Query: 654 PDLLDDQLRGLLAVQPLGAVRILLPMVTDVGELIRIRKRIDEFARELGRTEPIEVGVMIE 713 P +++DQLR LL +RI+ PMV V E R ++ E+ + +++G+M+E Sbjct: 755 PQVMEDQLRALLRAADQRPLRIMFPMVGQVHEWREARAMVERLRAEIPVAD-LQLGIMVE 813 Query: 714 VPSAALLADQLAQHADFLSIGTNDLTQYTLAMDRCQADLAAQADGLHPAVLRLIAATVQG 773 VPSAALLA QLA+ DF SIGTNDLTQYTLA+DR L+AQADGLHPAVL LI TV+ Sbjct: 814 VPSAALLAAQLAREVDFFSIGTNDLTQYTLAIDRGHPSLSAQADGLHPAVLSLIDMTVRA 873 Query: 774 ADKHGKWVGVCGALAGDPLAMPLLVGLGVTELSVDPVSVPGIKARVRNLDYQLCRQRAQD 833 A HGKWVGVCG LA DP A+ +L+GL V ELSV S+ +KA VR D+Q R A++ Sbjct: 874 AHAHGKWVGVCGELAADPQAVAVLLGLDVDELSVSARSIAEVKALVRQADHQTARALARE 933 Query: 834 ALALESAQAVRA 845 AL +SA AVRA Sbjct: 934 ALQQDSAAAVRA 945 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: 1746 Number of extensions: 85 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: 950 Length adjustment: 43 Effective length of query: 811 Effective length of database: 907 Effective search space: 735577 Effective search space used: 735577 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: 56 (26.2 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