Align The fructose-specific PTS Enzyme IIABC FruA (characterized)
to candidate WP_040535931.1 L248_RS09200 PTS transporter subunit EIIC
Query= TCDB::Q0S1N2 (700 letters) >NCBI__GCF_000469325.1:WP_040535931.1 Length = 475 Score = 299 bits (766), Expect = 2e-85 Identities = 192/484 (39%), Positives = 262/484 (54%), Gaps = 39/484 (8%) Query: 209 VAVTACPTGIAHTYMAADSLVAAGERAGVVVHVETQGSSG-STPLAPGVIAGASAVIFAT 267 V VT CP G+AHTYMAA+ L G+ G V +ETQG+SG L P + A VI A Sbjct: 5 VGVTKCPVGVAHTYMAAEKLQKVGQSLGYTVKIETQGASGVEDHLTPDDVKNADFVIIAA 64 Query: 268 DVGVKGKERFAGKPVVASGVKRAINEPDTMITEALRAGMNPSAAIVDAGSAGSAADEPA- 326 DV + G +RF K V+ S AI + +I +A +A + G AADE Sbjct: 65 DVEIDGMDRFTDKKVLFSTTAAAIKDSAALIDKAKKADIY--------GGKEDAADEKVE 116 Query: 327 GSIGWGTHLRQVLLTGVSYMIPFVAAGGLLIALGFLLGGYEISGPAEDIVLSNSLGQLPE 386 G + L + L+ GVS+MIPFV GGL IAL LGG+ A +V +++ Sbjct: 117 GDAHEQSPLIKQLMNGVSHMIPFVVVGGLFIALSITLGGHATK--AGMVVAPHTIW---- 170 Query: 387 GGLATYLGAVLFQLGSLAFSFLVPALAGYIAFAIADRPGLAPGFTAGAVA-------VFV 439 A + Q+G+L F+ ++P LAGYIA AIA R LAP + VA Sbjct: 171 --------ATMNQVGTLGFTLMIPILAGYIATAIAGRAALAPAMLSAMVANSPDILGTKA 222 Query: 440 GAGFIGGLVGGLIAGVVALWISRIPVPQWLRGLMPVVIIPLFATLIVGALMFLVLGRPLA 499 G GFIG ++ G AG + W + PVP+ LR +MP+ +IPL T I+ LG P++ Sbjct: 223 GTGFIGAIIVGFAAGYLVKWFNSWPVPKSLRAIMPIFVIPLLGTAIISGAFVFFLGGPIS 282 Query: 500 SITSGLTNWLNGLSGS--SVIFLGIILGLMMCFDLGGPVNKAAYAFAVAGLNVNDPASLR 557 + + LTN LN LS + + I LG++LG M+ D+GGP+NK A+ F VA + +P Sbjct: 283 WLMTALTNMLNVLSKNPQTSIILGLLLGAMVSIDMGGPINKVAFLFGVASITAGNP---E 339 Query: 558 IMAAVMAAGMVPPLAMALASTVLRPSLFSEAERENGKAAWLLGSAFISEGAIPFAAADPL 617 IM AV A VPPL+ +A T++R L S E G A L+G I+EGAIP A A+P Sbjct: 340 IMGAVACAIAVPPLSAGIA-TLIRSDLNSSEETAAGVPAILMGLIGITEGAIPLATANPK 398 Query: 618 RVIPSMMAGGAVTGALIMAFDVTLSAPHGG--IFVFFAIGNLLWFLVALAAGVVVAALCV 675 V P ++ G AV A+ M F +T + PHGG + V A NLL F +A+ GV V+A + Sbjct: 399 HVFPGIITGSAVAAAIGMFFKITDAVPHGGPIVGVLGATNNLLLFFLAIIIGVAVSAAII 458 Query: 676 VGAK 679 V K Sbjct: 459 VTLK 462 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: 785 Number of extensions: 49 Number of successful extensions: 8 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: 475 Length adjustment: 36 Effective length of query: 664 Effective length of database: 439 Effective search space: 291496 Effective search space used: 291496 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: 53 (25.0 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