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 WP_086509263.1 BZY95_RS07130 aldehyde dehydrogenase family protein
Query= SwissProt::Q02253 (535 letters) >NCBI__GCF_002151265.1:WP_086509263.1 Length = 496 Score = 258 bits (658), Expect = 5e-73 Identities = 161/473 (34%), Positives = 238/473 (50%), Gaps = 5/473 (1%) Query: 43 FIDGKFVESKSDKWIDIHNPAT-NEVVGRVPQSTKAEMEAAVAACKRAFPAWADTSILSR 101 +IDG++V S S + NPA ++++G S + A+AA RAF AW +T I R Sbjct: 22 YIDGQWVASGSGATFENRNPADQDDLLGLFQASGVDDARRAIAAADRAFTAWRETPISQR 81 Query: 102 QQVLLRYQQLIKENLKEIARLITLEQGKTLADAEGDVFRGLQVVEHACSVTSLMLGETMP 161 ++L R + EN+++ AR +T E+GK LA++ +V R Q + + GET P Sbjct: 82 AKILNRAADYLMENVEQFARELTREEGKLLANSRDEVTRSAQTLRFYAVEGQTITGETFP 141 Query: 162 SITKDMDLYSYRLPLGVCAGIAPFNFPAMIPLWMFPMAMVCGNTFLMKPSERVPGATMLL 221 M +Y+ R PLGV I P+NFP IP A++ GNT + KPS P L Sbjct: 142 QDDAKMTVYTQREPLGVATIITPWNFPISIPARKIAPALITGNTVVFKPSSDAPLIGYRL 201 Query: 222 AKLLQDSGAPDGTLNIIHGQHEAV-NFICDHPDIKAISFVGSNQAGEYIFERGSRNGKRV 280 A+ L +G P G N I G A+ I +P +KAISF GS AGE I R + R Sbjct: 202 AEALHHAGVPAGVFNFITGAASAIGEEITANPVVKAISFTGSTAAGERI-HRAAAMATRT 260 Query: 281 QANMGAKNHGVVMPDANKENTLNQLVGAAFGAAGQRCMALSTAVLVGEAK-KWLPELVER 339 Q +G KN +V+ DA+ + ++ V F GQ C S ++ K ++L LVE+ Sbjct: 261 QMELGGKNPLIVLEDADIDTAVDLTVKGGFSLTGQACTGTSRVLIARSRKQEYLTRLVEQ 320 Query: 340 AKNLRVNAGDQPGADLGPLITPQAKERVCNLIDSGAKEGASILLDGRKIKVKGYENGNFV 399 K L++ G G +GPL T Q + V +++G KE A+ + G + Y G +V Sbjct: 321 VKTLKIGNGMSEGIQIGPLATRQQLDTVLGYVETGRKE-ATHVYGGEHLTEGDYAKGFYV 379 Query: 400 GPTIISNVKPSMTCYKEEIFGPVLVVLETETLDEAIKIVNDNPYGNGTAIFTTNGAIARK 459 P I S+V M +EEIFGPV+ V+E + ++AI ND PYG + T N ++ Sbjct: 380 TPAIFSDVTQEMRIAREEIFGPVVAVIEVDGYEDAIAKANDTPYGLAAGLVTKNFDYIQR 439 Query: 460 YAHMVDVGQVGVNVPIPVPLPMFSFTGSRSSFRGDTNFYGKQGIQFYTQLKTI 512 + + G V +N L F G + S G+ G+ F+TQ KT+ Sbjct: 440 FPLDIQAGTVKINRTTTGNLVNAPFGGLKQSSTSTFRESGRAGLDFFTQTKTV 492 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: 551 Number of extensions: 30 Number of successful extensions: 6 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: 496 Length adjustment: 35 Effective length of query: 500 Effective length of database: 461 Effective search space: 230500 Effective search space used: 230500 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 24 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