Align Glyceraldehyde dehydrogenase medium chain; Glyceraldehyde dehydrogenase subunit B; Glyceraldehyde dehydrogenase subunit beta; EC 1.2.99.8 (characterized)
to candidate SM_b21011 SM_b21011 xanthine dehydrogenase
Query= SwissProt::Q4J6M6 (281 letters) >FitnessBrowser__Smeli:SM_b21011 Length = 495 Score = 118 bits (296), Expect = 2e-31 Identities = 81/241 (33%), Positives = 119/241 (49%), Gaps = 6/241 (2%) Query: 41 KLRVLSPDYILDINRLNELNYVKTSLNGVSIGALTRYHDILSNDIVKSKVPLMHHATRTI 100 ++R L+P ++ IN + EL +++S G++IGA Y +++ + S P I Sbjct: 244 QMRSLNP--VVFINGIAELQRIESSTAGLTIGAGVSY--TAAHEALSSAYPSFGRLLDRI 299 Query: 101 GDMQVRNMGTIGGAISNADPASDMPVVLTALNATIILSSASGSRSVKALDFFKGPFTTDT 160 G QVRNMGTIGG I+N P D P L L AT+ L S G R++ DFF D Sbjct: 300 GGDQVRNMGTIGGNIANGSPIGDSPPPLIVLGATVTLRSKDGQRTLPLEDFFIAYGKQDR 359 Query: 161 NKGELVTQIEVPVL--DGYKTVYKKVVRRAGDYALASVALAIKLKGNEIEDIKLAYGGVH 218 GE V + VP L D YK RR D + A I L G+ ++ ++A+GG+ Sbjct: 360 RPGEFVESLFVPALPADERFAAYKISKRRDEDISALLGAFRISLDGDRVKTARIAFGGMA 419 Query: 219 DKPFRAMEVEKNVIGKKLNDDLVKDIASKVSSQINPPSDHRGSSWYRREVVKVLTMKAFK 278 P RA VE +IG+ ++ V+ + + P +D R + YR K L M+ F Sbjct: 420 ATPKRAKTVEAALIGQAWTEETVRTAQAAFETDYQPITDWRATGAYRMLAAKNLLMRFFL 479 Query: 279 E 279 E Sbjct: 480 E 480 Lambda K H 0.316 0.134 0.372 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: 252 Number of extensions: 12 Number of successful extensions: 2 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: 281 Length of database: 495 Length adjustment: 30 Effective length of query: 251 Effective length of database: 465 Effective search space: 116715 Effective search space used: 116715 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 49 (23.5 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