Align glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate CCNA_02485 CCNA_02485 vanillin dehydrogenase
Query= BRENDA::Q88RC0 (480 letters) >FitnessBrowser__Caulo:CCNA_02485 Length = 470 Score = 290 bits (742), Expect = 7e-83 Identities = 164/451 (36%), Positives = 247/451 (54%), Gaps = 5/451 (1%) Query: 32 NPATGEVIGTVPKMGTAETRRAIEAADKALPAWRALTAKERSAKLRRWFELMIENQDDLA 91 +P TG V T M + R A++AA ALP W AL R A L + + DD Sbjct: 12 DPVTGAVATTSIAMTADQARVAVDAAQAALPTWSALGPNARRALLSKAAAALEARADDFV 71 Query: 92 RLMTTEQGKPLAEAKGEIAYAASFIEWFAEEAKRIYGDTIPGHQPDKRLIVIKQPIGVTA 151 M E G A+ + AAS + A ++ G+ IP +P + +++P+GV Sbjct: 72 AAMMGEIGATEGWARFNLMLAASMVREAAALTTQVSGEVIPSDKPGCLAMAVREPVGVIL 131 Query: 152 AITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPYSALALVELAHRAGIPAGVLSVVTG 211 I PWN P + R LA G T+VLK + P + + E AG+P G LS+VT Sbjct: 132 GIAPWNAPIILGVRAVATPLACGNTVVLKASESCPRTHELIAEAFAAAGLPEGALSIVTN 191 Query: 212 S---AGEVGGELTGNSLVRKLSFTGSTEIGRQLMEECAKDIKKVSLELGGNAPFIVFDDA 268 + A EV G L + VR+++FTGST +G+ + + A+ +K V LELGG AP IV +DA Sbjct: 192 APADAAEVVGALIDHPAVRRINFTGSTAVGKIIAKRAAEHLKPVLLELGGKAPLIVLEDA 251 Query: 269 DLDKAVEGAIISKYRNNGQTCVCANRIYVQDGVYDAFAEKLAAAVAKLKIGNGLEEGTTT 328 DLD+AV+ A + N GQ C+ RI V D + DAF K AA + L +G+ E T Sbjct: 252 DLDEAVKAAAFGAFMNQGQICMSTERIIVVDAIADAFVAKFAAKASSLAVGDPREGKTPL 311 Query: 329 GPLIDGKAVAKVQEHIEDAVSKGAKVLSGGKLIEGNFFEPTILVDVPKTAAVAKEETFGP 388 G ++D K V VQ + DA++ GA +SGG G T++ V + +EE+FGP Sbjct: 312 GAVVDLKTVTHVQGLVADALADGAVQVSGGP-ANGVLMPATVVDKVTPAMRLFREESFGP 370 Query: 389 LAPLFRFKDEAEVIAMSNDTEFGLASYFYARDMSRVFRVAEALEYGMVGINTGLISNEV- 447 + + R +DE IA++NDTE+GL++ + RD++R +VA ++ G+ +N + +E Sbjct: 371 VVAVIRARDEEHAIALANDTEYGLSASVFTRDIARGLKVARRIQSGICHVNGPTVHDEAQ 430 Query: 448 APFGGIKASGLGREGSKYGIEDYLEIKYLCI 478 PFGG+KASG GR G K G++ + E++++ + Sbjct: 431 MPFGGVKASGYGRFGGKAGVDAFTELRWITV 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: 549 Number of extensions: 19 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: 470 Length adjustment: 33 Effective length of query: 447 Effective length of database: 437 Effective search space: 195339 Effective search space used: 195339 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