Align PTS system, IIABC components (characterized, see rationale)
to candidate BWI76_RS16295 BWI76_RS16295 bifunctional PTS system maltose and glucose-specific transporter subunits IICB
Query= uniprot:Q836Y6 (722 letters) >FitnessBrowser__Koxy:BWI76_RS16295 Length = 530 Score = 223 bits (567), Expect = 2e-62 Identities = 169/554 (30%), Positives = 270/554 (48%), Gaps = 46/554 (8%) Query: 3 KMFSFEFWQKFGKALMVVVAVMPAAGLMISIGKSLPLIDP-------NLGLLVTTGGVLE 55 K+ +EF+Q+ GK M+ VA++ G+M+ IG SL D ++ LL + Sbjct: 8 KITLWEFFQQLGKTFMLPVALLSFCGIMLGIGSSLSSHDVLTLLPWLDVPLLQAVFIWMG 67 Query: 56 SIGWAIIGNLHLLFALAIGGSWAKDRAG-GAFAAGISFVLINRITGAIFGVTNEMLADEQ 114 +G L ++F +AI A++ G AFA + + ++N + + Sbjct: 68 KVGSFAFSFLPVMFCIAIPLGLARENKGVAAFAGFVGYAVMNLAVNFWLTAKGILPTTDA 127 Query: 115 AFTHTLFGTKIMVKGFFTSVLEAPALNMGVFVGIIAGFVGAMAYNKYYNYRKLPDALSFF 174 A ++ +++ +++ G+ +IAG + M + +++N R LPDAL+FF Sbjct: 128 A---------VLKANNIQNIIGIQSIDTGILGAVIAGIIVWMLHERFHNIR-LPDALAFF 177 Query: 175 NGKRFVPFVVILWSTIVSIALALIWPNIQAGINNFGLWIAQSQDSAPILAPFLYGTLERL 234 G RFVP + + +V + + LIWP GIN G Q +SA P ++GT ERL Sbjct: 178 GGTRFVPIITTVVLGLVGLVIPLIWPVFAMGINALG----QVINSAGDFGPMIFGTGERL 233 Query: 235 LLPFGLHHMLTIPINYTQLGGTYEILSGAQAGTQVFGQDPLWLAWATDLVNLKGAGDMSK 294 LLPFGLHH+L I +T+ GGT ++ + +G Q L G + S Sbjct: 234 LLPFGLHHILVALIRFTEAGGTMDVCGHSVSGALTIFQAQL------SCPTTHGFSE-SA 286 Query: 295 YQFVLENWTPARFKVGQMIGSSGILMGMALAMYRNVDADKKAKYKSMYFSAALAVFLTGV 354 +F+ + G+M G L G ALAMY + + K K + S +A + G Sbjct: 287 TRFLSQ---------GKMPAFLGGLPGAALAMYHCARPENRHKIKGLLISGVIACVVGGT 337 Query: 355 TEPLEFMFMFAAVPLYVIYAVIQGAAFAMADILPLRV-HSFGNIELLTRTPLAIKAGLGG 413 TEPLEF+F+F A LYVI+A++ G F M IL + + ++ GN+ + I GL Sbjct: 338 TEPLEFLFLFVAPVLYVIHALLTGLGFTMMAILGVTIGNTDGNV--IDFVVFGILHGLST 395 Query: 414 DLINFVLMVIIFGVVTYFLANFLIKKFNYATPGRNGNYDNDNSEEIASGAAGSGVVDQQI 473 ++ I+ V Y + F I +FN TPGR+ N E+ +G G + Sbjct: 396 KWYLVPVVAAIWFAVYYGIFRFAITRFNLKTPGRDIE-TNSAFEKAVTGVTGKS--GYNV 452 Query: 474 AQIVYLLGGKQNIKEVDACMTRLRVSVKDREKVGSEEAWKRAGAMGLI-VKDNGVQAVYG 532 I+ LGG +NI +D C+TRLR+SV D KV S A K A+G++ + + +Q V G Sbjct: 453 PAILAALGGAENIVSLDNCITRLRLSVNDMSKVDS-AALKANRAIGVVQLNQHNLQVVIG 511 Query: 533 PKADVLKSDIEDLL 546 P+ +K ++ L+ Sbjct: 512 PQVQSVKDEMAVLM 525 Lambda K H 0.322 0.138 0.404 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: 923 Number of extensions: 39 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: 722 Length of database: 530 Length adjustment: 37 Effective length of query: 685 Effective length of database: 493 Effective search space: 337705 Effective search space used: 337705 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 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