Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate PP_4667 PP_4667 methylmalonate-semialdehyde dehydrogenase
Query= BRENDA::Q02252 (535 letters) >FitnessBrowser__Putida:PP_4667 Length = 508 Score = 622 bits (1603), Expect = 0.0 Identities = 294/488 (60%), Positives = 383/488 (78%) Query: 34 SSSVPTVKLFIGGKFVESKSDKWIDIHNPATNEVIGRVPQATKAEMDAAIASCKRAFPAW 93 S+ V VKL I G++VESK+ +W DI NPAT EV+ RVP AT E+DAA+A+ +RAF W Sbjct: 9 STKVEQVKLLIDGQWVESKTTEWRDIVNPATQEVLARVPFATVEEVDAAVAAAQRAFQTW 68 Query: 94 ADTSVLSRQQVLLRYQQLIKENLKEIAKLITLEQGKTLADAEGDVFRGLQVVEHACSVTS 153 +T + +R +++L+ Q LI+E+ K IA++++ EQGKTLADAEGD+FRGL+VVEHA S+ + Sbjct: 69 RNTPIGARMRIMLKLQALIREHTKRIAQVLSAEQGKTLADAEGDIFRGLEVVEHAASIGT 128 Query: 154 LMMGETMPSITKDMDLYSYRLPLGVCAGIAPFNFPAMIPLWMFPMAMVCGNTFLMKPSER 213 L MGE ++ +D Y+ R P+GVCAGI PFNFPAMIPLWMFPMA+VCGNTF++KPSE+ Sbjct: 129 LQMGEFAENVAGGVDTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAIVCGNTFVLKPSEQ 188 Query: 214 VPGATMLLAKLLQDSGAPDGTLNIIHGQHEAVNFICDHPDIKAISFVGSNKAGEYIFERG 273 P +TMLL +L ++G P G LN++HG + V+ IC H DIKAISFVGS + G +++ G Sbjct: 189 DPLSTMLLVELALEAGVPAGVLNVVHGGKQVVDAICTHQDIKAISFVGSTEVGTHVYNLG 248 Query: 274 SRHGKRVQANMGAKNHGVVMPDANKENTLNQLVGAAFGAAGQRCMALSTAVLVGEAKKWL 333 S+HGKRVQ+ MGAKNH VV+PDAN+ T+N LVGAAFGAAGQRCMA S AVLVG+A++WL Sbjct: 249 SQHGKRVQSMMGAKNHAVVLPDANRTQTINALVGAAFGAAGQRCMATSVAVLVGKAREWL 308 Query: 334 PELVEHAKNLRVNAGDQPGADLGPLITPQAKERVCNLIDSGTKEGASILLDGRKIKVKGY 393 P++ E A L+VNAG +PG D+GP+++ +AKERV LI+SG KEGA + LDGR +KV GY Sbjct: 309 PDIKEAASKLKVNAGCEPGTDVGPVVSKRAKERVLGLIESGIKEGAKLELDGRDVKVPGY 368 Query: 394 ENGNFVGPTIISNVKPNMTCYKEEIFGPVLVVLETETLDEAIQIVNNNPYGNGTAIFTTN 453 E GNFVGPT+ S VK +M Y +EIFGPVLV LE +TLDEAI +VN NP+GNGT +FT + Sbjct: 369 EQGNFVGPTLFSGVKTDMQVYTQEIFGPVLVTLEVDTLDEAIALVNANPFGNGTGLFTQS 428 Query: 454 GATARKYAHLVDVGQVGVNVPIPVPLPMFSFTGSRSSFRGDTNFYGKQGIQFYTQLKTIT 513 GA ARK+ +D+GQVG+N+PIPVP+P FSFTGSR S GD YGKQ +QFYTQ KT+T Sbjct: 429 GAAARKFQSEIDIGQVGINIPIPVPVPFFSFTGSRGSKLGDLGPYGKQVVQFYTQTKTVT 488 Query: 514 SQWKEEDA 521 ++W ++D+ Sbjct: 489 ARWFDDDS 496 Lambda K H 0.318 0.133 0.391 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: 701 Number of extensions: 26 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: 535 Length of database: 508 Length adjustment: 35 Effective length of query: 500 Effective length of database: 473 Effective search space: 236500 Effective search space used: 236500 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:
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