Align The fructose-specific PTS Enzyme IIABC FruA (characterized)
to candidate WP_076477611.1 BW971_RS05975 PTS transporter subunit EIIA
Query= TCDB::Q0S1N2 (700 letters) >NCBI__GCF_900156495.1:WP_076477611.1 Length = 684 Score = 878 bits (2268), Expect = 0.0 Identities = 469/679 (69%), Positives = 531/679 (78%), Gaps = 35/679 (5%) Query: 14 IISEDLISLDTDLGASKEDVISALSRRLADAGRATEADALRDAALARESQSATGLPGGIA 73 II+ DL++LD D GA K +VI L RLA GR + A+ +AA+ARE+QSATGLPGGIA Sbjct: 5 IITTDLVALDVDAGAEKSEVIDFLVERLAADGRVHDTVAVNEAAMAREAQSATGLPGGIA 64 Query: 74 IPHCRSEAVVAASLGFARLAPKVDFGAPDGPADLVFLIAAPEGAGAEHMKLLSSLARALV 133 IPHCR+E V AA L FARLAP VDFGA DGPADLVFLIAAP G++HMKLLSSLARALV Sbjct: 65 IPHCRTEGVSAAGLSFARLAPAVDFGAKDGPADLVFLIAAPASGGSQHMKLLSSLARALV 124 Query: 134 RPAFVGALRDAKTPAEIVTLVNDVLAPAPAATPAAAAPAAAAAAAPAAAAAVPAPKPEPV 193 RP FV +LR+AK+ E+V LV+ + PAPA +PAAAA AA+ APA AA Sbjct: 125 RPDFVTSLRNAKSADEVVALVDQAINPAPATSPAAAAVPAASGGAPAKAAT--------- 175 Query: 194 APEKEPEPEVGPKHIVAVTACPTGIAHTYMAADSLVAAGERAGVVVHVETQGSSGSTPLA 253 +VA+TACPTGIAHTYMAAD+L A ERAGV + VETQGSS +TP Sbjct: 176 -------------RLVAITACPTGIAHTYMAADALKFAAERAGVDLVVETQGSSANTPTD 222 Query: 254 PGVIAGASAVIFATDVGVKGKERFAGKPVVASGVKRAINEPDTMITEALRAGMNPSAAIV 313 P VI A AVIFATDVGVK ++RFAGKPV+ASGVKRAINEPD MI EA+ A +P A+ V Sbjct: 223 PSVIRDADAVIFATDVGVKNRDRFAGKPVIASGVKRAINEPDVMIAEAVAAAGDPDASRV 282 Query: 314 DAGSAGSA-ADEPAGSIGWGTHLRQVLLTGVSYMIPFVAAGGLLIALGFLLGGYEIS--- 369 +A +A A G +GWGT LRQVLLTGVSYMIPFVAAGGLLIALGFLLGGY+I+ Sbjct: 283 GGDTAAAATASTAGGDLGWGTRLRQVLLTGVSYMIPFVAAGGLLIALGFLLGGYKIALAP 342 Query: 370 -GPAED-------IVLSNSLGQLPEGGLATYLGAVLFQLGSLAFSFLVPALAGYIAFAIA 421 G A+ I LSNSL LP GGLA YLGA+ F LG LAFSFLVPALAGYIA+AIA Sbjct: 343 PGSADGTEAIGKTIALSNSLWNLPSGGLAQYLGAICFTLGGLAFSFLVPALAGYIAYAIA 402 Query: 422 DRPGLAPGFTAGAVAVFVGAGFIGGLVGGLIAGVVALWISRIPVPQWLRGLMPVVIIPLF 481 DRPGLAPGFTAGAVAVFVGAGFIGGLVGGL+ G VALW+ RIP+P W RGLMPVVIIPL Sbjct: 403 DRPGLAPGFTAGAVAVFVGAGFIGGLVGGLLGGFVALWVGRIPLPAWARGLMPVVIIPLL 462 Query: 482 ATLIVGALMFLVLGRPLASITSGLTNWLNGLSGSSVIFLGIILGLMMCFDLGGPVNKAAY 541 ATL G +MFL LGRPLA + + LT+WLNGLSG+S I LGIILGLMMCFDLGGPVNKAAY Sbjct: 463 ATLATGGIMFLFLGRPLAWVNTSLTDWLNGLSGTSAIILGIILGLMMCFDLGGPVNKAAY 522 Query: 542 AFAVAGLNVNDPASLRIMAAVMAAGMVPPLAMALASTVLRPSLFSEAERENGKAAWLLGS 601 AFAV GL+ DPA LRIMAAVMAAGMVPPLA+ALA T LRP LF+E ERENGKAAWLLG+ Sbjct: 523 AFAVQGLSSGDPAQLRIMAAVMAAGMVPPLALALA-TALRPRLFTEPERENGKAAWLLGA 581 Query: 602 AFISEGAIPFAAADPLRVIPSMMAGGAVTGALIMAFDVTLSAPHGGIFVFFAIGNLLWFL 661 +FISEGAIPFAA DPLRVIPSMMAGGAVTGAL+MAFDVTL APHGGIFVFFA+GN+ FL Sbjct: 582 SFISEGAIPFAAVDPLRVIPSMMAGGAVTGALVMAFDVTLRAPHGGIFVFFAMGNVFGFL 641 Query: 662 VALAAGVVVAALCVVGAKE 680 ++L G+V++A V+ K+ Sbjct: 642 LSLLVGMVISATLVLALKQ 660 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: 1382 Number of extensions: 70 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: 700 Length of database: 684 Length adjustment: 39 Effective length of query: 661 Effective length of database: 645 Effective search space: 426345 Effective search space used: 426345 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: 54 (25.4 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