Align Malonate-semialdehyde dehydrogenase 1; MSA dehydrogenase 1; EC 1.2.1.-; Methylmalonate-semialdehyde dehydrogenase 1; MMSA dehydrogenase 1; MSDH 1; EC 1.2.1.27 (uncharacterized)
to candidate 8501416 DvMF_2146 delta-1-pyrroline-5-carboxylate dehydrogenase (RefSeq)
Query= curated2:Q5L025 (488 letters) >FitnessBrowser__Miya:8501416 Length = 1013 Score = 234 bits (596), Expect = 1e-65 Identities = 160/464 (34%), Positives = 240/464 (51%), Gaps = 16/464 (3%) Query: 10 VLKNYIGGQWVASSGTETLEVPNPAT-GEVLARVPISTKEDVDQAVQAAKKAFATWKDVP 68 V+ +IGG+ V + +T+ NPA EV+ARV K +VD A++AA+KAF W+D Sbjct: 518 VIPLFIGGKDVTTD--DTIASTNPAKPAEVIARVCQGGKPEVDAAIEAAQKAFPAWRDTS 575 Query: 69 VPKRARIMFSFHHLLNQHHEELAELVVQENGKAYKEAYGEIQRGIECVEFAAGAPTLLMG 128 RA + + + EL+ V E GK + +A+ ++ GI+ +++ A L Sbjct: 576 PADRAMFLHRAADIARRRMFELSAWQVLEVGKQWDQAFHDVGEGIDFLDYYAHEMLRLGT 635 Query: 129 ESLSNIAEEIDSEMFRYPLGVVAGITPFNFPMMVPLWMFPLAIVCGNTFVLKPSERTPIL 188 A + +F P G+ A I P+NFP + + M AIV GN + KPS + Sbjct: 636 PRRMGRAPGELNHLFYQPKGIAAVIAPWNFPFAIAIGMAAAAIVTGNPVIFKPSSIASRI 695 Query: 189 ANKLAELFTEAGAPPGVLNVVHGAHEVV-NALIDHEDIRAISFVGSQPVAKYVYERTA-- 245 L E+F EAG P GV N V G V+ + L++H + I F GS V + E+ A Sbjct: 696 GYNLTEIFREAGLPEGVFNYVPGRSSVMGDYLVEHPQVSMICFTGSMEVGLRIQEKAAKV 755 Query: 246 ----AQGKRVQALSGAKNHHIVMPDADVETAVQHVISSAFGSAGQRCMACSAVVIVGE-N 300 Q KRV A G KN I+ DAD++ AV V+ SAFG GQ+C ACS V+++ Sbjct: 756 QPGQMQCKRVIAEMGGKNAIIIDDDADLDEAVLQVLYSAFGFQGQKCSACSRVIVLDPIY 815 Query: 301 ETFVRRLKQKADELIIGNGMDPEVLLTPVIRQSHREKVLGYIQKGIEEGAVLLRDGRKEM 360 + FV RL + A + IG DP + PV S ++ +L Y++ +EG VL+ K Sbjct: 816 DRFVERLVKAAQAIKIGPSEDPANYMGPVADASLQKNILEYVKVAEQEGKVLV----KRT 871 Query: 361 DDRPEGNFLGPTIFDYVTPDMTIAKEEIFAPVLSLLRANDLDEALSYIRKSRYGNGATIY 420 D EG ++ TI + + P IA+EEIF PVL+++RA + DEAL+ +R+ ++ Sbjct: 872 DIPAEGCYVPLTIVEGIKPHHRIAQEEIFGPVLAVMRAGNFDEALAIANGTRFALTGGVF 931 Query: 421 TKDAKAVRKFREEADAGMLGINVGVPATMA-FFPFSGWKDSFYG 463 ++ + + K R E G L +N G M PF G+K S G Sbjct: 932 SRSPENLTKARREFRVGNLYLNRGSTGAMVERQPFGGFKMSGVG 975 Lambda K H 0.319 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: 1047 Number of extensions: 44 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: 488 Length of database: 1013 Length adjustment: 39 Effective length of query: 449 Effective length of database: 974 Effective search space: 437326 Effective search space used: 437326 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 (21.8 bits) S2: 54 (25.4 bits)
This GapMind analysis is from Sep 17 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