Align glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate WP_012468985.1 GLOV_RS04485 aldehyde dehydrogenase
Query= BRENDA::Q88RC0 (480 letters) >NCBI__GCF_000020385.1:WP_012468985.1 Length = 483 Score = 285 bits (730), Expect = 2e-81 Identities = 160/462 (34%), Positives = 257/462 (55%), Gaps = 11/462 (2%) Query: 12 QAYINGEWLDADNGQTIKVTNPATGEVIGTVPKMGTAETRRAIEAADKALPAWRALTAKE 71 Q YING W D+ +G NP TGE++ TV + A+ AA A P W A+ + Sbjct: 6 QMYINGTWQDSADGSWFDDFNPYTGEILTTVANGSQQDALLAVNAAADAFPDWAAVAPSQ 65 Query: 72 RSAKLRRWFELMIENQDDLARLMTTEQGKPLAEAKGEIAYAASFIEWFAEEAKRIYGDTI 131 + + +L+ + +D+L L+ E G A + A +++ +A R+ G + Sbjct: 66 KRLLFLKAADLLEKRKDELIDLLARETGAARPFAAYQAAAGPNYLREAGSQAHRVTGTIL 125 Query: 132 PGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPYSA-L 190 P + K +V++ P+GV A I+PWN P + R A+A G T+VLKP+ ++P S + Sbjct: 126 PS-ETTKVSMVMRHPVGVVAGISPWNCPVVLSLRAVCFAMAYGNTVVLKPSEESPVSGGI 184 Query: 191 ALVELAHRAGIPAGVLSVVT---GSAGEVGGELTGNSLVRKLSFTGSTEIGRQLMEECAK 247 L EL AG P GV ++VT G + EVG + V+++SFTGST +GR+L E+C + Sbjct: 185 LLAELFEEAGFPKGVFNIVTHGYGRSSEVGDLFIQDRRVKRISFTGSTRVGRELAEKCGR 244 Query: 248 DIKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRIYVQDGVYDAFAE 307 +K+++LELGGN P IV +DAD+D AV AI ++ + GQ C+ A R+ ++ V F Sbjct: 245 HLKRIALELGGNDPLIVLNDADMDHAVNAAIFGRFLHQGQVCMNAKRLIIEKTVAQEFTA 304 Query: 308 KLAAAVAKLKIGNGLEEGTTTGPLIDGKAVAKVQEHIEDAVSKGAKVLSGGKLIEGNFFE 367 + A + LK+GN L+ T GPLI+ K ++ + AV++GA++L GG G + Sbjct: 305 RFVARTSALKVGNPLDAATVIGPLINHKQYETLEGQVNRAVAEGAELLCGG-YGNGLCYH 363 Query: 368 PTILVDVPKTAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYARDMSRVFRV 427 PT+L +V + ++ EETFGP+AP+ +D + + ++N + +GL++ +M + + Sbjct: 364 PTVLGNVREDMSIFHEETFGPVAPIIVAEDADDALRLANSSAYGLSAGILTNNMQQGLAL 423 Query: 428 AEALEYGMVGINTGLISNEV-APFGGIKASGLGREGSKYGIE 468 A +E G +N + E AP GG+ SG G K+GIE Sbjct: 424 ARRIESGACHVNDSPLYGETHAPLGGVNNSGWG----KFGIE 461 Lambda K H 0.317 0.134 0.384 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: 564 Number of extensions: 18 Number of successful extensions: 6 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: 483 Length adjustment: 34 Effective length of query: 446 Effective length of database: 449 Effective search space: 200254 Effective search space used: 200254 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: 52 (24.6 bits)
This GapMind analysis is from Sep 24 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