Align Glyceraldehyde dehydrogenase medium chain; Glyceraldehyde dehydrogenase subunit B; Glyceraldehyde dehydrogenase subunit beta; EC 1.2.99.8 (characterized)
to candidate PP_3309 PP_3309 promiscuous aromatic aldehyde dehydrogenase, FAD-binding subunit
Query= SwissProt::Q4J6M6 (281 letters) >FitnessBrowser__Putida:PP_3309 Length = 333 Score = 86.7 bits (213), Expect = 6e-22 Identities = 87/306 (28%), Positives = 130/306 (42%), Gaps = 55/306 (17%) Query: 6 FSYVRAESLQEALKFLEGNDNTRPLAGGQSLIPMLKLRVLSPDYILDINRLNELNYVKTS 65 FSY + S+ EA+ + + + +AGG +L+ ++K V+ P ++DI+ L LN + + Sbjct: 4 FSYHKPASISEAVSLADASSHF--IAGGTNLVDLMKENVVRPKRLIDISGLG-LNGIHPT 60 Query: 66 LNG-VSIGALTRYHDILSNDIVKSKVPLMHHATRTIGDMQVRNMGTIGG----------- 113 LNG + IGAL D+ + +++ PL+ A Q+RNM + GG Sbjct: 61 LNGGLLIGALVSNADLAWHPMIEQHYPLLSDAILAGASPQLRNMASTGGNLLQRTRCYYF 120 Query: 114 --------------------------AISNADPA------SDMPVVLTALNATIILSSAS 141 AI A A SDM V L AL A + + Sbjct: 121 YDTGTPCNKREPGSGCPARTGSNRIHAILGASDACVATHPSDMCVALAALEAVVHVQGPR 180 Query: 142 GSRSVKALDFFKGPFTTDTNKG-----ELVTQIEV--PVLDGYKTVYKKVVRRAGDYALA 194 G R + F + P T ELV IE+ PV + + K R + +AL Sbjct: 181 GERQIPFAAFHRLPEDTPERDNQLAIDELVVAIELPPPVFEKHYRYLKIRDRASYAFALV 240 Query: 195 SVALAIKLKGNEIEDIKLAYGGVHDKPFRAMEVEKNVIGKKLNDDLVKDIASKVSSQINP 254 SVA A+ G I +LA GGV KP+R VE+ + G+ + L A+K Q Sbjct: 241 SVAAALSFDGQVIRQARLALGGVAHKPWRDPVVERMLAGQAPCEALFTR-AAKTLLQGAK 299 Query: 255 PSDHRG 260 P H G Sbjct: 300 PLSHNG 305 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: 185 Number of extensions: 7 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