Align N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized)
to candidate H281DRAFT_02007 H281DRAFT_02007 phosphoenolpyruvate--protein phosphotransferase
Query= reanno::BFirm:BPHYT_RS02740 (854 letters) >FitnessBrowser__Burk376:H281DRAFT_02007 Length = 582 Score = 276 bits (707), Expect = 2e-78 Identities = 197/573 (34%), Positives = 288/573 (50%), Gaps = 19/573 (3%) Query: 292 TLAGVCAAPGVAVGKLVRWDDADIDPPEKANGTSAAESRL--LDKAIATVDADLDTTVRD 349 TL G+ + G+A+G+ A +D + ES + A V +LD D Sbjct: 4 TLHGIPVSRGIAIGRAYLIAPAALDVDHYLIEPAQIESEVERFRAAQQRVHEELDALRAD 63 Query: 350 ASQRGAVGEAGIF-SVHRVLLEDPTLLDAARDLISLGK-SAGFAWREAIRAQIAILTNIE 407 + A E G F +VH ++L D L+ DLI + + +A E + +IE Sbjct: 64 LAA-DAPSEMGAFINVHSMILNDAMLVQETIDLIRTRRYNVEWALTEQLERLSRHFDDIE 122 Query: 408 DALLAERAADLRDIEKRVLRALGYTSAT----ARTLPEEAVLAAEEFTPSDLSTLDRSRV 463 D L ER AD+ + +RVL+AL S + +E ++ A + P+D+ Sbjct: 123 DEYLRERKADIEQVVERVLKALAGASGSLVNGVHGACDEMIVVAHDIAPADMMQFKTQTF 182 Query: 464 TALVMARGGATSHAAILARQAGIPALVAVGDALHAIPEGTQVVVNATTGRLEFAPTELDV 523 V GG TSH AI+AR GIPA V V A I + ++V+ G + P + + Sbjct: 183 QGFVTDLGGRTSHTAIVARSLGIPAAVGVQHASALIRQDDLIIVDGDHGIVIVDPAPIVL 242 Query: 524 ERARLERTRLADVREANRRTSQQAAVTSDGRAIEVAANIATLDDAKTAVENGADSVGLLR 583 E ++ A + +R T G IE+ ANI +DA+ AV+ GA VGL R Sbjct: 243 EEYSYRQSEKALEQRKLQRLKFSPTQTLCGTRIELCANIELPEDARAAVDAGATGVGLFR 302 Query: 584 TELLFI-HRAAAPTTDEHRQSYQAIVDALSGRTAIIRTLDVGADKEVDYLT----LPPEP 638 TE LF+ H+ P +E ++Y+ V+ ++G IRT+DVGADK +D ++ Sbjct: 303 TEFLFMNHKHRMPEEEEQFEAYRRAVELMNGLPVTIRTIDVGADKPLDSMSGGDGYETAA 362 Query: 639 NPALGLRGIRLAQVRPDLLDDQLRGLLAVQPLGAVRILLPMVTDVGELIRIRKRIDEFAR 698 NPALGLR IR + P + QLR +L G V+IL+PM+ E+ + I E R Sbjct: 363 NPALGLRAIRWSLSEPQMFLTQLRAILRASAFGTVKILVPMLAHAQEIDQTLDLIREAKR 422 Query: 699 ELGRT----EP-IEVGVMIEVPSAALLADQLAQHADFLSIGTNDLTQYTLAMDRCQADLA 753 +L +P ++VG MIE+P+AA+ + DFLSIGTNDL QYTLA+DR +A Sbjct: 423 QLDDAGIAYDPNVQVGAMIEIPAAAIALPLFLKRLDFLSIGTNDLIQYTLAIDRADNSVA 482 Query: 754 AQADGLHPAVLRLIAATVQGADKHGKWVGVCGALAGDPLAMPLLVGLGVTELSVDPVSVP 813 D LHPAVL LIA T++ A + G V VCG +AGDP LL+G+G+TE S+ P + Sbjct: 483 HLYDPLHPAVLHLIAFTLREAKRAGVPVSVCGEMAGDPSLTRLLLGMGLTEFSMHPSQLL 542 Query: 814 GIKARVRNLDYQLCRQRAQDALALESAQAVRAA 846 +K V + + D LA + V+AA Sbjct: 543 VVKQEVLRSHLKTLEKPVADVLASFEPEEVQAA 575 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: 1017 Number of extensions: 52 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: 854 Length of database: 582 Length adjustment: 39 Effective length of query: 815 Effective length of database: 543 Effective search space: 442545 Effective search space used: 442545 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