Align Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate GFF3484 PS417_17840 betaine-aldehyde dehydrogenase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_495 (480 letters) >FitnessBrowser__WCS417:GFF3484 Length = 486 Score = 330 bits (847), Expect = 5e-95 Identities = 180/461 (39%), Positives = 269/461 (58%), Gaps = 17/461 (3%) Query: 32 NPATGEILGTVPKMGAAETRRAIEAADKALPAWRALTAKERATKLRRWYELIIENQDDLA 91 NPATGE +G V GA E A+ AA +A P W AKERA +R+ ELI +N LA Sbjct: 21 NPATGEAIGEVASGGAEEVALAVAAAKEAFPKWANTPAKERARLMRKLGELIEQNVPHLA 80 Query: 92 RLMTLEQGKPLAEAKGEIVYAASF-IEWFAEEAKRIYGDVIPGHQPDKRLI--VIKQPIG 148 L TL+ G P+ + K ++ AS ++FAE R+ G P D +++ + QP+G Sbjct: 81 ELETLDTGLPIHQTKNVLIPRASHNFDFFAEVCTRMDGHSYP---VDDQMLNYTLYQPVG 137 Query: 149 VTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPFSAFALAELAQRAGIPAGVFSV 208 V ++PWN P T K P LA G T VLK + +P +A L LA AGIP GV +V Sbjct: 138 VCGLVSPWNVPFMTATWKTAPCLALGNTAVLKMSELSPLTANELGRLAVEAGIPNGVLNV 197 Query: 209 VSGSAGDIGSELTSNPIVRKLSFTGSTEIGRQLMSECAKDIKKVSLELGGNAPFIVFDDA 268 + G G L +P VR +SFTG T G+++M +KK S+ELGG +P ++F+DA Sbjct: 198 IQGYGATAGDALVRHPDVRAISFTGGTATGKKIMQTAG--LKKYSMELGGKSPVLIFEDA 255 Query: 269 DLDKAVEGAIISKYRNNGQTCVCANRLYIQDGVYDAFAEKLKVAVAKLKIGNGLEAGTTT 328 DL++A++ A+ + + NG+ C +R++IQ+ VY F + +L +G+ + T Sbjct: 256 DLERALDSALFTIFSLNGERCTAGSRIFIQESVYPQFVAEFAARAKRLIVGDPQDPKTQV 315 Query: 329 GPLIDEKAVAKVQEHIADALSKGATVLAGG--KPM-------EGNFFEPTILTNVPNNAA 379 G +I + KV +I + +GAT+LAGG +P +G F +PT+ +V N Sbjct: 316 GSMITQAHYDKVTGYIKIGIEEGATLLAGGLDRPANLPAHLSKGQFIQPTVFADVNNKMR 375 Query: 380 VAKEETFGPLAPLFRFKDEADVIAMSNDTEFGLASYFYARDLGRVFRVAEALEYGMVGVN 439 +A+EE FGP+ L FKDEA+ + ++NDTE+GLASY + +D+G+ R+A +E GMV +N Sbjct: 376 IAQEEIFGPVVCLIPFKDEAEALQLANDTEYGLASYIWTQDIGKAHRLARGIEAGMVFIN 435 Query: 440 TGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCLGI 480 + + + PFGG+K SG GREG +Y E + EIK +C+ + Sbjct: 436 SQNVRDLRQPFGGVKGSGTGREGGQYSFEVFAEIKNVCISM 476 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: 603 Number of extensions: 26 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: 486 Length adjustment: 34 Effective length of query: 446 Effective length of database: 452 Effective search space: 201592 Effective search space used: 201592 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