Align Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate GFF2074 PGA1_c21070 betaine aldehyde dehydrogenase BetB
Query= reanno::pseudo13_GW456_L13:PfGW456L13_495 (480 letters) >FitnessBrowser__Phaeo:GFF2074 Length = 488 Score = 310 bits (794), Expect = 7e-89 Identities = 173/472 (36%), Positives = 264/472 (55%), Gaps = 7/472 (1%) Query: 12 QAFIDGAWVDADNGQTIKVNNPATGEILGTVPKMGAAETRRAIEAADKAL--PAWRALTA 69 Q +I G + +D + +PA+GE+ +P+ A++ A+ AA A P W +TA Sbjct: 5 QQYIGGVF--SDGSARFESRDPASGEVWAMMPEARASDVEAAVAAARAAFHAPDWAGMTA 62 Query: 70 KERATKLRRWYELIIENQDDLARLMTLEQGKPLAEAKGEIVYAASFIEWFAEEAKRIYGD 129 R L R +LI EN + LA+L T + GK + E +I Y A + ++A A +I G Sbjct: 63 TGRGKLLYRLADLIAENAETLAQLETRDTGKIIRETSAQIAYVADYYRYYAGLADKIEGA 122 Query: 130 VIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPFSA 189 +P +PD + + ++P+GV AA+ PWN + K GPALAAGCT+VLK + + P Sbjct: 123 HLPIDKPDMEVWLRREPLGVVAAVVPWNSQLFLAAVKIGPALAAGCTVVLKASEEAPAPL 182 Query: 190 FALAELAQRAGIPAGVFSVVSGSAGDIGSELTSNPIVRKLSFTGSTEIGRQLMSECAKDI 249 A + +AG P GV +V++G D G+ LT++P + ++FTG + R ++ A+++ Sbjct: 183 LEFARIFDQAGFPRGVLNVITGFGADCGAVLTAHPGIDHIAFTGGPDTARHVVRNSAENL 242 Query: 250 KKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYIQDGVYDAFAEKL 309 SLELGG +PFIVF+D D+D AV + + + GQ+CV +RL I + + F +L Sbjct: 243 ASTSLELGGKSPFIVFEDVDIDSAVNAQVSAIFAATGQSCVAGSRLIISNQIKAQFLHRL 302 Query: 310 KVAVAKLKIGNGLEAGTTTGPLIDEKAVAKVQEHIADALSKGATVLAGGKPM--EGNFFE 367 K ++IG T GPL + + + E +A +L+ GA ++ GG+P+ EGNFF Sbjct: 303 KEKAENIRIGAPELPETEVGPLCTDAQMRRAVELVAASLAAGARIVTGGQPLEGEGNFFP 362 Query: 368 PTIL-TNVPNNAAVAKEETFGPLAPLFRFKDEADVIAMSNDTEFGLASYFYARDLGRVFR 426 PTIL + A +EE FGP+ + F EA+ +A++NDT GLAS + RDL R R Sbjct: 363 PTILDCSEAPEAPCLREEFFGPVLSVCGFDTEAEALALANDTAHGLASGVFTRDLTRAHR 422 Query: 427 VAEALEYGMVGVNTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCL 478 + + G+V VNT + +APFGG SG GREG DY +K + L Sbjct: 423 MIRGIRAGIVWVNTYRAVSPIAPFGGQGLSGHGREGGLQAALDYTRVKTVWL 474 Lambda K H 0.317 0.135 0.390 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: 532 Number of extensions: 20 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: 480 Length of database: 488 Length adjustment: 34 Effective length of query: 446 Effective length of database: 454 Effective search space: 202484 Effective search space used: 202484 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