Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate WP_010532044.1 ON01_RS16145 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::P25553 (479 letters) >NCBI__GCF_000224785.1:WP_010532044.1 Length = 480 Score = 337 bits (865), Expect = 4e-97 Identities = 181/469 (38%), Positives = 286/469 (60%), Gaps = 5/469 (1%) Query: 9 MYIDGQFVTWRGDAWIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIER 68 M I+GQ+V D ++VVNPA + +P+G ++A +A++AA A W L A +R Sbjct: 10 MSINGQWVGSDLDT-LNVVNPANGETVGTVPNGGEKEAEQAVNAAYDAFESWSNLTAHDR 68 Query: 69 ASWLRKISAGIRERASEISALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYEGEIIQ 128 A +L+K++ + E E++ ++ E GK + EV + A +I++ AE +R +G +I Sbjct: 69 AVYLKKLNQLMLENQEELAQMMTIEMGKPINESRGEVKYAASFIEWFAEEGKRIDGAVIP 128 Query: 129 SDRPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAIAF 188 + G+ + ++K+ +GV I PWNFP ++ RKM PAL +G T ++KPS +P A+ Sbjct: 129 THAAGKRLQVWKKPVGVAAAITPWNFPAAMLTRKMGPALASGCTFIMKPSSESPLTAVKL 188 Query: 189 AKIVDEIGLPRGVFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNITKV 248 ++ ++ G P+GV NLV G + + + N KV V+ TGS G+ ++ +A + K+ Sbjct: 189 MELCEQAGFPKGVVNLVTGSSSKIAKVVMENSKVRKVTFTGSTEVGKTLIRQSADQVKKL 248 Query: 249 CLELGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRLGEA 308 LELGG AP +V+DDAD++LAVK V S+ N+GQ C CA R+YVQ+G+YD++V +L +A Sbjct: 249 SLELGGHAPLVVLDDADVDLAVKGTVASKFRNAGQTCICANRIYVQEGVYDEYVEKLTKA 308 Query: 309 MQAVQFGNPA-ERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAV-EGKGYYYP 366 ++ ++ G+ E NDI GPLIN L++V++ V A +GA + GGKAV + G +Y Sbjct: 309 VEELKAGDGTDESNDI--GPLINQDGLDKVKRHVDDATSKGASITTGGKAVTDNGGLFYQ 366 Query: 367 PTLLLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVAMKA 426 PT+L DV Q M IM EETFGPV PV + E+A+ ++ND+ YGL + ++T N+ + Sbjct: 367 PTVLKDVDQSMVIMEEETFGPVTPVEKISSDEEAVKLSNDTPYGLAAYVFTSNVARGYQL 426 Query: 427 IKGLKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQTQVV 475 I+ L FG N A Q G ++SGIG G G+ E++++Q V Sbjct: 427 IEKLDFGIVGWNEGGPSAAQVPFGGMKESGIGREGGHEGIEEFVESQYV 475 Lambda K H 0.318 0.135 0.392 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: 555 Number of extensions: 20 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: 479 Length of database: 480 Length adjustment: 34 Effective length of query: 445 Effective length of database: 446 Effective search space: 198470 Effective search space used: 198470 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: 51 (24.3 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