Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate RR42_RS01580 RR42_RS01580 methylmalonate-semialdehyde dehydrogenase
Query= reanno::pseudo5_N2C3_1:AO356_23175 (500 letters) >FitnessBrowser__Cup4G11:RR42_RS01580 Length = 505 Score = 770 bits (1987), Expect = 0.0 Identities = 367/494 (74%), Positives = 424/494 (85%) Query: 7 VGHYIDGRIQASDNARLSNVFNPATGAVQARVALAEPSTVDAAVASALAAFPAWSEQSSL 66 + HYI G ++A+ + R ++VFNPATGAV RVAL VDAAVA+A AAFPAWSE + L Sbjct: 12 IAHYIGGTVRAASSDRFADVFNPATGAVAGRVALGSAQDVDAAVAAAHAAFPAWSETAPL 71 Query: 67 RRSRVMFKFKELLDRHHDELAQIISREHGKVLSDAHGEVTRGIEIVEYACGAPNLLKTDF 126 +R+R++FKFKELLDRHHD+LA +I+REHGKV SDA GEVTRG+EIVE+ACG PNLLKTDF Sbjct: 72 KRARILFKFKELLDRHHDDLAALITREHGKVFSDAKGEVTRGVEIVEFACGIPNLLKTDF 131 Query: 127 SDNIGGGIDNWNLRQPLGVCAGVTPFNFPVMVPLWMIPLALVAGNCFILKPSERDPSASL 186 +DNIGGGIDNWNLRQPLGV AG+TPFNFPVMVP+WM P+AL GN F+LKPSERDPS SL Sbjct: 132 TDNIGGGIDNWNLRQPLGVVAGITPFNFPVMVPMWMFPVALACGNTFVLKPSERDPSPSL 191 Query: 187 LMARLLTEAGLPDGVFNVVQGDKVAVDALLQHPDIEAISFVGSTPIAEYIHQQGTAQGKR 246 L+A LL +AGLPDGVFNVVQG K AVDALL H D++A+SFVGSTPIAEYI+ +GT +GKR Sbjct: 192 LIADLLKQAGLPDGVFNVVQGGKEAVDALLAHKDVQALSFVGSTPIAEYIYTEGTRRGKR 251 Query: 247 VQALGGAKNHMIVMPDADLDQAADALIGAAYGSAGERCMAISIAVAVGDVGDELIAKLLP 306 VQALGGAKNH++VMPDADLDQA DALIGAAYGSAGERCMAIS+AVAVGDV D+L+ +L Sbjct: 252 VQALGGAKNHLVVMPDADLDQAVDALIGAAYGSAGERCMAISVAVAVGDVADKLVPRLAE 311 Query: 307 RIDQLKIGNGQQPGTDMGPLVTAEHKAKVEGFIDAGVAEGARLIVDGRGFKVPGAEQGFF 366 R LKI NG Q +MGPLVTA HKAKVEG+I GV EGA+L+ DGRG KV G E GF+ Sbjct: 312 RARSLKIRNGMQDDAEMGPLVTAAHKAKVEGYIAKGVEEGAKLVTDGRGHKVDGHENGFY 371 Query: 367 VGATLFDQVTAEMSIYQQEIFGPVLGIVRVPDFATAVALINAHEFGNGVSCFTRDGGIAR 426 VG TLFD VT +M+IY++EIFGPVL +VRV D A AV LIN HE+GNGVSC+T DGG+AR Sbjct: 372 VGGTLFDNVTPDMTIYKEEIFGPVLSVVRVHDLAEAVDLINGHEYGNGVSCYTSDGGVAR 431 Query: 427 AFARSIKVGMVGINVPIPVPMAWHSFGGWKRSLFGDHHAYGEEGLRFYSRYKSVMQRWPD 486 AF+R I+VGMVGINVPIPVPMAWHSFGGWKRSLFGDHHAYGEEG+RFY+RYKS+MQRWPD Sbjct: 432 AFSRQIQVGMVGINVPIPVPMAWHSFGGWKRSLFGDHHAYGEEGIRFYTRYKSIMQRWPD 491 Query: 487 SIAKGPEFSMPTAQ 500 SI KG EF+MP A+ Sbjct: 492 SIGKGAEFTMPVAK 505 Lambda K H 0.320 0.137 0.412 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: 833 Number of extensions: 28 Number of successful extensions: 1 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: 500 Length of database: 505 Length adjustment: 34 Effective length of query: 466 Effective length of database: 471 Effective search space: 219486 Effective search space used: 219486 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