Align glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate BWI76_RS07615 BWI76_RS07615 betaine-aldehyde dehydrogenase
Query= BRENDA::Q88RC0 (480 letters) >lcl|FitnessBrowser__Koxy:BWI76_RS07615 BWI76_RS07615 betaine-aldehyde dehydrogenase Length = 490 Score = 313 bits (801), Expect = 1e-89 Identities = 174/483 (36%), Positives = 274/483 (56%), Gaps = 9/483 (1%) Query: 6 AQLFRQQAYINGEWLDADNGQTIKVTNPATGEVIGTVPKMGTAETRRAIEAADKALPAWR 65 +++ QQ YI+G ++ A +G+T + NPA GEV+ TV G + RA+++A K W Sbjct: 2 SRMAEQQLYIDGGYVSATSGKTFETINPANGEVLATVQAAGREDVDRAVKSAQKGQKIWA 61 Query: 66 ALTAKERSAKLRRWFELMIENQDDLARLMTTEQGKPLAE-AKGEIAYAASFIEWFAEEAK 124 A++A ERS LR+ +++ D+LARL T + GKPL+E A +I A +E++A Sbjct: 62 AMSAMERSRILRKAVDILRARNDELARLETLDTGKPLSETAAVDIVTGADVLEYYAGLIP 121 Query: 125 RIYGDTIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQ 184 + G IP + + ++P+GV A I WN+P + K+ PALAAG M+ KP+ Sbjct: 122 ALEGSQIP-LRDSSFVYTRREPLGVVAGIGAWNYPIQIALWKSAPALAAGNAMIFKPSEV 180 Query: 185 TPYSALALVELAHRAGIPAGVLSVVTGSAGEVGGELTGNSLVRKLSFTGSTEIGRQLM-E 243 TP +AL L E+ AG+PAGV +V+ G+ E G LT + + K+SFTG G+++M Sbjct: 181 TPLTALKLAEIYREAGLPAGVFNVLPGTGAETGQYLTEHPDIAKISFTGGVASGKKVMAN 240 Query: 244 ECAKDIKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRIYVQDGVYD 303 A +K+V++ELGG +P IV +DA LD A + A+++ + ++GQ C R++V + Sbjct: 241 AAASSLKEVTMELGGKSPLIVCEDASLDLAADIAMMANFYSSGQVCTNGTRVFVPTRLKA 300 Query: 304 AFAEKLAAAVAKLKIGNGLEEGTTTGPLIDGKAVAKVQEHIEDAVSKGAKVLSGGKLIEG 363 AF EK+ A VA+++ G+ E T GPL+ V +IE +GA++L GG+ ++G Sbjct: 301 AFEEKILARVARIRPGDLFAESTNFGPLVSFPHRDNVLRYIETGKQEGARLLCGGEALKG 360 Query: 364 NFFE------PTILVDVPKTAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFY 417 F+ PT+ D + +EE FGP+ + + DE E + +N TE+GLA+ Sbjct: 361 EGFDRGAWVAPTVFTDCDDQMTIVREEIFGPVMSILSYDDEEEALRRANATEYGLAAGVV 420 Query: 418 ARDMSRVFRVAEALEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLC 477 D++R R+ LE G+ INT S P GG K SG+GRE + Y +IK + Sbjct: 421 TPDLNRAHRLIHRLEAGICWINTWGESPAEMPVGGYKHSGIGRENGVQTLHSYTQIKSIQ 480 Query: 478 ISV 480 + + Sbjct: 481 VEM 483 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: 565 Number of extensions: 25 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: 490 Length adjustment: 34 Effective length of query: 446 Effective length of database: 456 Effective search space: 203376 Effective search space used: 203376 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 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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