Align The fructose-specific PTS Enzyme IIABC FruA (characterized)
to candidate WP_067471936.1 BJL86_RS06275 PTS transporter subunit EIIA
Query= TCDB::Q0S1N2 (700 letters) >NCBI__GCF_001659785.1:WP_067471936.1 Length = 726 Score = 678 bits (1749), Expect = 0.0 Identities = 369/698 (52%), Positives = 467/698 (66%), Gaps = 33/698 (4%) Query: 14 IISEDLISLDTDLGASKEDVISALSRRLADAGRATEADALRDAALARESQSATGLPGGIA 73 +I + LD DLG +KE V+ L+ D GRA + D +A LARE ++ATG+ GG A Sbjct: 6 LIETGTVRLDADLGDNKEGVLRTLAGAFVDTGRANDLDGAVEALLAREEKAATGMKGGFA 65 Query: 74 IPHCRSEAVVAASLGFARLAPKVDFGAPDGPADLVFLIAAPEGAGAEHMKLLSSLARALV 133 IPHC+S A+ SL FARL+ VDFGA DGPADLVF++ AP+G G H+K+LS LAR+LV Sbjct: 66 IPHCKSAAIDTPSLAFARLSNPVDFGAADGPADLVFMLGAPDGEGKAHLKMLSKLARSLV 125 Query: 134 RPAFVGALRDAKTPAEIVTLVNDVLAPAPAA--------TPAAAAPAAAAAAAPAAAAAV 185 R FV +LR +T +E V ++ D + P + T AA A AA AA A AA Sbjct: 126 RKDFVESLRQVETDSEAVKIILDAVEDKPKSDGGSGSEDTAAAGAAGAAGAATVGAGAAA 185 Query: 186 PAPKPEPVAPEKEPEPEVGPKHIVAVTACPTGIAHTYMAADSLVAAGERAGVVVHVETQG 245 + IVAVT+C TGIAHTYMAAD+L + G+ VE QG Sbjct: 186 AGASASAGIDDSGSAKVDDAVRIVAVTSCATGIAHTYMAADALTQTAKDKGIDFAVEPQG 245 Query: 246 SSGSTPLAPGVIAGASAVIFATDVGVKGKERFAGKPVVASGVKRAINEPDTMITEALRAG 305 SSG+TPL I A AVIFATDVGV+ K RFAGKPVV VKR I+ P+ M+ +A++A Sbjct: 246 SSGTTPLTAEQIDKADAVIFATDVGVRDKGRFAGKPVVEGPVKRGIDAPEKMLDDAVKAA 305 Query: 306 MNPSAAIVDAGSAGSAADEPAGSIG--WGTHLRQVLLTGVSYMIPFVAAGGLLIALGFLL 363 +P+A V A S G G W L++ +++GVSYMIPFVAAGGLL+ALGFL Sbjct: 306 RDPNATRVKAASGSGEESASGGGKGEHWARTLQRGVMSGVSYMIPFVAAGGLLMALGFLF 365 Query: 364 GGYEISGPAEDIVLSNSLGQLP-------EG---------------GLATYLGAVLFQLG 401 GGY+++G +DIV + SL LP EG G+ Y+G V F +G Sbjct: 366 GGYDMAGVYQDIVTTYSLTDLPPQLFTDGEGLVAAGASGAEALDRTGMMLYMGVVFFAIG 425 Query: 402 SLAFSFLVPALAGYIAFAIADRPGLAPGFTAGAVAVFVGAGFIGGLVGGLIAGVVALWIS 461 A SF++P L+GYIA IADRPGLAPGF GA+++ + AGF+G L+ G++AG + W+S Sbjct: 426 QAAMSFMIPVLSGYIAMGIADRPGLAPGFVGGAISLTLDAGFLGALITGILAGFLMRWMS 485 Query: 462 RIPVPQWLRGLMPVVIIPLFATLIVGALMFLVLGRPLASITSGLTNWLNGLSGSSVIFLG 521 VP WLRGLMPVV+ PL +LI+G +MFL+LG+P+A + LT+ L+ +SGSS I LG Sbjct: 486 SWSVPSWLRGLMPVVLFPLLGSLIIGLVMFLLLGQPIAWLMETLTDGLSSMSGSSAILLG 545 Query: 522 IILGLMMCFDLGGPVNKAAYAFAVAGLNVNDPASLRIMAAVMAAGMVPPLAMALASTVLR 581 +ILGLMMCFDLGGPVNKAAY FA AGL V++P++LRIMAAVMAAGMVPP+A+++A T +R Sbjct: 546 LILGLMMCFDLGGPVNKAAYVFATAGLVVDEPSTLRIMAAVMAAGMVPPIALSIA-TFVR 604 Query: 582 PSLFSEAERENGKAAWLLGSAFISEGAIPFAAADPLRVIPSMMAGGAVTGALIMAFDVTL 641 LF+ AERENG+AAWLLG +FISEGAIPFAAADPLRVIPSMM GGA TGAL MAF V Sbjct: 605 KHLFTPAERENGRAAWLLGLSFISEGAIPFAAADPLRVIPSMMLGGATTGALSMAFSVES 664 Query: 642 SAPHGGIFVFFAIGNLLWFLVALAAGVVVAALCVVGAK 679 APHGGIFV FAI + + V++ AGVVV+ + VV AK Sbjct: 665 YAPHGGIFVIFAIHPIWGYFVSILAGVVVSTIAVVIAK 702 Lambda K H 0.320 0.136 0.395 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: 1379 Number of extensions: 66 Number of successful extensions: 5 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: 700 Length of database: 726 Length adjustment: 39 Effective length of query: 661 Effective length of database: 687 Effective search space: 454107 Effective search space used: 454107 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 (21.8 bits) S2: 55 (25.8 bits)
This GapMind analysis is from Sep 24 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