Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate RR42_RS34225 RR42_RS34225 methylmalonate-semialdehyde dehydrogenase
Query= metacyc::MONOMER-15203 (503 letters) >FitnessBrowser__Cup4G11:RR42_RS34225 Length = 506 Score = 740 bits (1911), Expect = 0.0 Identities = 367/499 (73%), Positives = 414/499 (82%), Gaps = 4/499 (0%) Query: 5 RIEHYINGHKTNGVADSHQEVTNPATGQVTGQVALASQADVDSAVAAAQAAFPAWSDTPP 64 ++ HYING + + Q+V NPATG VAL S + +AVAAA AAF AW+DTPP Sbjct: 12 QLGHYINGSRVASASGRAQDVFNPATGAAARSVALGSADEAGTAVAAAAAAFAAWADTPP 71 Query: 65 IRRARVMFKFLELLNAHKDELAEAITREHGKVFTDAQGEVARGIDIVEFACGIPQLLKGD 124 IRRARVM +FL+L+N H+D LA IT EHGKVF+DAQGEV+RGIDI+EFACGIPQLLKGD Sbjct: 72 IRRARVMQRFLQLMNQHRDTLAAMITAEHGKVFSDAQGEVSRGIDIIEFACGIPQLLKGD 131 Query: 125 YTEQVSTGIDNWTTRQPLGVVAGITPFNFPVMVPMWMFPLAIAAGNSFVLKPSPLDPSAS 184 YT+QVSTG+DNWT RQPLGVV GITPFNFP MVP WMFP+A+AAGN+FVLKPS DPSAS Sbjct: 132 YTDQVSTGMDNWTLRQPLGVVVGITPFNFPCMVPCWMFPIALAAGNTFVLKPSERDPSAS 191 Query: 185 LMMADLLKQAGLPDGVFNVVQGDKDSVEALIDHPDVKALSFVGSTPIANLIYERGARSGK 244 L MADLL +AGLP GVFNVVQGDK V+ALI HP+VKA+SFVGSTPIA I ER A GK Sbjct: 192 LFMADLLTEAGLPAGVFNVVQGDKVVVDALIAHPEVKAVSFVGSTPIAQYISERSAHFGK 251 Query: 245 RIQALGGAKNHMVVMPDANLDKAVDALIGAAYGSAGERCMAISVAVLVGDVADKIVPRLA 304 R+QALGGAKNH+VVMPDA++++AVDALIGA YGSAGERCMAIS+AVLVGDVADKI+P LA Sbjct: 252 RVQALGGAKNHLVVMPDADIEQAVDALIGAGYGSAGERCMAISIAVLVGDVADKILPLLA 311 Query: 305 ERARDLKIKNGLELDAEMGPIVTSQAHQRITGYIEKGVAEGAEMVVDGRDFDSSVTGEGC 364 ER + L I NG+ +AEMGPIVT QA +RI GY+ GVAEGA +VVDGRD G Sbjct: 312 ERVKALVIGNGMNAEAEMGPIVTRQALERIEGYVGLGVAEGATLVVDGRD----CRVPGH 367 Query: 365 ADGFWMGGTLFDHVTPEMTIYREEIFGPVLACVRVPDVATAIQLINDHEFGNGVSCFTES 424 GF+ GGTLFD+VTP M IY+EEIFGPVL CVRV D A A+QL+NDHEFGNGV+C+T Sbjct: 368 EAGFFTGGTLFDNVTPAMRIYKEEIFGPVLGCVRVKDFAQAVQLVNDHEFGNGVACYTSD 427 Query: 425 GSVAREFGRRIQVGMVGINVPIPVPMAWHGFGGWKRSMFGDTHAYGEEGVRFYTKQKSIM 484 G VAREF RRIQVGMVGINVPIPVPMAWHGFGGWKRS+FGDTHAYGEEGVRFYTKQKS+M Sbjct: 428 GGVAREFARRIQVGMVGINVPIPVPMAWHGFGGWKRSLFGDTHAYGEEGVRFYTKQKSVM 487 Query: 485 QRWSDSIDAGAEFAMPTAK 503 QRW DSI GAEFAMPTAK Sbjct: 488 QRWPDSIGKGAEFAMPTAK 506 Lambda K H 0.319 0.136 0.406 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: 840 Number of extensions: 27 Number of successful extensions: 2 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: 503 Length of database: 506 Length adjustment: 34 Effective length of query: 469 Effective length of database: 472 Effective search space: 221368 Effective search space used: 221368 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