Align glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate Ga0059261_0516 Ga0059261_0516 vanillin dehydrogenase (EC 1.2.1.67)
Query= BRENDA::Q88RC0 (480 letters) >FitnessBrowser__Korea:Ga0059261_0516 Length = 478 Score = 293 bits (749), Expect = 1e-83 Identities = 170/461 (36%), Positives = 252/461 (54%), Gaps = 8/461 (1%) Query: 25 GQTIKVTNPATGEVIGTVPKMGTAETRRAIEAADKALPAWRALTAKERSAKLRRWFELMI 84 G+T NP TGEV + A+EAA A PAW L R A L + E + Sbjct: 10 GKTFARLNPVTGEVATEAQAFTVDQANEAVEAAAAAFPAWSTLGPNARRAALNKAAEALA 69 Query: 85 ENQDDLARLMTTEQGKPLAEAKGEIAYAASFIEWFAEEAKRIYGDTIPGHQPDKRLIVIK 144 +D M E G A+ + A S + A +I G+ IP +P + I+ Sbjct: 70 AKAEDFVEAMNGEIGATEGWARFNLMLAVSMVREAAALTTQIGGEVIPSDKPGCIAMAIR 129 Query: 145 QPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPYSALALVELAHRAGIPAG 204 +P+GV I PWN P + R LA G T+VLK + Q P + + E A +P G Sbjct: 130 EPVGVMLGIAPWNAPIILGVRAVAAPLACGNTVVLKASEQCPRTHSLIAEAFDEA-LPKG 188 Query: 205 VLSVVTGS---AGEVGGELTGNSLVRKLSFTGSTEIGRQLMEECAKDIKKVSLELGGNAP 261 +S+VT + A E+ G L N +R+++FTGST +GR + + A+ +K V LELGG AP Sbjct: 189 AVSIVTNAPEDAPEIVGALIDNPHIRRINFTGSTAVGRIIAKRAAEHLKPVLLELGGKAP 248 Query: 262 FIVFDDADLDKAVEGAIISKYRNNGQTCVCANRIYVQDGVYDAFAEKLAAAVAKLKIGNG 321 +V +DADLD+AV+ A + N GQ C+ RI V D V DAF EK AA V + +G+ Sbjct: 249 MLVLEDADLDEAVKAAAFGAFMNQGQICMSTERIIVVDAVADAFVEKFAAKVGTMPVGDP 308 Query: 322 LEEGTTTGPLIDGKAVAKVQEHIEDAVSKGAKVLSGGKLIE--GNFFEPTILVD-VPKTA 378 E T G ++D K VA V+ I DA++ GA ++GG ++E G P ++D V Sbjct: 309 REGKTPLGAVVDQKTVAHVKALIGDALAAGAVQVNGGGVLEGTGGVLMPAHVIDHVTPDM 368 Query: 379 AVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYARDMSRVFRVAEALEYGMVGI 438 + ++E+FGP+ + R +DEA I ++NDTE+GL++ + RD +R RVA ++ G+ + Sbjct: 369 KLFRDESFGPVVGVIRARDEAHAILLANDTEYGLSASVFTRDTARGLRVARQIKSGICHV 428 Query: 439 NTGLISNEV-APFGGIKASGLGREGSKYGIEDYLEIKYLCI 478 N + +E PFGG+KASG GR G K GI+ + E++++ I Sbjct: 429 NGPTVHDEAQMPFGGVKASGYGRFGGKAGIDAFTELRWITI 469 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: 600 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: 478 Length adjustment: 34 Effective length of query: 446 Effective length of database: 444 Effective search space: 198024 Effective search space used: 198024 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: 51 (24.3 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