Align N-acetylglucosamine-specific PTS system, IIBC components (nagE) (characterized)
to candidate BWI76_RS16295 BWI76_RS16295 bifunctional PTS system maltose and glucose-specific transporter subunits IICB
Query= reanno::BFirm:BPHYT_RS02745 (591 letters) >FitnessBrowser__Koxy:BWI76_RS16295 Length = 530 Score = 295 bits (754), Expect = 4e-84 Identities = 193/518 (37%), Positives = 276/518 (53%), Gaps = 65/518 (12%) Query: 10 QRLGRALMLPIAVLPVAGLLLRLGQP----DVFNIKMIADA-------------GGAIFD 52 Q+LG+ MLP+A+L G++L +G DV + D G F Sbjct: 16 QQLGKTFMLPVALLSFCGIMLGIGSSLSSHDVLTLLPWLDVPLLQAVFIWMGKVGSFAFS 75 Query: 53 NLPLLFAIGVAVGFAKDNNGVAGLAGAIGYLI------------------EVAVMKDIN- 93 LP++F I + +G A++N GVA AG +GY + + AV+K N Sbjct: 76 FLPVMFCIAIPLGLARENKGVAAFAGFVGYAVMNLAVNFWLTAKGILPTTDAAVLKANNI 135 Query: 94 ------DKLNMGVLSGIVAGIVAGLLYNRYKDIKLPDYLAFFGGKRFVPIVTGVVCLVLG 147 ++ G+L ++AGI+ +L+ R+ +I+LPD LAFFGG RFVPI+T VV ++G Sbjct: 136 QNIIGIQSIDTGILGAVIAGIIVWMLHERFHNIRLPDALAFFGGTRFVPIITTVVLGLVG 195 Query: 148 IAFGYVWQPVQAVIDTAGHWLTTAGALGAFVFGVLNRLLLVTGLHHILNSLTWFV-FGTF 206 + +W I+ G + +AG G +FG RLLL GLHHIL +L F G Sbjct: 196 LVIPLIWPVFAMGINALGQVINSAGDFGPMIFGTGERLLLPFGLHHILVALIRFTEAGGT 255 Query: 207 TPPGGAAVTGDLHRFFA--GDPTAGTF--------MTGFFPVMMFGLPAACLAMFHEAPK 256 G +V+G L F A PT F G P + GLP A LAM+H A Sbjct: 256 MDVCGHSVSGALTIFQAQLSCPTTHGFSESATRFLSQGKMPAFLGGLPGAALAMYHCARP 315 Query: 257 ERRAVVGGLLFSMALTSFLTGVTEPIEFSFMFLAPVLYVIHALLTGISLAICSALGIHLG 316 E R + GLL S + + G TEP+EF F+F+APVLYVIHALLTG+ + + LG+ +G Sbjct: 316 ENRHKIKGLLISGVIACVVGGTTEPLEFLFLFVAPVLYVIHALLTGLGFTMMAILGVTIG 375 Query: 317 FTFSAGAIDYV---LNYGLSTRGWWAIP-IGLVYMVVYYGLFRFFIRKFNMATPGREPAA 372 T ID+V + +GLST+ W+ +P + ++ VYYG+FRF I +FN+ TPGR Sbjct: 376 NT-DGNVIDFVVFGILHGLSTK-WYLVPVVAAIWFAVYYGIFRFAITRFNLKTPGR---- 429 Query: 373 ADEQVDSFAAGGFVSPVAGTAVPRAQRYIAALGGASNLSVVDACTTRLRLSVVDSNKVSE 432 D + +S A V+ V G + +AALGGA N+ +D C TRLRLSV D +KV Sbjct: 430 -DIETNS-AFEKAVTGVTGKSGYNVPAILAALGGAENIVSLDNCITRLRLSVNDMSKVDS 487 Query: 433 NELKTIGARGVLKRGSTNVQVIIGPEADIIADEIRTVI 470 LK A GV++ N+QV+IGP+ + DE+ ++ Sbjct: 488 AALKANRAIGVVQLNQHNLQVVIGPQVQSVKDEMAVLM 525 Score = 36.2 bits (82), Expect = 3e-06 Identities = 23/68 (33%), Positives = 34/68 (50%), Gaps = 4/68 (5%) Query: 513 LAVFGGAGNVLSLDAIAATRLRIVVRDPSAVDRQRL---ATLDTAWISADTFHIVVGDAA 569 LA GGA N++SLD TRLR+ V D S VD L + ++ +V+G Sbjct: 456 LAALGGAENIVSLDN-CITRLRLSVNDMSKVDSAALKANRAIGVVQLNQHNLQVVIGPQV 514 Query: 570 QRYAEKLA 577 Q +++A Sbjct: 515 QSVKDEMA 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: 978 Number of extensions: 53 Number of successful extensions: 7 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