Align D-tagatose-1,6-bisphosphate aldolase subunit GatY; TBPA; TagBP aldolase; D-tagatose-bisphosphate aldolase class II; Tagatose-bisphosphate aldolase; EC 4.1.2.40 (characterized)
to candidate BWI76_RS27560 BWI76_RS27560 hypothetical protein
Query= SwissProt::Q8VS16 (284 letters) >FitnessBrowser__Koxy:BWI76_RS27560 Length = 286 Score = 186 bits (471), Expect = 7e-52 Identities = 102/283 (36%), Positives = 162/283 (57%), Gaps = 4/283 (1%) Query: 3 IISSKNMLLKAQRLGYAVPAFNIHNLETMQVVVETAAELRSPLILAGTPGTYSYAGTGNV 62 ++S +L + G+A+ AFN+ + ++ VVE A +P I++ P + + G Sbjct: 2 LVSMHELLKPTREHGFAIGAFNVADSCFIRAVVEEAEATNTPAIISIHPSEHDFVGDA-F 60 Query: 63 VAIARDLAKIWDLPLAVHLDHHEDLADITRKVQAGIRSVMIDGSHSPFEENVALVKSVVE 122 + RD+ + +P +HLDH + + R +Q G SVMIDGS P+EENVAL + VV Sbjct: 61 FSYVRDITQRSRVPFTLHLDHGASVEHVLRAIQCGFTSVMIDGSLLPYEENVALTREVVR 120 Query: 123 LSHRYDASVEAELGRLGGVEDDLGVDAKDALYTNPEQGREFVARTGIDSLAVVIGTAHGL 182 L+H SVE ELG +G + + YT+P Q +FVARTG+D+LAV IGTAHG+ Sbjct: 121 LAHAVGVSVEGELGTIGQTGTSVEGGVSEVTYTDPAQAEDFVARTGVDTLAVAIGTAHGI 180 Query: 183 Y--AAEPKLGFAALPPISERVDVPLVLHGASKLPDSDIRRAISLGVCKVNVATELKIAFS 240 Y +PKL L I+ R+ +PLVLHG S PD++I +++LGV K+N+++++K A+ Sbjct: 181 YPKGMQPKLQMHILRDIAGRLSIPLVLHGGSANPDAEIAESVTLGVGKINISSDMKYAYF 240 Query: 241 DALKHYFEENPDANEPRHYMKPAKAAMKDVVRKVIHVCGCEGQ 283 + + + Y +P AA ++V+R + + G G+ Sbjct: 241 QKAREILAKETWWDPNVIYPEPINAA-REVIRHKMKLFGSTGK 282 Lambda K H 0.319 0.135 0.389 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: 219 Number of extensions: 10 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: 284 Length of database: 286 Length adjustment: 26 Effective length of query: 258 Effective length of database: 260 Effective search space: 67080 Effective search space used: 67080 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 (21.7 bits) S2: 47 (22.7 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