Align Glyceraldehyde dehydrogenase medium chain; Glyceraldehyde dehydrogenase subunit B; Glyceraldehyde dehydrogenase subunit beta; EC 1.2.99.8 (characterized)
to candidate AO356_15625 AO356_15625 FAD-binding molybdopterin dehydrogenase
Query= SwissProt::Q4J6M6 (281 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_15625 Length = 333 Score = 90.9 bits (224), Expect = 3e-23 Identities = 84/320 (26%), Positives = 139/320 (43%), Gaps = 55/320 (17%) Query: 6 FSYVRAESLQEALKFLEGNDNTRPLAGGQSLIPMLKLRVLSPDYILDINRLNELNYVKTS 65 F Y + +++Q A+ + +R +AGG +L+ ++K + P++++DI L + +T Sbjct: 4 FQYSKPDTVQAAVDL--SSPVSRFIAGGTNLLDLMKENITRPEHLIDITGLPLADLSETP 61 Query: 66 LNGVSIGALTRYHDILSNDIVKSKVPLMHHATRTIGDMQVRNMGTIGGAISN-------- 117 GV IGAL D+ + ++ + PL+ A Q+RNM + GG + Sbjct: 62 SGGVMIGALVSNADLAWHPWIERRYPLLAQAILAGASPQLRNMASTGGNLLQRTRCYYFY 121 Query: 118 -----------------------------------ADPASDMPVVLTALNATIILSSASG 142 A SDM V L AL A + + G Sbjct: 122 DASVPCNKRRPGSGCPARNGLNRIHAIFGASDQCVATHPSDMCVALAALEAVVHVLGRGG 181 Query: 143 SRSVKALDFFKGPFTTDTNKG-----ELVTQIEVPVLD-GYKTVYKKVVRRAG-DYALAS 195 +R+++ DF + P EL+T IE+P + Y K+ RA +AL S Sbjct: 182 ARTIEFADFHRLPGDAPERDNQLADDELITAIELPAAGFADHSHYLKIRDRASYAFALVS 241 Query: 196 VALAIKLKGNEIEDIKLAYGGVHDKPFRAMEVEKNVIGKKLNDDLVKDIASKVSSQINPP 255 VA A++L G I +LA GGV KP+R VE + G+ ++ + +A+ Q P Sbjct: 242 VAAALELDGPVIRQARLALGGVAHKPWRDRAVESWLTGQTVSRETF-TVAADALLQNAEP 300 Query: 256 SDHRGSS--WYRREVVKVLT 273 +H G RR +V+ L+ Sbjct: 301 LEHNGFKVRLARRAIVRALS 320 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: 170 Number of extensions: 10 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 281 Length of database: 333 Length adjustment: 27 Effective length of query: 254 Effective length of database: 306 Effective search space: 77724 Effective search space used: 77724 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: 48 (23.1 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