Align N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized)
to candidate 1937187 b3947 fused predicted PTS enzymes: Hpr component/enzyme I component/enzyme IIA component (NCBI)
Query= reanno::pseudo3_N2E3:AO353_04460 (838 letters) >FitnessBrowser__Keio:1937187 Length = 833 Score = 348 bits (894), Expect = e-100 Identities = 214/671 (31%), Positives = 343/671 (51%), Gaps = 25/671 (3%) Query: 183 GLHARPAALIRQTAHLFNSKSQLHF--AGKSASCDSLIGLMGLGIGEQDEVQVSCKGADA 240 G+HARPA+ + + F+S+ + H + + S + L+G D Q+ GAD Sbjct: 14 GVHARPASHVETLCNTFSSQIEWHNLRTDRKGNAKSALALIGTDTLAGDNCQLLISGADE 73 Query: 241 KAALQALLNALSTAVNDDSHAAAPT---------PIAQRTRTAEAGVLNGVCAAPGLVGG 291 + A Q L L ++ H AP P+ ++ G GG Sbjct: 74 QEAHQRLSQWLR---DEFPHCDAPLAEVKSDELEPLPVSLTNLNPQIIRARTVCSGSAGG 130 Query: 292 PLFQLAAIPLPEDTGKHNAEEQLQALDRALEQVRSEIRETLSHAKKHKHTEEEQIFAAHL 351 L ++++ L G A + + A ALE + + + + I AH Sbjct: 131 ILTPISSLDL-NALGNLPAAKGVDAEQSALENGLTLVLKNIEFRLLDSDGATSAILEAHR 189 Query: 352 ALLEDPALLEAAIQSIDQGSAATHAWSQSIEAQCEVLQQLGNPLLAERANDLRDLRQRVL 411 +L D +L E + + G + A S CE + + L ERA D+RD+ ++L Sbjct: 190 SLAGDTSLREHLLAGVSAGLSCAEAIVASANHFCEEFSRSSSSYLQERALDVRDVCFQLL 249 Query: 412 RALLGQDWHYDVPAG----AIVAAHELTPSDLLQLSQQGVAGLCMAEGGATSHVAILARG 467 + + G+ + P AI A ELTPS L+L + + GL + GG TSH ILAR Sbjct: 250 QQIYGEQ-RFPAPGKLTQPAICMADELTPSQFLELDKNHLKGLLLKSGGTTSHTVILARS 308 Query: 468 KGLPCLVALSASLLQQPQGQSVVLDADGGRLELTPDSQRLEQVAQAQREHLQRRERQQAQ 527 +P LV + L Q Q++ +D + G + + P Q R RE+Q+ Sbjct: 309 FNIPTLVGVDIDALTPWQQQTIYIDGNAGAIVVEPGEAVARYYQQEARVQDALREQQRVW 368 Query: 528 AHTPAHTRDGLRIEVAANVASSNEAADALKGGADGVGLLRTEFLFVDRQTAPDEQEQRQA 587 A T DG+RIE+AAN+A S EA A GA+GVGL RTE L++DR +AP E E Sbjct: 369 LTQQARTADGIRIEIAANIAHSVEAQAAFGNGAEGVGLFRTEMLYMDRTSAPGESELYNI 428 Query: 588 YQAVLDAMGDKSVIIRTIDVGGDKQLDYLPLPAEANPVLGLRGIRMAQVRPELLDQQLRA 647 + L++ +S+I+RT+D+GGDK +DYL +PAEANP LG R +R+ + L QLR+ Sbjct: 429 FCQALESANGRSIIVRTMDIGGDKPVDYLNIPAEANPFLGYRAVRIYEEYASLFTTQLRS 488 Query: 648 LLQVSPLQRCRILLPMVTEVDELLYIRQRLDALCAEL-----ALTQRLELGVMIEVPAAA 702 +L+ S +I++PM++ ++E+L+++++L +L ++++LG+M+EVP+ Sbjct: 489 ILRASAHGSLKIMIPMISSMEEILWVKEKLAEAKQQLRNEHIPFDEKIQLGIMLEVPSVM 548 Query: 703 LLAEQLAEHADFLSIGTNDLSQYTLAMDRDHAGLAARVDALHPALLRLIAQTCIGAAKHQ 762 + +Q E DF SIG+NDL+QY LA+DRD+A + ++L+PA LR + + Sbjct: 549 FIIDQCCEEIDFFSIGSNDLTQYLLAVDRDNAKVTRHYNSLNPAFLRALDYAVQAVHRQG 608 Query: 763 RWVGVCGALASDPLATPVLIGLGISELSVSPPQVGEIKERVRQLDAADCRRFSATLLNLS 822 +W+G+CG L + P+L+GLG+ ELS+S P + K R+ QLD+ +CR+ + Sbjct: 609 KWIGLCGELGAKGSVLPLLVGLGLDELSMSAPSIPAAKARMAQLDSRECRKLLNQAMACR 668 Query: 823 SATAVRHACHQ 833 ++ V H Q Sbjct: 669 TSLEVEHLLAQ 679 Lambda K H 0.318 0.133 0.379 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: 1342 Number of extensions: 58 Number of successful extensions: 4 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: 838 Length of database: 833 Length adjustment: 42 Effective length of query: 796 Effective length of database: 791 Effective search space: 629636 Effective search space used: 629636 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