Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate WP_043879642.1 AZC_RS20260 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::P25553 (479 letters) >NCBI__GCF_000010525.1:WP_043879642.1 Length = 493 Score = 315 bits (806), Expect = 3e-90 Identities = 170/465 (36%), Positives = 262/465 (56%), Gaps = 1/465 (0%) Query: 11 IDGQFVTWRGDAWIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIERAS 70 I G +V A I+V NPAT A+I IP + R+AI+AA A W A A ERAS Sbjct: 25 IGGAWVDADSGATIEVNNPATGAIIGTIPQAGRAETRRAIEAAADAFKIWRAKTAAERAS 84 Query: 71 WLRKISAGIRERASEISALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYEGEIIQSD 130 L K++ I +++ L+ E GK A+ EV +A Y+ + AE ARR G+ I S Sbjct: 85 ALHKLADIILANQDDLARLLTTEQGKPFAEAKGEVGASAAYVRWFAEEARRLYGDTIPSP 144 Query: 131 RPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAIAFAK 190 G I++ K +GV I PWNFP ++ARK+ AL G T+V KP+E TP + +A+ Sbjct: 145 WAGRRIMVTKEPVGVVAAITPWNFPSSMLARKVGAALAAGCTVVAKPAELTPYSGLAWGV 204 Query: 191 IVDEIGLPRGVFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNITKVCL 250 + + G+P G N+V G + +G E+ NP V V+ TGS G+ +M +A + K+ + Sbjct: 205 LAEMAGIPAGCVNIVTGDAKEIGLEMTSNPIVKKVTFTGSTPVGKLLMKQSADTMKKISM 264 Query: 251 ELGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRLGEAMQ 310 ELGG AP IV DDADL+ AV+ + S+ NSGQ C CA R+YVQ GI+D F + EA++ Sbjct: 265 ELGGNAPFIVFDDADLDAAVEGAIASKFRNSGQTCVCANRIYVQAGIHDAFAEKFAEAVR 324 Query: 311 AVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAVEGKGYYYPPTLL 370 ++ GN + + + GPLI A+ +VE+ + A ++G + GGK ++ PT++ Sbjct: 325 KLKIGNGFD-DGVVAGPLIEEKAVAKVERLLKDATDKGGTIVTGGKRSPLGLTFFEPTVI 383 Query: 371 LDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVAMKAIKGL 430 + Q+M EE FGP+ P+ F+T E+ + AN ++YGL +T++L A + + L Sbjct: 384 ANATQDMGFAREEIFGPMAPLFKFETEEEVVRYANSTEYGLACYFFTKDLGRAFRVSEAL 443 Query: 431 KFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQTQVV 475 ++G+ +N G ++SG+G K+G +YL + + Sbjct: 444 EYGQVGVNAGVITTEVAPFGGVKESGVGREGSKYGCDDYLNIKYI 488 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: 546 Number of extensions: 27 Number of successful extensions: 4 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: 493 Length adjustment: 34 Effective length of query: 445 Effective length of database: 459 Effective search space: 204255 Effective search space used: 204255 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