Align Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)
to candidate PfGW456L13_2360 Aldehyde dehydrogenase (EC 1.2.1.3)
Query= SwissProt::Q9I6M5 (483 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2360 Length = 496 Score = 325 bits (834), Expect = 2e-93 Identities = 186/470 (39%), Positives = 266/470 (56%), Gaps = 9/470 (1%) Query: 15 VDGAWVDADNGQTIKVNNPATGEIIGSVPKMGAAETRRAIEAADKALP--AWRALTAKER 72 + G WV+A +GQT+ ++NPATGE++ VP+ + RA+ AA +A AW +ER Sbjct: 22 IGGDWVEAADGQTMPLHNPATGEVLCVVPRATPEDVDRAVLAARQAFDDSAWTRTRPRER 81 Query: 73 ANKLRRWFDLMIENQDDLARLMTIEQGKPLAEAKG-EIAYAASFLEWFGEEAKRIYGDTI 131 N L + DLM + + LA+L + GK A A+ ++ A FL + A +I G T+ Sbjct: 82 QNLLWKLADLMQRDAELLAQLECLNNGKSAAVAQVMDVQLAIDFLRYMAGWATKIEGSTV 141 Query: 132 PGHQP-----DKRIIVIKQPIGVTAAITPWNFPSAMITRKAGPALAAGCTMVLKPASQTP 186 P + ++ +GV AI WNFP + K GPALA GCT+VLKPA +TP Sbjct: 142 DVSAPLMPNDQFHSFIRREAVGVVGAIVAWNFPLLLACWKLGPALATGCTVVLKPADETP 201 Query: 187 YSALALAELAERAGIPKGVFSVVTGSAGEVGGELTSNPIVRKLTFTGSTEIGRQLMAECA 246 +AL LAEL AG P+GVF+VVTG+ G LT NP+V KLTFTGST +G+Q+ Sbjct: 202 LTALKLAELVLEAGYPEGVFNVVTGTGITAGSALTHNPLVDKLTFTGSTAVGKQIGKIAM 261 Query: 247 QDIKKVSLELGGNAPFIVFDDADLDAAVEGALISKYRNNGQTCVCANRLYVQDGVYDAFV 306 + +V+LELGG +P IV DADL A GA + + N GQ C +RLYVQ +D V Sbjct: 262 DSMTRVTLELGGKSPTIVMADADLKTAAAGAASAIFFNQGQVCCAGSRLYVQRKHFDNVV 321 Query: 307 DKLKAAVAKLNIGNGLEAGVTTGPLIDAKAVAKVEEHIADAVSKGAKVVSGGKPHALGGT 366 + + +GNGL+ V GPLI A+ +V +I GA + GG+ G Sbjct: 322 ADISDIANAMKLGNGLDPSVDMGPLISARQQERVYGYIEKGRESGATIACGGEQFG-PGF 380 Query: 367 FFEPTILVDVPKNALVSKDETFGPLAPVFRFKDEAEVIAMSNDTEFGLASYFYARDLARV 426 F +PT++VDV + + ++E FGP+ F DEA+ + M+ND+ +GL + ++ DLA V Sbjct: 381 FVKPTVIVDVDQKHSLVQEEIFGPVLVAIPFDDEADALRMANDSPYGLGASIWSNDLAAV 440 Query: 427 FRVAEQLEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIK 476 R+ +++ G V +N + PFGG K SG+GRE IE Y E+K Sbjct: 441 HRMIPRIKSGSVWVNCHSALDPALPFGGYKMSGVGREMGYAAIEHYTELK 490 Lambda K H 0.317 0.135 0.391 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: 588 Number of extensions: 23 Number of successful extensions: 4 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: 483 Length of database: 496 Length adjustment: 34 Effective length of query: 449 Effective length of database: 462 Effective search space: 207438 Effective search space used: 207438 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 (21.7 bits) S2: 52 (24.6 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