Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate H281DRAFT_01202 H281DRAFT_01202 methylmalonate-semialdehyde dehydrogenase [acylating]
Query= BRENDA::Q02252 (535 letters) >FitnessBrowser__Burk376:H281DRAFT_01202 Length = 502 Score = 603 bits (1554), Expect = e-177 Identities = 280/482 (58%), Positives = 366/482 (75%) Query: 39 TVKLFIGGKFVESKSDKWIDIHNPATNEVIGRVPQATKAEMDAAIASCKRAFPAWADTSV 98 TVKL I G+FV+S++ +W D+ NPAT +V+ RVP AT E+D AI S AF W DT + Sbjct: 8 TVKLLINGEFVDSRTTEWRDVVNPATQQVLARVPFATAGEVDEAIRSAHAAFKTWKDTPI 67 Query: 99 LSRQQVLLRYQQLIKENLKEIAKLITLEQGKTLADAEGDVFRGLQVVEHACSVTSLMMGE 158 +R +++L+YQ LI+E++ IAK ++ EQGKT+ DAEGD+FRGL+VVEHACS+ SL GE Sbjct: 68 GARMRIMLKYQALIREHMPRIAKTLSAEQGKTIPDAEGDIFRGLEVVEHACSIGSLQQGE 127 Query: 159 TMPSITKDMDLYSYRLPLGVCAGIAPFNFPAMIPLWMFPMAMVCGNTFLMKPSERVPGAT 218 ++ +D Y+ R PLGVCAGI PFNFPAMIPLWMFPMA+VCGNTF++KPSE+ P +T Sbjct: 128 FAENVAGGVDTYTLRQPLGVCAGITPFNFPAMIPLWMFPMAIVCGNTFVLKPSEQDPMST 187 Query: 219 MLLAKLLQDSGAPDGTLNIIHGQHEAVNFICDHPDIKAISFVGSNKAGEYIFERGSRHGK 278 M L +L ++G P G LN++HG + V+ +C H +KA+SFVGS G +++ GS HGK Sbjct: 188 MQLVELALEAGVPKGVLNVVHGGKDVVDALCTHELVKAVSFVGSTAVGTHVYRLGSEHGK 247 Query: 279 RVQANMGAKNHGVVMPDANKENTLNQLVGAAFGAAGQRCMALSTAVLVGEAKKWLPELVE 338 RVQ+ MGAKNH VV+PDAN+E TLN L GA FGAAGQRCMA S VLVG A++WLPE+V Sbjct: 248 RVQSMMGAKNHAVVLPDANREQTLNALAGAGFGAAGQRCMATSVVVLVGAAQQWLPEIVA 307 Query: 339 HAKNLRVNAGDQPGADLGPLITPQAKERVCNLIDSGTKEGASILLDGRKIKVKGYENGNF 398 AK L+VNAG++P D+GP+++ AKER+ LI++G KEGA++ LDGR + V GYE GNF Sbjct: 308 KAKTLKVNAGNEPNTDIGPVVSRAAKERILGLIEAGVKEGATLALDGRDVTVPGYEQGNF 367 Query: 399 VGPTIISNVKPNMTCYKEEIFGPVLVVLETETLDEAIQIVNNNPYGNGTAIFTTNGATAR 458 +GPTI S+V M Y+ EIFGPVL+VL TLD+AI +VN+NP+GNG +FT +GA AR Sbjct: 368 IGPTIFSDVSTEMEIYRTEIFGPVLLVLNAATLDDAIALVNSNPFGNGVGLFTQSGAAAR 427 Query: 459 KYAHLVDVGQVGVNVPIPVPLPMFSFTGSRSSFRGDTNFYGKQGIQFYTQLKTITSQWKE 518 K+ +DVGQVG+N+PIPVP+P FSFTGSR S GD YGKQ +QFYTQ KT+T++W + Sbjct: 428 KFQSEIDVGQVGINIPIPVPVPFFSFTGSRGSKLGDLGPYGKQVVQFYTQTKTVTARWFD 487 Query: 519 ED 520 +D Sbjct: 488 DD 489 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: 678 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: 535 Length of database: 502 Length adjustment: 35 Effective length of query: 500 Effective length of database: 467 Effective search space: 233500 Effective search space used: 233500 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