Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate 3608018 Dshi_1425 aldehyde dehydrogenase (RefSeq)
Query= reanno::WCS417:GFF2142 (499 letters) >FitnessBrowser__Dino:3608018 Length = 484 Score = 208 bits (529), Expect = 4e-58 Identities = 147/489 (30%), Positives = 230/489 (47%), Gaps = 29/489 (5%) Query: 2 TTTIEHYINDQRVSRDDRYQDVFNPATGEKTGRVALASRQTVSEAVAAAQAAFAGWADTP 61 T H IN V ++ VFNPAT E ASR V +A+AAA+AA GWA Sbjct: 16 TGPYRHAINGALVDSAGSFE-VFNPATDEVVAHAPNASRDQVEQAIAAAKAAQPGWAALS 74 Query: 62 PIRRARVLFEYLHLLRERKDDLARIIVAEHGKV-FTDAQGEVDRGIDILEFACGIPNLLK 120 R + Y L K +L ++ E GK + A EV+ I + + K Sbjct: 75 QDERGAYIAAYADALDAHKQELITLLTTEQGKPRHSMATTEVEYAI------FWVREVAK 128 Query: 121 GEHSDQVSRGMDNWTMR---QPLGVVAGVTPFNFPVMVPMWMYPIAIAAGNTFILKPSPT 177 D+V T++ PLGVV +TP+NFPV++ +W + GNT ++KPSP Sbjct: 129 RRLEDEVIEDTPEHTVKVAHTPLGVVGAITPWNFPVLLGLWKIAPCLVTGNTMVMKPSPY 188 Query: 178 DPSASLFMAELLREAGLPKGVFNVVQGDKESVDALIEHPDVKAVSFVGSTPIAQYIYETG 237 P +L E+ ++ P GV NVV G E L EHPD+ +SF GST + + + Sbjct: 189 TPLCTLRFGEIAQQV-FPAGVLNVVAGGNEQGAWLTEHPDIAKISFTGSTATGRKVMASS 247 Query: 238 ARNGKRVQGLGGAKNHMVVMPDADIEKTVDALMGAAYGSAGERCMAISVAVLVGDVGDKV 297 + N KR+ G + +++P D + + L AAYG++G+ C+A+ + + D Sbjct: 248 SCNLKRITLELGGNDPAILLPGTDYKPLIPTLFDAAYGNSGQWCIAVKRLYVHESLYDDF 307 Query: 298 IAALTERAKHLRITDGRDLKAEMGPIVSRAALERISGYIEQGVQAGAQLLLDGRDYVPTE 357 + A + +G D ++GPI ++ ++ G + L G +P Sbjct: 308 LRDFVAHAAEKTVGNGMDPNTDLGPIQNKMQYGKLKDLFADVKAQGLSVPLGGE--IPDG 365 Query: 358 PGLENGFWLGATLFDHVTEEMSIYREEIFGPVLACVRVNDFAEAIKLVNAHEFGNGVSCF 417 P G ++ T+ D+ ++ + REE FGP+L ++ +D E ++ N EFG S + Sbjct: 366 P----GNFVPITIVDNPPKDSRVVREEPFGPILPIIKWSDLDEVVRDANDTEFGLAASVW 421 Query: 418 TRDGNIAREFARRIEVGMVGINV----PISVPMAWHGFGGWKKSLFGDMHAYGTEGVRFY 473 D + A A R+E G V +N I +P FGG K+S G + G EG++ + Sbjct: 422 GPDRDTAIGVANRLEAGTVWVNEIHIHGIDIP-----FGGHKQSGMGVEN--GQEGLKEF 474 Query: 474 TKQKSIMQR 482 T K+ M R Sbjct: 475 TNTKTYMFR 483 Lambda K H 0.320 0.136 0.407 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: 29 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: 499 Length of database: 484 Length adjustment: 34 Effective length of query: 465 Effective length of database: 450 Effective search space: 209250 Effective search space used: 209250 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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