Align 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized)
to candidate 6938547 Sama_2650 methylmalonate-semialdehyde dehydrogenase (RefSeq)
Query= metacyc::MONOMER-20632 (478 letters) >lcl|FitnessBrowser__SB2B:6938547 Sama_2650 methylmalonate-semialdehyde dehydrogenase (RefSeq) Length = 496 Score = 265 bits (676), Expect = 3e-75 Identities = 149/472 (31%), Positives = 245/472 (51%), Gaps = 3/472 (0%) Query: 4 TLRHYIGGERVAADAPAESLNPSNTNDVVAKVPMGGQAEVDAAVDAARKAFPAWADASPE 63 ++ H++ G+ A A +++ T + A+V + EV A+ A+ AF +W+ +P Sbjct: 3 SITHFVNGQHTAPSARTQTVFEPATGEARAQVSLASTQEVGEAIAVAKAAFESWSQMTPL 62 Query: 64 VRSDLLDKVGSTIIARSADIGRLLAREEGKTLAEGIGETVRAGRIFKYFAGEALRRHGQN 123 R+ +L K + + A ++ +L+ RE GK L + GE +R + ++ G G++ Sbjct: 63 NRARILFKFKALVEANMDELAQLITREHGKVLDDAKGELIRGLEVVEFACGIPHLLKGEH 122 Query: 124 LESTRPGVEIQTYRQAVGVYGLITPWNFPIAIPAWKAAPALAFGNTVVIKPAGPTPATAN 183 GV+ Q +GV I P+NFP+ +P W A+A GNT ++KP+ P++ Sbjct: 123 TAQVGTGVDAWAVNQPLGVVAGIAPFNFPVMVPMWMFPIAIACGNTFIMKPSEKDPSSVM 182 Query: 184 VLADIMAECGAPAGVFNMLFGRGSMGDALIKHKDVDGVSFTGSQGVGAQVAAAAVARQAR 243 +A+++ E G P GVFN++ G D L+ HKD+ VSF GS + + A A A R Sbjct: 183 RIAELLKEAGLPDGVFNVVNGDKEAVDTLLTHKDIQAVSFVGSTPIAEYIYATASAHGKR 242 Query: 244 VQLEMGGKNPLIVLDDADLERAVAIALDGSFFATGQRCTASSRLIVQDGIHDKFVALLAE 303 VQ G KN ++++ DADL++AV + ++ + G+RC A S ++ D V L Sbjct: 243 VQALGGAKNHMLLMPDADLDQAVNALMGAAYGSAGERCMAISVVLAVGDAGDALVEKLLP 302 Query: 304 KVAALRVGDALDPNTQIGPAVSEDQMETSYRYIDIAASEGGRVVTGGDRIKLDNP--GWY 361 K+AAL+VG+ L P+ ++GP +S ++ Y++ EG ++ G + +++ G++ Sbjct: 303 KIAALKVGNGLIPDMEMGPLISAQHLDKVSSYVEAGVREGASLLVDGRELSMEDKANGYF 362 Query: 362 VRPTLIADTQAGMRINNEEVFGPVASTIRVKSYEEALEIANGVEFGLSAGIATTSLKHAR 421 + L M I EE+FGPV S +RV Y AL++ N EFG I T S + AR Sbjct: 363 LGACLFDHVTPQMSIYKEEIFGPVLSIVRVPDYNSALQLINDHEFGNGTAIFTQSGEAAR 422 Query: 422 HFQRYARAGMTMVNLATAGVDYHVPFGGTKSSSYG-AREQGFAAVEFFTQTK 472 HF + + GM VN+ FGG K S +G G V F+T+ K Sbjct: 423 HFCHHVQVGMVGVNVPIPVPMAFHSFGGWKRSLFGPLHMHGPDGVRFYTKRK 474 Lambda K H 0.317 0.133 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: 527 Number of extensions: 14 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: 478 Length of database: 496 Length adjustment: 34 Effective length of query: 444 Effective length of database: 462 Effective search space: 205128 Effective search space used: 205128 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 (21.7 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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