Align N-acetylglucosamine-specific PTS system, IIBC components (nagE) (characterized)
to candidate 15742 b1621 fused maltose and glucose-specific PTS enzymes: IIB component -! IIC component (NCBI)
Query= reanno::BFirm:BPHYT_RS02745 (591 letters) >FitnessBrowser__Keio:15742 Length = 530 Score = 291 bits (745), Expect = 5e-83 Identities = 190/514 (36%), Positives = 271/514 (52%), Gaps = 65/514 (12%) Query: 10 QRLGRALMLPIAVLPVAGLLLRLGQP----DVFNI-------------KMIADAGGAIFD 52 Q+LG+ MLP+A+L G++L +G DV + ++ G F Sbjct: 16 QQLGKTFMLPVALLSFCGIMLGIGSSLSSHDVITLIPVLGNPVLQAIFTWMSKIGSFAFS 75 Query: 53 NLPLLFAIGVAVGFAKDNNGVAGLAGAIGYLI------------------EVAVMKDIN- 93 LP++F I + +G A++N GVA AG IGY + + AV+K N Sbjct: 76 FLPVMFCIAIPLGLARENKGVAAFAGFIGYAVMNLAVNFWLTNKGILPTTDAAVLKANNI 135 Query: 94 ------DKLNMGVLSGIVAGIVAGLLYNRYKDIKLPDYLAFFGGKRFVPIVTGVVCLVLG 147 ++ G+L ++AGI+ +L+ R+ +I+LPD LAFFGG RFVPI++ +V ++G Sbjct: 136 QSILGIQSIDTGILGAVIAGIIVWMLHERFHNIRLPDALAFFGGTRFVPIISSLVMGLVG 195 Query: 148 IAFGYVWQPVQAVIDTAGHWLTTAGALGAFVFGVLNRLLLVTGLHHILNSLTWFV-FGTF 206 + VW I GH + +AG G +FG RLLL GLHHIL +L F G Sbjct: 196 LVIPLVWPIFAMGISGLGHMINSAGDFGPMLFGTGERLLLPFGLHHILVALIRFTDAGGT 255 Query: 207 TPPGGAAVTGDLHRFFA--GDPTAGTF--------MTGFFPVMMFGLPAACLAMFHEAPK 256 G V+G L F A PT F G P + GLP A LAM+H A Sbjct: 256 QEVCGQTVSGALTIFQAQLSCPTTHGFSESATRFLSQGKMPAFLGGLPGAALAMYHCARP 315 Query: 257 ERRAVVGGLLFSMALTSFLTGVTEPIEFSFMFLAPVLYVIHALLTGISLAICSALGIHLG 316 E R + GLL S + + G TEP+EF F+F+APVLYVIHALLTG+ + S LG+ +G Sbjct: 316 ENRHKIKGLLISGLIACVVGGTTEPLEFLFLFVAPVLYVIHALLTGLGFTVMSVLGVTIG 375 Query: 317 FTFSAGAIDYV---LNYGLSTRGWWAIP-IGLVYMVVYYGLFRFFIRKFNMATPGREPAA 372 T ID+V + +GLST+ W+ +P + ++ VVYY +FRF I +FN+ TPGR+ Sbjct: 376 NT-DGNIIDFVVFGILHGLSTK-WYMVPVVAAIWFVVYYVIFRFAITRFNLKTPGRDSEV 433 Query: 373 ADEQVDSFAAGGFVSPVAGTAVPRAQRYIAALGGASNLSVVDACTTRLRLSVVDSNKVSE 432 A ++ AG G + + ALGGA N+ +D C TRLRLSV D + V+ Sbjct: 434 A-SSIEKAVAG-----APGKSGYNVPAILEALGGADNIVSLDNCITRLRLSVKDMSLVNV 487 Query: 433 NELKTIGARGVLKRGSTNVQVIIGPEADIIADEI 466 LK A GV++ N+QV+IGP+ + DE+ Sbjct: 488 QALKDNRAIGVVQLNQHNLQVVIGPQVQSVKDEM 521 Score = 35.8 bits (81), Expect = 5e-06 Identities = 26/90 (28%), Positives = 43/90 (47%), Gaps = 4/90 (4%) Query: 491 AAPVAASVAQGSGPLDPDPLRWLAVFGGAGNVLSLDAIAATRLRIVVRDPSAVDRQRL-- 548 A+ + +VA G + L GGA N++SLD TRLR+ V+D S V+ Q L Sbjct: 434 ASSIEKAVAGAPGKSGYNVPAILEALGGADNIVSLDN-CITRLRLSVKDMSLVNVQALKD 492 Query: 549 -ATLDTAWISADTFHIVVGDAAQRYAEKLA 577 + ++ +V+G Q +++A Sbjct: 493 NRAIGVVQLNQHNLQVVIGPQVQSVKDEMA 522 Lambda K H 0.325 0.141 0.426 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: 986 Number of extensions: 52 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 591 Length of database: 530 Length adjustment: 36 Effective length of query: 555 Effective length of database: 494 Effective search space: 274170 Effective search space used: 274170 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 53 (25.0 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