Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate WP_022948198.1 H035_RS0106590 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::P25553 (479 letters) >NCBI__GCF_000421465.1:WP_022948198.1 Length = 486 Score = 325 bits (832), Expect = 3e-93 Identities = 177/464 (38%), Positives = 270/464 (58%), Gaps = 1/464 (0%) Query: 10 YIDGQFVTWRGDAWIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIERA 69 YI GQ+V G A ++VVNP+ + ++ +PD + R AI AA W A ER Sbjct: 17 YIGGQWVDADGGATLEVVNPSDQQILGTVPDMAEAETRGAIAAAREGFEVWRKKTAAERG 76 Query: 70 SWLRKISAGIRERASEISALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYEGEIIQS 129 L + + ++ L+ E GK A+ E+A+ A ++ + AE +RR G+ I + Sbjct: 77 EILYRWYELMMALQDDLGRLMTLEQGKPLPEAKGEIAYAAGFLKWFAEESRRAYGDTIPA 136 Query: 130 DRPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAIAFA 189 +PG++I++ K+ +GV+ I PWNFP +I RK AL G ++V+KP+ TP +A+A A Sbjct: 137 AKPGQHIVVIKQPVGVSVAITPWNFPSAMITRKAGAALAAGCSMVVKPAAETPFSALALA 196 Query: 190 KIVDEIGLPRGVFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNITKVC 249 ++ + GLP GV N++ G +GQ L + V +S TGS G K+MA A++I K+ Sbjct: 197 ELGERAGLPNGVLNVITGDAVRIGQTLTSSATVRKLSFTGSTEVGRKLMAQCAEHIQKIS 256 Query: 250 LELGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRLGEAM 309 LELGG AP +V DDADL+ AV+ + S+ N+GQ C CA R VQ+G++D FV +L AM Sbjct: 257 LELGGNAPFLVFDDADLDKAVEGAMASKFRNTGQTCVCANRFLVQEGVHDAFVEKLKTAM 316 Query: 310 QAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAVEGKGYYYPPTL 369 + ++ GN E + LIN AA+++V++ + AV +GAR+ GG+A G Y P L Sbjct: 317 ETLRVGNGLEEG-VNQSALINQAAVDKVDEHLRDAVGKGARLILGGEAHPLGGTYVQPAL 375 Query: 370 LLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVAMKAIKG 429 L V +M + HEETFGPV V+ F T E+AI +AND+ YGL S Y+++++ + + Sbjct: 376 LTGVTPDMQLCHEETFGPVAAVMKFQTEEEAIRLANDTPYGLASYFYSRDIHRVWRVAEA 435 Query: 430 LKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQTQ 473 L+ G IN G ++SGIG K+G+ EYL+ + Sbjct: 436 LEAGIVGINEGLISNPVAPFGGVKESGIGREGSKYGMEEYLEVK 479 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: 565 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: 479 Length of database: 486 Length adjustment: 34 Effective length of query: 445 Effective length of database: 452 Effective search space: 201140 Effective search space used: 201140 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