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 WP_083831993.1 AZO_RS11360 aldehyde dehydrogenase
Query= curated2:Q5L025 (488 letters) >NCBI__GCF_000061505.1:WP_083831993.1 Length = 478 Score = 232 bits (592), Expect = 2e-65 Identities = 159/478 (33%), Positives = 240/478 (50%), Gaps = 16/478 (3%) Query: 15 IGGQWVASSGTETLEVPNPATGEVLARVPISTKEDVDQAVQAAKKAFAT--WKDVPVPKR 72 IG +W A+ ETL V +PATG+ A VP D+D+AV AA++AF + W + R Sbjct: 3 IGAEWSAAVSGETLAVLDPATGQAFATVPAGGAADIDRAVAAARRAFESGEWPKMRPVDR 62 Query: 73 ARIMFSFHHLLNQHHEELAELVVQENGKAYKEA-YGEIQRGIECVEFAAGAPTLLMGESL 131 R++ F L+ + +ELAE+ +NGK A + ++ ++ + + AG T + G ++ Sbjct: 63 ERLLLKFADLIEANAQELAEIEALDNGKPVMMARHVDVALVVDFLRYMAGWATKIEGSTM 122 Query: 132 S-NIAEEIDSEMF----RYPLGVVAGITPFNFPMMVPLWMFPLAIVCGNTFVLKPSERTP 186 ++ D E+F R P+GVV I P+NFP+++ W A+ G T VLKP+E TP Sbjct: 123 DVSVPLMRDRELFGFTRREPVGVVGAIIPWNFPLLMAAWKVGPALTSGCTMVLKPAEETP 182 Query: 187 ILANKLAELFTEAGAPPGVLNVVHGAHEVVN-ALIDHEDIRAISFVGSQPVAKYVYERTA 245 + A + AEL EAG P GVLNVV G + AL H+ I ++F GS + K V + Sbjct: 183 LTALRFAELALEAGYPAGVLNVVTGHGDTAGAALASHKGIEKVAFTGSTEIGKLVGKAAI 242 Query: 246 AQGKRVQALSGAKNHHIVMPDADVETAVQHVISSAFGSAGQRCMACSAVVI-VGENETFV 304 RV G K+ IV+ DAD A + F + GQ C A S + I E V Sbjct: 243 DNMTRVSLELGGKSPVIVLDDADPAMAAAGAAQAIFFNQGQVCTAGSRLFIHKSRFEKVV 302 Query: 305 RRLKQKADELIIGNGMDPEVLLTPVIRQSHREKVLGYIQKGIEEGAVLLRDGRKEMDDRP 364 L A + +G G+DP + P++ +++VLGYI+ G+ EGA G + Sbjct: 303 EGLSGIAASMKLGPGIDPSTQIGPLVSAVQQQRVLGYIESGLAEGARAATGGGAGGE--- 359 Query: 365 EGNFLGPTIFDYVTPDMTIAKEEIFAPVLSLLRANDLDEALSYIRKSRYGNGATIYTKDA 424 G F+ PT+ M + +EEIF PV+ + DLDE + YG A+I++ D Sbjct: 360 AGYFVKPTVLVNAHDAMKVVREEIFGPVVVAMPYEDLDEVAHRANDTPYGLAASIWSNDL 419 Query: 425 KAVRKFREEADAGMLGINVGVPATMAFFPFSGWKDSFYGDLHVNGKDGVNFYTRKKMI 482 V + + AG + +N A PF G+K S G G+ ++ YT K + Sbjct: 420 TRVHRLIPKIKAGTVWVNCHNILDNA-MPFGGYKQSGIG--REMGRAVLDMYTESKSV 474 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: 529 Number of extensions: 25 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: 478 Length adjustment: 34 Effective length of query: 454 Effective length of database: 444 Effective search space: 201576 Effective search space used: 201576 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: 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