Align Methylmalonate-semialdehyde dehydrogenase [acylating], mitochondrial; MMSDH; Malonate-semialdehyde dehydrogenase [acylating]; Aldehyde dehydrogenase family 6 member A1; EC 1.2.1.18; EC 1.2.1.27 (characterized)
to candidate Pf1N1B4_2417 Betaine aldehyde dehydrogenase (EC 1.2.1.8)
Query= SwissProt::Q02253 (535 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2417 Length = 490 Score = 227 bits (579), Expect = 7e-64 Identities = 136/437 (31%), Positives = 225/437 (51%), Gaps = 7/437 (1%) Query: 41 KLFIDGKFVESKSDKWIDIHNPATNEVVGRVPQSTKAEMEAAVAACKRAFPAWADTSILS 100 KL+IDG + ++ SD + NPA EV+ V ++TK ++E AV + ++ WA + + Sbjct: 8 KLYIDGGYSDASSDATFEAINPANGEVLATVQRATKEDVERAVVSAEKGQKIWAAMTAME 67 Query: 101 RQQVLLRYQQLIKENLKEIARLITLEQGKTLADAEG-DVFRGLQVVEHACSVTSLMLGET 159 R ++L R +++E E+A L TL+ GK ++ D+ G V+E+ + + GE Sbjct: 68 RSRILRRAVDILRERNDELAALETLDTGKAYSETRYVDIVTGADVLEYYAGLVPAIEGEQ 127 Query: 160 MPSITKDMDLYSYRLPLGVCAGIAPFNFPAMIPLWMFPMAMVCGNTFLMKPSERVPGATM 219 +P T +Y+ R PLG+ AGI +N+P I LW A+ GN + KPSE T+ Sbjct: 128 IPLRTTSF-VYTRREPLGIVAGIGAWNYPIQIALWKSAPALAAGNAMIFKPSEVTSLTTL 186 Query: 220 LLAKLLQDSGAPDGTLNIIHGQ-HEAVNFICDHPDIKAISFVGSNQAGEYIFERGSRNG- 277 LA++ ++G P G N++ G E ++ +HP I+ ISF G G+ + S + Sbjct: 187 KLAEIYTEAGLPAGVFNVLTGSGREVGTWLTEHPRIEKISFTGGTDTGKKVMASASGSSL 246 Query: 278 KRVQANMGAKNHGVVMPDANKENTLNQLVGAAFGAAGQRCMALSTAVLVGEAKK--WLPE 335 K V +G K+ ++ DA+ + + + A F ++GQ C T V V K + + Sbjct: 247 KDVTMELGGKSPLIIFDDADLDRAADTAMMANFYSSGQVCTN-GTRVFVPSHLKAAFEAK 305 Query: 336 LVERAKNLRVNAGDQPGADLGPLITPQAKERVCNLIDSGAKEGASILLDGRKIKVKGYEN 395 +VER +RV + + GPL++ E V I G +EGA +L G ++ + Sbjct: 306 IVERVARIRVGNPEDENTNFGPLVSFAHMESVLGYIAKGKEEGARLLCGGDRLTDGEFAK 365 Query: 396 GNFVGPTIISNVKPSMTCYKEEIFGPVLVVLETETLDEAIKIVNDNPYGNGTAIFTTNGA 455 G FV PT+ ++ MT +EEIFGPV+ +L ET +E I+ ND +G + T + Sbjct: 366 GAFVAPTVFTDCTDEMTIVREEIFGPVMSILTYETEEEVIRRANDTEFGLAAGVVTKDLN 425 Query: 456 IARKYAHMVDVGQVGVN 472 A + H ++ G +N Sbjct: 426 RAHRVIHQLEAGICWIN 442 Lambda K H 0.318 0.133 0.389 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: 560 Number of extensions: 28 Number of successful extensions: 5 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: 490 Length adjustment: 35 Effective length of query: 500 Effective length of database: 455 Effective search space: 227500 Effective search space used: 227500 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