Align Glyceraldehyde dehydrogenase medium chain; Glyceraldehyde dehydrogenase subunit B; Glyceraldehyde dehydrogenase subunit beta; EC 1.2.99.8 (characterized)
to candidate WP_011426360.1 RHE_RS15975 xanthine dehydrogenase small subunit
Query= SwissProt::Q4J6M6 (281 letters) >NCBI__GCF_000092045.1:WP_011426360.1 Length = 488 Score = 114 bits (285), Expect = 4e-30 Identities = 82/242 (33%), Positives = 114/242 (47%), Gaps = 7/242 (2%) Query: 41 KLRVLSPDYILDINRLNELNYVKTSLNGVSIGALTRYHDILSNDIVKSKVPLMHHATRTI 100 ++R LSP ++ IN L+EL V S +G++IGA Y + + K+P + I Sbjct: 236 QMRRLSP--VVFINHLSELQSVTESEDGITIGAGVSYTGAFA--AISKKIPALGRLIDRI 291 Query: 101 GDMQVRNMGTIGGAISNADPASDMPVVLTALNATIILSSASGSRSVKALDFFKGPFTTDT 160 QVRNMGTIGG I+N P D P L AL AT+ L S G R + DFF D Sbjct: 292 AGEQVRNMGTIGGNIANGSPIGDSPPPLIALGATLTLRSLEGQRKMPLEDFFIAYGKQDR 351 Query: 161 NKGELVTQIEVPVLDGYK--TVYKKVVRRAGDYALASVALAIKLKGNEI-EDIKLAYGGV 217 GE V + VP YK RR D A + L EI DI++AYGG+ Sbjct: 352 RPGEFVESVFVPYPKATSRFAAYKITKRRDEDITAVLGAFLLTLDDAEIVTDIRIAYGGM 411 Query: 218 HDKPFRAMEVEKNVIGKKLNDDLVKDIASKVSSQINPPSDHRGSSWYRREVVKVLTMKAF 277 P RA VE +IG+ + ++ + P +D R ++ YR+ K L + + Sbjct: 412 AATPKRARTVEAELIGRPWTEATIQAARPAFDADFQPLTDWRATAEYRQLTAKNLLTRFY 471 Query: 278 KE 279 E Sbjct: 472 LE 473 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: 243 Number of extensions: 7 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: 488 Length adjustment: 30 Effective length of query: 251 Effective length of database: 458 Effective search space: 114958 Effective search space used: 114958 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 Apr 09 2024. 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