Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate WP_013134994.1 ARNIT_RS05955 aldehyde dehydrogenase
Query= BRENDA::P42412 (487 letters) >NCBI__GCF_000092245.1:WP_013134994.1 Length = 482 Score = 245 bits (625), Expect = 3e-69 Identities = 151/482 (31%), Positives = 251/482 (52%), Gaps = 6/482 (1%) Query: 1 MAEIRKLKNYINGEWVESKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFKTW 60 M+E++ + YINGE++ + E V+NP+ K+++ +P T++D++ A ++A EA +W Sbjct: 1 MSEVKVYQMYINGEFINHV--EKEPVINPSDKQIISYIPKGTEDDVNQAVESAQEAQSSW 58 Query: 61 SKVAVPRRARILFNFQQLLSQHKEELAHLITIENGKNTKEALGEVGRGIENVEFAAGAPS 120 K+ R L + + ++ + LA +IT E GK AL EV + +++ A Sbjct: 59 EKLPAVERGNYLKKIAKKIRENADMLARVITEEQGKVLGLALVEVNFTADYMDYVAEWAR 118 Query: 121 LMMGDSLASIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSER 180 G+ + S + ++ PIGV GI P+NFP + A+ GNT ++KPS Sbjct: 119 RYEGEIIQSDRPNENIFLFKLPIGVAAGILPWNFPFFLIARKLAPALLTGNTIVIKPSSD 178 Query: 181 TPLLTEKLVELFEKAGLPKGVFNVVYGAH-DVVNGILEHPEIKAISFVGSKPVGEYVYKK 239 TP + +L ++ GLPKGVFN++ G +V + H ++ +SF GS P G + + Sbjct: 179 TPNNAFEFAKLVDEVGLPKGVFNLISGTGAEVGTPLAGHEKVGIVSFTGSVPTGVKIMEA 238 Query: 240 GSENLKRVQSLTGAKNHTIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIADE 299 ++N+ +V G K IV+ DANL+ V I + + G+ C V V + IA E Sbjct: 239 AAKNVTKVSLELGGKAPAIVMADANLDLAVEAIKNSRVINNGQVCNCAERVYVHKSIAKE 298 Query: 300 FMAKLQEKVADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGRENVSD 359 F K+ + + GN L + V +GP+I ED S ++ +E GA + G+ D Sbjct: 299 FSEKMTKAMEATTYGNPLKEEVDMGPLINEDAITHVQSLVDSAVEAGATITTGGKRAERD 358 Query: 360 DGYFVGPTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTSNS 419 DG++ PT+ +V +M+I ++EIF PVL ++ + L EAI +AN SEF + ++T N Sbjct: 359 DGFYYEPTVIVDVKQDMSIIQEEIFGPVLPIMTFETLDEAIALANDSEFGLTSSIYTQNI 418 Query: 420 NAIRYFRENIDAGMLGINLGVPAPMAFFPFSGWKSSFFGTLHANGKDSVDFYTRKKVVTA 479 + + I G IN M F +GW+ S G A+GK ++ + + KVV Sbjct: 419 DVAMRACKEIKFGETYINRENFEAMQGF-HAGWRKSGIG--GADGKHGLEEFLQTKVVYL 475 Query: 480 RY 481 +Y Sbjct: 476 QY 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: 553 Number of extensions: 31 Number of successful extensions: 3 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: 482 Length adjustment: 34 Effective length of query: 453 Effective length of database: 448 Effective search space: 202944 Effective search space used: 202944 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