Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate Ac3H11_2357 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27)
Query= BRENDA::Q02252 (535 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2357 Length = 507 Score = 612 bits (1578), Expect = e-179 Identities = 297/487 (60%), Positives = 374/487 (76%), Gaps = 1/487 (0%) Query: 38 PTVKLFIGGKFVESKSDKWIDIHNPATNEVIGRVPQATKAEMDAAIASCKRAFPAWADTS 97 PTVKL IGGKFVESK+ +W D+ NPAT EV+ RVP AT E+DAA+AS + AF W T+ Sbjct: 12 PTVKLLIGGKFVESKTTQWRDVVNPATQEVLARVPFATPEEIDAAVASAQEAFKTWKKTA 71 Query: 98 VLSRQQVLLRYQQLIKENLKEIAKLITLEQGKTLADAEGDVFRGLQVVEHACSVTSLMMG 157 + +R ++ L+YQQLI+EN+ E+A ++T EQGKTL DAEGDVFRGL+VVEHA S+ +L +G Sbjct: 72 IGARARIFLKYQQLIRENMAELAAILTAEQGKTLPDAEGDVFRGLEVVEHAASIGNLQLG 131 Query: 158 ETMPSITKDMDLYSYRLPLGVCAGIAPFNFPAMIPLWMFPMAMVCGNTFLMKPSERVPGA 217 E ++ +D Y+ PLGVCAGI PFNFPAMIPLWMFPMA+ GNTF++KPSE+ P Sbjct: 132 ELANNVAGGVDTYTLMQPLGVCAGITPFNFPAMIPLWMFPMAIATGNTFVLKPSEQDPMV 191 Query: 218 TMLLAKLLQDSGAPDGTLNIIHGQHEAVNFICDHPDIKAISFVGSNKAGEYIFERGSRHG 277 TM L +L ++G P G LN+IHG AVN ICDH DIKAISFVGS K G +++ R S +G Sbjct: 192 TMRLVELALEAGIPPGVLNVIHGGEAAVNAICDHKDIKAISFVGSTKVGTHVYNRASLNG 251 Query: 278 KRVQANMGAKNHGVVMPDANKENTLNQLVGAAFGAAGQRCMALSTAVLVGEAKKWLPELV 337 KRVQ MGAKNH +VMPDANKE TLN L GAAFGAAGQRCMALS VLVGEA+KW+PELV Sbjct: 252 KRVQCMMGAKNHAIVMPDANKEQTLNALAGAAFGAAGQRCMALSVVVLVGEAQKWIPELV 311 Query: 338 EHAKNLRVNAGDQPGADLGPLITPQAKERVCNLIDSGTKEGASILLDGRKIKVKGYENGN 397 AK L+V+AG + G D+GP+++ AK+RV +LI+ G +GA++ LDGR +V GYE GN Sbjct: 312 AKAKTLKVSAGVEKGTDVGPVVSCAAKDRVQSLIERGIADGATLELDGRNPEVAGYEKGN 371 Query: 398 FVGPTIISNVKPNMTCYKEEIFGPVLVVLETETLDEAIQIVNNNPYGNGTAIFTTNGATA 457 FVGPT+ S VKP M+ Y +EIFGPVL + +DEAI +N+NP GNGTAIFT +GA A Sbjct: 372 FVGPTVFSGVKPGMSIYDQEIFGPVLCLSAAADIDEAIAFINDNPNGNGTAIFTQSGAAA 431 Query: 458 RKYAHLVDVGQVGVNVPIPVPLPMFSFTGSRSSFRGDTNFYGKQGIQFYTQLKTITSQWK 517 RK+ +DVGQVG+NVPIPVP+P+FSF+GSR+S GD YGKQ + FYTQ KT+T++W Sbjct: 432 RKFQEEIDVGQVGINVPIPVPVPLFSFSGSRASKLGDLGPYGKQVVLFYTQTKTVTARW- 490 Query: 518 EEDATLS 524 +D+T+S Sbjct: 491 FDDSTIS 497 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: 709 Number of extensions: 33 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: 535 Length of database: 507 Length adjustment: 35 Effective length of query: 500 Effective length of database: 472 Effective search space: 236000 Effective search space used: 236000 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