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) >FitnessBrowser__SB2B:6938547 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 Apr 09 2024. 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