Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate WP_011770382.1 PING_RS10720 betaine-aldehyde dehydrogenase
Query= BRENDA::P42412 (487 letters) >NCBI__GCF_000015285.1:WP_011770382.1 Length = 488 Score = 261 bits (668), Expect = 3e-74 Identities = 169/482 (35%), Positives = 255/482 (52%), Gaps = 10/482 (2%) Query: 1 MAEIRKLKNYINGEWVESKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFKTW 60 M+ + +NYI+G+++ + T + +V+NPAT +V V + + A ++A F TW Sbjct: 1 MSSLVVYQNYIHGQYIPNDTGETFEVINPATGQVSYLVETADQAVQQAAIESAKSGFATW 60 Query: 61 SKVAVPRRARILFNFQQLLSQHKEELAHLITIENGKNTKEA-LGEVGRGIENVEFAAGAP 119 SK+ R+RIL LL +H +ELA ++ GK +EA + +V G + +EF AG Sbjct: 61 SKMTPIERSRILLKAVALLREHNDELAVGEVLDTGKPWQEASVVDVVTGTDTIEFFAGLA 120 Query: 120 SLMMGDSLASIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSE 179 + G+ + D R P+G+ GI +N+P+ + CW A+A GN I KPSE Sbjct: 121 PSIEGNQ-QQVGDDFYYTR-REPLGICAGIGAWNYPLQIACWKAAPALACGNVMIFKPSE 178 Query: 180 RTPLLTEKLVELFEKAGLPKGVFNVVYGAHDVVNGILEHPEIKAISFVGSKPVGEYVYKK 239 TP +L E+F AG+P GVFNVV G V + H +I +SF G G+ V Sbjct: 179 ETPRGAMRLAEIFTLAGVPDGVFNVVQGDGRVGAWLTGHEDIAKVSFTGEVGTGKKVMAA 238 Query: 240 GSENLKRVQSLTGAKNHTIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIADE 299 + +LK V G K+ I+ NDA+LE+ V+ + F + GE C V V+E I Sbjct: 239 AAGSLKAVTMELGGKSPLIIFNDADLENAVSAAMLGNFYTQGEVCTNGTRVFVQEEIYPR 298 Query: 300 FMAKLQEKV-ADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGRE--- 355 F+ +L E+ +I G+ +D GP+I +D++++ L YI G EGA L+ G++ Sbjct: 299 FIKRLVERTEQNIICGDPMDPETNFGPLISKDHQQKVLDYITIGKAEGATLLTGGKKLHP 358 Query: 356 NVSDDGYFVGPTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLF 415 + DGYFV PTIF + T EMT+ K+EIF PV+SV+ + E + AN + A LF Sbjct: 359 ENAPDGYFVAPTIFTDCTDEMTLTKEEIFGPVMSVLTFSDEDEVVRRANDTRLGLAAGLF 418 Query: 416 TSNSNAIRYFRENIDAGMLGINLGVPAPMAFFPFSGWKSSFFGTLHANGKDSVDFYTRKK 475 T + IDAG+ IN +P A P G+K S G NG +++ YT+ K Sbjct: 419 TQDITRAHRVIHQIDAGICWINSFGASP-AEMPVGGYKMS--GVGRENGSETLKSYTQIK 475 Query: 476 VV 477 V Sbjct: 476 AV 477 Lambda K H 0.318 0.136 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: 587 Number of extensions: 31 Number of successful extensions: 4 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: 487 Length of database: 488 Length adjustment: 34 Effective length of query: 453 Effective length of database: 454 Effective search space: 205662 Effective search space used: 205662 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