Align Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) (characterized)
to candidate WP_086509263.1 BZY95_RS07130 aldehyde dehydrogenase family protein
Query= reanno::pseudo3_N2E3:AO353_05990 (507 letters) >NCBI__GCF_002151265.1:WP_086509263.1 Length = 496 Score = 259 bits (661), Expect = 2e-73 Identities = 165/473 (34%), Positives = 243/473 (51%), Gaps = 7/473 (1%) Query: 18 IDGQWVESQTTEWHDIVNPATQQVLAKVPFATPAEVDA--AISAAHRAFQTWKLTPIGAR 75 IDGQWV S + + NPA Q L + F DA AI+AA RAF W+ TPI R Sbjct: 23 IDGQWVASGSGATFENRNPADQDDLLGL-FQASGVDDARRAIAAADRAFTAWRETPISQR 81 Query: 76 MRIMLKLQALIREHSKRIAVVLSAEQGKTIADAEGDIFRGLEVVEHACSIGSLQMGEFAE 135 +I+ + + E+ ++ A L+ E+GK +A++ ++ R + + G GE Sbjct: 82 AKILNRAADYLMENVEQFARELTREEGKLLANSRDEVTRSAQTLRFYAVEGQTITGETFP 141 Query: 136 NVAGGVDTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAIACGNTFVLKPSEQDPMSTMLL 195 + YT R+P+GV ITP+NFP IP A+ GNT V KPS P+ L Sbjct: 142 QDDAKMTVYTQREPLGVATIITPWNFPISIPARKIAPALITGNTVVFKPSSDAPLIGYRL 201 Query: 196 VELAIEAGIPAGVLNVVHGGKDVV-DALCTHKDIKAVSFVGSTAVGTHVYDLAGKHGKRV 254 E AG+PAGV N + G + + + + +KA+SF GSTA G ++ A R Sbjct: 202 AEALHHAGVPAGVFNFITGAASAIGEEITANPVVKAISFTGSTAAGERIHRAAAM-ATRT 260 Query: 255 QSMMGAKNHAVVLPDANREQALNALVGAGFGAAGQRCMATSVVVLVGAAKQ-WLPDLKAL 313 Q +G KN +VL DA+ + A++ V GF GQ C TS V++ + KQ +L L Sbjct: 261 QMELGGKNPLIVLEDADIDTAVDLTVKGGFSLTGQACTGTSRVLIARSRKQEYLTRLVEQ 320 Query: 314 AQKLKVNAGSEPGTDVGPVISKRAKARILDLIESGIKEGAKLELDGRDITVPGYEKGNFV 373 + LK+ G G +GP+ +++ +L +E+G KE + G +T Y KG +V Sbjct: 321 VKTLKIGNGMSEGIQIGPLATRQQLDTVLGYVETGRKEATHV-YGGEHLTEGDYAKGFYV 379 Query: 374 GPTLFSGVTTDMQIYTQEIFGPVLVVLEVDTLDQAIALVNANPFGNGTGLFTQSGAAARK 433 P +FS VT +M+I +EIFGPV+ V+EVD + AIA N P+G GL T++ ++ Sbjct: 380 TPAIFSDVTQEMRIAREEIFGPVVAVIEVDGYEDAIAKANDTPYGLAAGLVTKNFDYIQR 439 Query: 434 FQNEIDVGQVGINIPIPVPVPFFSFTGSRGSKLGDLGPYGKQVVQFYTQTKTV 486 F +I G V IN + F G + S G+ + F+TQTKTV Sbjct: 440 FPLDIQAGTVKINRTTTGNLVNAPFGGLKQSSTSTFRESGRAGLDFFTQTKTV 492 Lambda K H 0.319 0.135 0.396 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: 585 Number of extensions: 27 Number of successful extensions: 7 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: 507 Length of database: 496 Length adjustment: 34 Effective length of query: 473 Effective length of database: 462 Effective search space: 218526 Effective search space used: 218526 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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