Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate WP_011423489.1 RHE_RS00470 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::P25553 (479 letters) >NCBI__GCF_000092045.1:WP_011423489.1 Length = 494 Score = 353 bits (905), Expect = e-101 Identities = 193/466 (41%), Positives = 279/466 (59%), Gaps = 7/466 (1%) Query: 10 YIDGQFVTWRGDA---WIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPAI 66 YI+G + GDA DV+NPAT +++ +PD A + R AIDAA AQP W A PA Sbjct: 23 YINGVWTP--GDAAAKTFDVLNPATGELLASLPDMGAAETRAAIDAAYAAQPAWAARPAK 80 Query: 67 ERASWLRKISAGIRERASEISALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYEGEI 126 ER+ LRK I A ++A++ E GK A E+ + A YI++ AE A+R GE Sbjct: 81 ERSQILRKWFDLIVANADALAAILTAEMGKPFPEARGEILYAAAYIEWYAEEAKRIYGET 140 Query: 127 IQSDRPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAI 186 I + + +++ K+ +GV I PWNFP +IARK+APAL G T+V KP+E TP AI Sbjct: 141 IPAPSQDKRMIVIKQPVGVVGTITPWNFPAAMIARKIAPALAVGCTVVSKPAEQTPLTAI 200 Query: 187 AFAKIVDEIGLPRGVFNLVLG-RGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNI 245 A A + ++ G+P GVFNL++G G +G+EL GN KV +S TGS G +M A I Sbjct: 201 ALAVLAEQAGIPAGVFNLIVGLDGPAIGRELCGNDKVRKISFTGSTEVGRILMRQCADQI 260 Query: 246 TKVCLELGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRL 305 KV LELGG AP IV DDADL+ AV+ + S+ N+GQ C CA R+Y+Q G+YD F +L Sbjct: 261 KKVSLELGGNAPFIVFDDADLDAAVEGAIASKYRNAGQTCVCANRLYIQSGVYDAFAAKL 320 Query: 306 GEAMQAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAVEGKGYYY 365 + + G+ R + +GPLI+ L +VE V AV +GA++ GGK ++G G ++ Sbjct: 321 AAKVADMSVGD-GFRPGVEIGPLIDEQGLAKVEDHVGDAVAKGAKILTGGKRIDGAGTFF 379 Query: 366 PPTLLLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVAMK 425 PT+L V ++M++ EETFGPV P+ F+T ED I+ AND+++GL + Y +L + Sbjct: 380 APTVLTGVTRDMTVAREETFGPVAPLFRFETAEDVITQANDTEFGLAAYFYAGDLKKVWR 439 Query: 426 AIKGLKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQ 471 + L++G IN + G ++SG+G +HG +YL+ Sbjct: 440 VAEALEYGMVGINTGLMSSEMAPFGGIKQSGLGREGSRHGADDYLE 485 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: 19 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: 494 Length adjustment: 34 Effective length of query: 445 Effective length of database: 460 Effective search space: 204700 Effective search space used: 204700 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