Align Malonate-semialdehyde dehydrogenase; MSA dehydrogenase; EC 1.2.1.-; Methylmalonate-semialdehyde dehydrogenase; MMSA dehydrogenase; MSDH; EC 1.2.1.27 (uncharacterized)
to candidate WP_011612882.1 TERY_RS16535 L-glutamate gamma-semialdehyde dehydrogenase
Query= curated2:A7BJC4 (487 letters) >NCBI__GCF_000014265.1:WP_011612882.1 Length = 993 Score = 246 bits (629), Expect = 2e-69 Identities = 161/485 (33%), Positives = 253/485 (52%), Gaps = 16/485 (3%) Query: 11 INGEWVESKTDQYEDVVNPA-TKEVLCQVPISTKEDIDYAAQTAAEAFETWSKVAVPRRA 69 INGE+ + T Q D +NP+ +KEV+ ++ + + E + A Q A AF +W K V R Sbjct: 508 INGEY--TNTAQIVDSLNPSNSKEVVGKIGLISVEQAEQAIQAAKAAFPSWKKTPVRERT 565 Query: 70 RILFNFQQLLSQHKEELAHLITIENGKNTKEALGEVGRGIENVEFAAGAPSLMMGDSLAS 129 RIL L+ + + ELA + +E GK + EV I+ + A + Sbjct: 566 RILRKAADLMEKRRHELAAWMVLEVGKPLNQGNAEVSEAIDFCRYYADEMERLEQGYNYD 625 Query: 130 IATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTPLLTEKLV 189 +A + + Y+ P G+ I+P+NFP+ +P M ++ GN +LKP+ + ++ K+ Sbjct: 626 VAGETDRYYYQ-PRGISLVISPWNFPLAIPTGMTVSSLVTGNCTLLKPAAVSSVIASKIS 684 Query: 190 ELFEKAGLPKGVFNVVYGAHDVVNGIL-EHPEIKAISFVGSKPVGEYVYKKGS------E 242 E+ +AG PKGVF V G V + +HP + +I+F GS VG ++Y + + + Sbjct: 685 EILLEAGFPKGVFQFVPGNGSTVGDFMVKHPSVNSITFTGSMEVGCHIYAQAAVLQPRQK 744 Query: 243 HLKRVQSLTGAKNHTIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIADEFMA 302 HLKRV + G KN IV A+L+ V +V +AFG +G++C AC+ V V I D F+ Sbjct: 745 HLKRVIAEMGGKNAIIVDESADLDQAVAGVVYSAFGYSGQKCSACSRVVVLATIYDSFVN 804 Query: 303 KLQEKVADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGRENVSDDGY 362 +L E + IG+ +GPVI E +KR YI KG +E + + DGY Sbjct: 805 RLVEATRSLNIGDAEKPSTQVGPVIDEKAQKRIQEYIVKGKQEAEVAI---EMSAPKDGY 861 Query: 363 FVGPTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTSNSNAI 422 FVGP IF +V+ TI ++EIF PVL+V++ N +A+EIAN + FA L++ + I Sbjct: 862 FVGPVIFKDVSPSATIAQEEIFGPVLAVMKADNFTQALEIANGTNFALTGGLYSRTPSHI 921 Query: 423 RYFRENIDAGMLGINLGVP-APMAFFPFSGWKSSFFGTLHANGKDSVDFYTRKKVVTARF 481 + + G L IN G+ A ++ PF G+K S G+ A G D + + + +T Sbjct: 922 EQAKAEFEVGNLYINRGITGAIVSRQPFGGFKLSGVGS-KAGGPDYLLQFLEPRTITENI 980 Query: 482 PAPDF 486 F Sbjct: 981 QRQGF 985 Lambda K H 0.318 0.136 0.397 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: 976 Number of extensions: 50 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: 487 Length of database: 993 Length adjustment: 39 Effective length of query: 448 Effective length of database: 954 Effective search space: 427392 Effective search space used: 427392 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: 54 (25.4 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